compositions comprising circular polyribonucleotides and their uses

专利摘要:
This invention relates generally to pharmaceutical compositions and preparations of circular polyribonucleotides and their uses.
公开号:BR112020011670A2
申请号:R112020011670-0
申请日:2018-12-14
公开日:2020-11-17
发明作者:Morag Helen STEWART；Catherine CIFUENTES-ROJAS；Ki Young PAEK；Avak Kahvejian；Nicholas McCartney Plugis；Alexandra Sophie De Boer；Erica Gabrielle Weistein；Sebastian TROUSIL
申请人:Flagship Pioneering Innovations Vi, Llc.；
IPC主号:

专利说明:

[0001] [0001] This claim claims the benefit of U.S. Provisional Application No. 62 / 599,547, filed on December 15, 2017, and U.S. Provisional Application No. 62 / 676,688, filed on May 25, 2018, each of which is incorporated herein by reference in its entirety. BACKGROUND
[0002] [0002] Certain circular polyribonucleotides are ubiquitously present in human tissues and cells, including tissues and cells from healthy individuals. SUMMARY
[0003] [0003] In one aspect, the invention includes a pharmaceutical composition comprising a circular polyribonucleotide that comprises at least one structural element selected from a) an encryptogen; b) a staggered element; c) a regulatory element; d) an element of replication; f) secondary structure of almost double tape; and g) expression sequence; and at least one functional feature selected from: a) greater translation efficiency than a linear counterpart; b) a stoichiometric translation efficiency of multiple translation products; c) less immunogenicity than a counterpart without an encryptogen; d) increased half-life in relation to a linear counterpart; and e) persistence during cell division.
[0004] [0004] In some embodiments, the circular polyribonucleotide is competent for translation. In such an embodiment, the quasi-helical structure comprises at least one segment of double-stranded RNA with at least one non-double-stranded segment. In another such embodiment, the quasi-helical structure comprises a first sequence and a second sequence linked to a repetitive sequence, e.g., an A-rich sequence.
[0005] [0005] In some embodiments, the circular polyribonucleotide comprises an encryptogen. In some embodiments, the encryptogen comprises at least one modified ribonucleotide, e.g., pseudouridine, N (6) methyladenosine (m6A). In some embodiments, encryptogen comprises a protein-binding site, e.g., ribonucleotide-binding protein. In some embodiments, encryptogen comprises an immunoprotein binding site, e.g., to escape immune responses, e.g., CTL responses.
[0006] [0006] In some embodiments, the circular polyribonucleotide comprises at least one modified ribonucleotide.
[0007] [0007] In some embodiments, the circular polyribonucleotide has at least 2x less immunogenicity than a counterpart without the encryptogen, eg, as assessed by expression or signaling or activation of at least one of
[0008] [0008] In some embodiments, the circular polyribonucleotide additionally comprises a riboswitch.
[0009] [0009] In some embodiments, the circular polyribonucleotide additionally comprises an aptazime.
[0010] [0010] In some embodiments, the circular polyribonucleotide comprises a translation initiation sequence, eg, start codon GUG, CUG, eg, expression under stress conditions.
[0011] [0011] In some embodiments, the circular polyribonucleotide comprises at least one expression sequence, e.g., encoding a polypeptide. In such an embodiment, the expression sequence encodes a peptide or polynucleotide. In some embodiments, the circular polyribonucleotide comprises a plurality of expression sequences, the same or different.
[0012] [0012] In some embodiments, the circular polyribonucleotide comprises a stepped element, eg, 2A.
[0013] [0013] In some embodiments, the circular polyribonucleotide comprises a regulatory nucleic acid, e.g., a non-coding RNA. In some embodiments, the circular polyribonucleotide comprises a regulatory element, e.g., that alters the expression of an expression sequence.
[0014] [0014] In some embodiments, the circular polyribonucleotide has a size in the range of about 20 bases to about 20 kb.
[0015] [0015] In some embodiments, the circular polyribonucleotide is synthesized through the circularization of a linear polynucleotide.
[0016] [0016] In some embodiments, the circular polyribonucleotide is substantially resistant to degradation, eg, exonuclease.
[0017] [0017] In some embodiments, the circular polyribonucleotide does not have at least one of: a) a 5'-RTU; b) a 3'-RTU; c) a poly-A sequence; d) a 5 'cap; e) a terminating element; f) an internal ribosomal entry site; g) susceptibility to degradation by exonucleases and h) binding to a cap binding protein.
[0018] [0018] In one aspect, the invention includes a method of producing the composition comprising a circular polyribonucleotide described herein.
[0019] [0019] In one aspect, the invention includes a pharmaceutical composition comprising a pharmaceutically acceptable carrier or excipient and a circular polyribonucleotide comprising one or more expression sequences, in which the circular polyribonucleotide is competent for translation of a rolling circle.
[0020] [0020] In some embodiments, each of the one or more expression sequences is separated from a subsequent expression sequence by a stepped element in the circular polyribonucleotide, wherein the rolling circle translation of one or more expression sequences generates at least two polypeptide molecules, e.g., stepped elements interrupt or stop the ribosome so that the elongated polypeptide falls off the ribosome. In some embodiments, the scaled element prevents the generation of a single polypeptide (a) from two translation rounds of a single expression sequence or (b) from one or more translation rounds of two or more expression sequences . For example, the stepped element can prevent the generation of a single polypeptide from two or more translation rounds of two or more expression sequences, eg, the stepped element for the ribosome and / or allows the stretched polypeptide fall from the ribosome after a circuit around the circular polyribonucleotide.
[0021] [0021] In some embodiments, the scaled element is a sequence separate from one or more expression sequences.
[0022] [0022] In some embodiments, the scaled element comprises a portion of an expression sequence from one or more expression sequences.
[0023] [0023] In one aspect, the invention includes a pharmaceutical composition comprising a pharmaceutically acceptable carrier or excipient and a circular polyribonucleotide that comprises one or more expression sequences and is competent for translation of a circular circle, in which the circular polyribonucleotide is configured so that at least 10%, 20%, 30%, 40%, 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% of the total polypeptides (molar / molar) generated during the rolling circle translation of the circular polyribonucleotide are discrete polypeptides and where each of the discrete polypeptides is generated from a single translation round or less than a single translation round of one or more expression strings.
[0024] [0024] In some embodiments, the circular polyribonucleotide is configured so that at least 10%, 20%, 30%, 40%, 50%, at least 60%, at least 70%, at least 80%, at least 90 %, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% of the total polypeptides (molar / molar) generated during translation of circular polyribonucleotide are the discrete polypeptides, and where the ratio of quantities between discrete products and total polypeptides is tested in an in vitro translation system.
[0025] [0025] In some embodiments, the in vitro translation system comprises rabbit reticulocyte lysate.
[0026] [0026] In some embodiments, the stepped element is downstream of or 3 'with respect to at least one of the one or more expression sequences, in which the stepped element is configured to interrupt a ribosome during the polyribonucleotide rolling circle translation Circular.
[0027] [0027] In one aspect, the invention provides a pharmaceutical composition comprising a pharmaceutically acceptable carrier or excipient and a circular polyribonucleotide comprising one or more expression sequences and a stepped element downstream of or 3 'with respect to at least one of the one or more expression strings. In some embodiments, the stepped element is configured to interrupt a ribosome during the translation of a circular circle of the circular polyribonucleotide.
[0028] [0028] In some embodiments, the scaled element encodes a peptide sequence selected from the group consisting of a 2A sequence and a type 2A sequence.
[0029] [0029] In some embodiments, the scaled element encodes a sequence with a C-terminal sequence that is GP.
[0030] [0030] In some embodiments, the scaled element encodes a sequence with a C-terminal consensus sequence that is D (V / I) ExNPG P, where x = any amino acid.
[0031] [0031] In some modalities, the scaled element encodes at least one of GDVESNPGP, GDIEENPGP, VEPNPGP, IETNPGP, GDIESNPGP, GDVELNPGP, GDIETNPGP, GDVENPGP, GDVEENPGP, GDVEQPGPG, GDNPPPG, HDD, PGNPP, HDD, and DSEFNPGP.
[0032] [0032] In some modalities, the scaled element is downstream of or 3´ in relation to each one of the one or more expression sequences.
[0033] [0033] In some embodiments, the stepped element of a first expression sequence in the circular polyribonucleotide is upstream of (5 'with respect to) a first translation initiation sequence for an expression sequence that succeeds the first expression sequence in circular polyribonucleotide, and where a distance between the stepped element and the first translation initiation sequence allows for continuous translation of the first expression sequence and the subsequent expression sequence. In some embodiments, the stepped element comprises a terminating element for a first expression sequence in the circular polyribonucleotide that has a distance upstream (5 'from) a translation initiation sequence for an expression sequence that succeeds the first expression sequence in the circular polyribonucleotide, and where the distance allows continuous translation of the first expression sequence and its subsequent expression sequence.
[0034] [0034] In some embodiments, a staggered first element is upstream of (5 'with respect to) a first translation initiation sequence for a first expression sequence in the circular polyribonucleotide, in which the circular polyribonucleotide is continuously translated, in which a corresponding circular polyribonucleotide comprises a second stepped element upstream of a second translation initiation sequence of a second expression sequence in the corresponding circular polyribonucleotide that is not continuously translated, and in which the second stepped element in the corresponding circular polyribonucleotide is at a distance greater than the second translation initiation sequence, eg at least 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x, than a distance between the first stepped element and the first translation initiation in the circular polyribonucleotide.
[0035] [0035] In some modalities, the distance between the first stepped element and the first translation initiation is at least 2 nt, 3 nt, 4 nt, 5 nt, 6 nt, 7 nt, 8 nt, 9 nt, 10 nt, 11 nt, 12 nt, 13 nt, 14 nt, 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, 25 nt, 30 nt, 35 nt, 40 nt, 45 nt, 50 nt, 55 nt , 60 nt, 65 nt, 70 nt, 75 nt or greater. In some embodiments, the distance between the second staggered element and the second translation initiation is at least 2 nt, 3 nt, 4 nt, 5 nt, 6 nt, 7 nt, 8 nt, 9 nt, 10 nt, 11 nt, 12 nt, 13 nt, 14 nt, 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, 25 nt, 30 nt, 35 nt, 40 nt, 45 nt, 50 nt, 55 nt, 60 nt , 65 nt, 70 nt, 75 nt or greater than the distance between the first stepped element and the first translation initiation.
[0036] [0036] In some embodiments, the circular polyribonucleotide comprises more than one expression sequence.
[0037] [0037] In some embodiments, the circular polyribonucleotide has a translation efficiency of at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50% at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 2 times, at least 3 times, at least 4 times, at least 5 times at least 6 times, at least 7 times, at least 8 times, at least 9 times, at least 10 times, at least 20 times, at least 50 times or at least 100 times greater than a linear counterpart.
[0038] [0038] In some embodiments, the circular polyribonucleotide has a translation efficiency at least 5 times greater than that of a linear counterpart.
[0039] [0039] In some embodiments, the circular polyribonucleotide does not have an internal ribosomal entry site.
[0040] [0040] In some embodiments, the one or more expression sequences comprise a Kozak initiation sequence.
[0041] [0041] In some embodiments, one or more expression sequences encode a peptide.
[0042] [0042] In some embodiments, the circular polyribonucleotide comprises a regulatory nucleic acid, e.g., a non-coding RNA. In some embodiments, the circular polyribonucleotide comprises a regulatory element, e.g., that alters the expression of an expression sequence.
[0043] [0043] In one aspect, the invention provides a circular polyribonucleotide from any of the pharmaceutical compositions provided herein.
[0044] [0044] In one aspect, the invention includes a method of producing the pharmaceutical composition provided herein, comprising combining the circular polyribonucleotide described herein and the pharmaceutically acceptable carrier or excipient described herein.
[0045] [0045] In one aspect, the invention includes a method of administering the composition comprising a circular polyribonucleotide described herein.
[0046] [0046] In one aspect, the invention includes a method for expressing proteins, comprising translating at least one region of the circular polyribonucleotide provided herein.
[0047] [0047] In some embodiments, the translation of at least one region of the circular polyribonucleotide takes place in vitro. In some embodiments, the translation of at least one region of the circular polyribonucleotide takes place in vivo.
[0048] [0048] In one aspect, the invention includes a polynucleotide, e.g., a DNA vector, encoding the circular polyribonucleotide provided here.
[0049] [0049] In one aspect, the invention includes a method of producing the circular polyribonucleotide as provided herein.
[0050] [0050] In some embodiments, the method comprises circularization mediated by splint binding of a linear polyribonucleotide.
[0051] [0051] In some embodiments, circularization, eg circularization mediated by splint bonding, has an efficiency of at least 2%, at least 5%, at least 10%, at least 15%, at least 20% at least 25%, at least 30%, at least 32%, at least 34%, at least 36%, at least 38%, at least 40%, at least 42%, at least 44%, at least 46% , at least 48% or at least 50%. In some embodiments, splint-mediated circularization has an efficiency of about 40% to about 50% or more than 50%.
[0052] [0052] The present invention will be described with respect to particular modalities and with reference to certain figures, but the invention is not limited to them, but only by the claims. The terms as presented hereinafter will generally be understood in their common sense, unless otherwise indicated.
[0053] [0053] The terms "obtainable by", "produceable by" or similar are used to indicate that a claim or modality refers to a compound, composition, product, etc. per se, i.e., that compound, composition, product, etc. it can be obtained or produced by a method that is described for making the compound, composition, product, etc., but that the compound, composition, product, etc. it can also be obtained or produced by methods other than that described. The terms "obtained by", "produced by" or similar indicate that the compound, composition, product, is obtained or produced by a specific method recited. It is to be understood that the terms "obtainable by", "produceable by" and the like also disclose the terms "obtained by", "produced by" and similar as a preferred modality of "obtainable by", "produceable by" and the like.
[0054] [0054] The expression “compound, composition, product, etc. for treatment, modulation, etc. ” is to be understood as referring to a compound, composition, product, etc. per se that it is suitable for the indicated purposes of treatment, modulation, etc. The expression “compound, composition, product,
[0055] [0055] The expression “compound, composition, product, etc. for use in ... ”or“ use of a compound, composition, product, etc. in the manufacture of a medicine, pharmaceutical composition, veterinary composition, diagnostic composition, etc. for ... ”indicates that such compounds, compositions, products, etc. they are to be used in therapeutic methods that can be practiced on the human or animal body. They are considered as an equivalent disclosure of modalities and claims pertaining to treatment methods, etc. If a modality or claim thus refers to “a compound for use in the treatment of a human or animal being suspected of suffering from a disease”, this is considered to also be a disclosure of a “use of a compound in the manufacture of a medicine for treating a human or animal being suspected of suffering from a disease ”or a“ treatment method for administering a compound to a human or animal being suspected of suffering from a disease ”. The expression “compound, composition, product, etc. for treatment, modulation, etc. ” is to be understood as referring to a compound, composition, product, etc. per se that it is suitable for the indicated purposes of treatment, modulation, etc.
[0056] [0056] The term "pharmaceutical composition" is also intended to disclose that the circular polyribonucleotide comprised within a pharmaceutical composition can be used to treat the human or animal body by therapy. So it is intended to be equivalent to “a circular polyribonucleotide for use in therapy”.
[0057] [0057] Circular polyribonucleotides, compositions comprising such circular polyribonucleotides, methods using such circular polyribonucleotides, etc., as described here, are based in part on the examples illustrating how circular polyribonucleotide effectors comprising different elements, for example a replication element, an expression sequence, a stepped element and an encryptogen (see, eg, example 1) or for example an expression sequence, a stepped element and a regulatory element (see, eg, examples 30 and 38) can be used to achieve different technical effects (eg, increased translation efficiency than a linear counterpart in examples 1 and 38 and increased half-life compared to a linear counterpart in example 38). It is on the basis of these examples inter alia that the description hereafter contemplates several variations of the findings and specific combinations considered in the examples.
[0058] [0058] As used here, the terms "circRNA" or "circular polyribonucleotide" or "circular RNA" are used interchangeably and can refer to a polyribonucleotide that forms a circular structure through covalent or non-covalent bonds.
[0059] [0059] As used here, the term "encryptogen" can refer to a nucleic acid sequence or structure of the circular polyribonucleotide that aids in the reduction, escape and / or avoidance of detection by an immune cell and / or reduces the induction of a immune response against circular polyribonucleotide.
[0060] [0060] As used herein, the term "expression sequence" can refer to a nucleic acid sequence that encodes a product, e.g., a peptide or polypeptide, or a regulatory nucleic acid. An exemplary expression sequence encoding a peptide or polypeptide can comprise a plurality of triad of nucleotides, each of which can encode an amino acid and is referred to as a "codon".
[0061] [0061] As used here, the term "immunoprotein binding site" can refer to a nucleotide sequence that binds to an immunoprotein. In some embodiments, the immunoprotein binding site aids in masking the circular polyribonucleotide as exogenous, for example, the immunoprotein binding site can be linked by a protein (eg, a competitive inhibitor) that prevents the circular polyribonucleotide is recognized and linked by an immunoprotein, thereby reducing or avoiding an immune response against the circular polyribonucleotide. As used here, the term "immunoprotein" can refer to any protein or peptide that is associated with an immune response, eg, such as against an immunogen, eg, the circular polyribonucleotide. Non-limiting examples of immunoprotein include T cell receptors (TCRs), antibodies (immunoglobulins), major histocompatibility complex (MHC) proteins, complement proteins and RNA-binding proteins.
[0062] [0062] As used here, the term "modified ribonucleotide" can refer to a nucleotide with at least one modification in the sugar, nucleobase or internucleoside bond.
[0063] [0063] As used here, the phrase "quasi-helical structure" can refer to a higher-order structure of the circular polyribonucleotide, in which at least a portion of the circular polyribonucleotide folds into a helical structure.
[0064] [0064] As used here, the phrase "secondary double-stranded structure" can refer to a higher-order structure of the circular polyribonucleotide, in which at least a portion of the circular polyribonucleotide creates an internal double strand.
[0065] [0065] As used here, the term "regulatory element" can refer to a fraction, such as a nucleic acid sequence, that modifies the expression of an expression sequence within the circular polyribonucleotide.
[0066] [0066] As used here, the term "repetitive nucleotide sequence" can refer to a repetitive nucleic acid sequence within a stretch of DNA or RNA or along a genome. In some embodiments, the repetitive nucleotide sequence includes poly CA or poly TG (UG) sequences. In some embodiments, the repetitive nucleotide sequence includes repeated sequences in the Alu family of introns.
[0067] [0067] As used here, the term "element of replication" can refer to a sequence and / or motifs useful for replication or that initiate transcription of the circular polyribonucleotide.
[0068] [0068] As used here, the term "scaled element" can refer to a fraction, such as a sequence of nucleotides, which induces ribosomal pause during translation. In some modalities, the scaled element is a non-conserved sequence of amino acids with a strong alpha-helical propensity followed by the consensus sequence -D (V / I) ExNPG P, where x = any amino acid. In some embodiments, the scaled element may include a chemical moiety, such as glycerol, a binding fraction other than nucleic acid, a chemical modification, a modified nucleic acid or any combination thereof.
[0069] [0069] As used here, the term "substantially resistant" can refer to one that has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95 %, 96%, 97%, 98% or 99% resistance compared to a reference.
[0070] [0070] As used here, the term "stoichiometric translation" can refer to a substantially equivalent production of expression products translated from the circular polyribonucleotide. For example, for a circular polyribonucleotide having two expression sequences, the stoichiometric translation of the circular polyribonucleotide can mean that the expression products of the two expression sequences can have substantially equivalent amounts, e.g., the difference in quantities between the two sequences expression (eg molar difference) can be about 0 or less than 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15% or 20%.
[0071] [0071] As used here, the term "translation initiation sequence" can refer to a nucleic acid sequence that initiates the translation of an expression sequence in the circular polyribonucleotide.
[0072] [0072] As used here, the term "terminating element" can refer to a fraction, such as a nucleic acid sequence, which terminates the translation of the expression sequence in the circular polyribonucleotide.
[0073] [0073] As used here, the term "translation efficiency" can refer to a rate or amount of production of proteins or peptides from a ribonucleotide transcript. In some embodiments, translation efficiency can be expressed as the amount of protein or peptide produced by a given amount of transcript encoding the protein or peptide, eg, in a given period of time, eg, in a given translation system, e.g., an in vitro translation system such as rabbit reticulocyte lysate or an in vivo translation system such as a eukaryotic cell or a prokaryotic cell.
[0074] [0074] As used here, the term "circularization efficiency" can refer to a measurement of the resulting circular polyribonucleotide versus its starting material.
[0075] [0075] As used here, the term "immunogenic" can refer to a potential to induce an immune response to a substance. In some embodiments, an immune response can be induced when an organism's immune system or a certain type of immune cell is exposed to an immunogenic substance. The term "non-immunogenic" can refer to a lack of or an absence of an immune response above a detectable threshold for a substance. In some embodiments, no immune response is detected when an organism's immune system or a certain type of immune cell is exposed to a non-immunogenic substance. In some embodiments, a non-immunogenic circular polyribonucleotide as provided herein does not induce an immune response above a predetermined threshold when measured by an immunogenicity assay. For example, when an immunogenicity assay is used to measure antibodies raised against a circular polyribonucleotide or inflammatory markers, a non-immunogenic polyribonucleotide as provided herein can lead to the production of antibodies or markers at a level below a predetermined threshold. The predetermined threshold can be, for example, a maximum of 1.5 times, 2 times, 3 times, 4 times or 5 times the level of antibodies or markers created by a control reference. INCORPORATION BY REFERENCE
[0076] [0076] All publications, patents and patent applications mentioned in this specification are incorporated herein by reference to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference. BRIEF DESCRIPTION OF THE DRAWINGS
[0077] [0077] The following detailed description of the modalities of the invention will be better understood when read in conjunction with the attached drawings. For the purpose of illustrating the invention modalities are shown in the drawings, which are presently exemplified. It should be understood, however, that the invention is not limited to the precise disposition and instrumentalities of the modalities shown in the drawings.
[0078] [0078] Figure 1 shows different exemplary circularization methods.
[0079] [0079] Figure 2 shows a schematic of an exemplary in vitro production process of a circular RNA containing a start codon, an ORF (open reading frame) encoding GFP, a stepped element (2A), an encryptogen and a IRES (internal ribosomal entry site).
[0080] [0080] Figure 3 shows a schematic of an exemplary in vivo production process for a circular RNA.
[0081] [0081] Figure 4 shows the design of an exemplary circular RNA comprising a start codon, an ORF encoding GFP, a stepped element (2A) and an encryptogen.
[0082] [0082] Figures 5A and 5B are schematics showing stoichiometric expression of proteins in vivo from two different circular RNAs.
[0083] [0083] Figure 6 shows a scheme of a circular control RNA that has an intron and expresses GFP.
[0084] [0084] Figure 7 shows a schematic of an exemplary circular RNA that has a synthetic riboswitch (in red) regulating GFP expression from the circular RNA in the presence or absence of ligands for the riboswitch.
[0085] [0085] Figure 8 is a schematic demonstrating expression of protein in vivo in a mouse model from exemplary circular RNAs.
[0086] [0086] Figure 9 is a schematic demonstrating in vivo biodistribution of an exemplary circular RNA in a mouse model.
[0087] [0087] Figure 10 is a schematic demonstrating expression of protein in vivo in a mouse model from an exemplary circular RNA that houses an encryptogen (intron).
[0088] [0088] Figure 11 shows a schematic of an exemplary circular RNA that has a double-stranded RNA segment, which can be subjected to dot blot analysis for its structural information.
[0089] [0089] Figure 12 shows a schematic of an exemplary circular RNA that has an almost helical structure (HDVmin), which can be subjected to SHAPE analysis for its structural information.
[0090] [0090] Figure 13 shows a schematic of an exemplary circular RNA that has a functional almost helical structure (HDVmin), which demonstrates HDAg binding activity.
[0091] [0091] Figure 14 is a schematic showing transcription, autocleavage and binding of an exemplary self-replicating circular RNA.
[0092] [0092] Figure 15 shows a schematic of an exemplary circular RNA that is expressed in vivo and has improved in vivo stability.
[0093] [0093] Figure 16 shows an outline of an exemplary circular RNA that is preserved during mitosis and persists in daughter cells. BrdU pulse as shown is used for labeling the divided cells.
[0094] [0094] Figure 17 is an image of denaturing PAGE gel demonstrating in vitro production of different exemplary circular RNAs.
[0095] [0095] Figure 18 is a graph summarizing the circularization efficiencies of different exemplary circular RNAs.
[0096] [0096] Figure 19 is an image of denaturing PAGE gel demonstrating susceptibility to decreased degradation of an exemplary circular RNA compared to its linear counterpart.
[0097] [0097] Figure 20 is an image of denaturing PAGE gel demonstrating exemplary circular RNAs after an exemplary purification process.
[0098] [0098] Figure 21 is a Western blot image demonstrating Flag protein expression (~ 15 kDa) by an exemplary circular RNA that lacks IRES, cap, 5 'and 3' UTRs.
[0099] [0099] Figure 22 is a Western transfer image showing a circular circle translation of an exemplary circular RNA.
[0100] [0100] Figure 23 shows Western transfer images demonstrating production of discrete proteins or long continuous peptides from different exemplary circular RNAs with or without an exemplary stepped element.
[0101] [0101] Figure 24A is a Western blot image showing the comparison of protein expression between different exemplary circular RNAs with an exemplary stepped element or a terminating element (stop codon).
[0102] [0102] Figure 24B is a graph summarizing signal strength from the Western blot analysis of protein products translated from the two exemplary circular RNAs.
[0103] [0103] Figure 25 is a graph summarizing the luciferase activity of translation products from an exemplary circular RNA and its linear counterpart, compared to a vehicle control RNA.
[0104] [0104] Figure 26 is a graph summarizing amounts of RNA at different times of collection in an experiment over time testing the half-life of an exemplary circular RNA.
[0105] [0105] Figure 27A is a graph showing qRT-PCR analysis of linear and circular RNA levels 24 hours after administration to cells using primers that captured both linear and circular RNA.
[0106] [0106] Figure 27B is a graph showing qRT-PCR analysis of linear and circular RNA levels using a specific circular RNA primer.
[0107] [0107] Figure 28 is an image showing a blot of lysates of circular RNA and linear RNA probed for EGF protein and a beta-tubulin load control.
[0108] [0108] Figure 29 is a graph showing qRT-PCR analysis of immunorelated genes from 293T cells transfected with circular RNA or linear RNA.
[0109] [0109] Figure 30 is a graph showing protein luciferase activity expressed from circular RNA through rolling circle translation.
[0110] [0110] Figure 31 is a graph showing protein luciferase activity expressed from circular RNA or linear RNA.
[0111] [0111] Figure 32 is a graph showing protein luciferase activity expressed from linear RNA or circular RNA through rolling circle translation.
[0112] [0112] Figure 33 is a graph showing protein luciferase activity expressed from circular RNA through initiation of IRES translation.
[0113] [0113] Figure 34 is a graph showing protein luciferase activity expressed from circular RNA through IRES initiation and rolling circle translation.
[0114] [0114] Figure 35 is an image showing a protein blot of expression products from circular RNA or linear RNA.
[0115] [0115] Figure 36 is an image showing a protein blot of expression products from circular RNA or linear RNA.
[0116] [0116] Figure 37 shows the predicted structure with an almost double stranded structure of an exemplary circular RNA.
[0117] [0117] Figure 38 shows the predicted structure with an almost helical strand structure of an exemplary circular RNA.
[0118] [0118] Figure 39 shows the predicted structure with an almost helical chain structure linked with a repetitive sequence of an exemplary circular RNA.
[0119] [0119] Figure 40 demonstrates experimental data that RNAse H degradation of an exemplary circular RNA produced nucleic acid degradation products consistent with a circular, non-concatemeric RNA.
[0120] [0120] Figure 41 shows an electrophoresis image of the different lengths of DNA that were generated to create a wide variety of lengths of RNA.
[0121] [0121] Figure 42 shows experimental data that confirmed the circularization of RNAs using RNAse R treatment and qPCR analysis against circular junctions of a wide variety of lengths.
[0122] [0122] Figure 43 shows the generation of exemplary circular RNA with a miRNA binding site.
[0123] [0123] Figure 44 shows the generation of exemplary circular RNA by self-splicing.
[0124] [0124] Figure 45 shows the generation of exemplary circular RNA with a protein binding site.
[0125] [0125] Figure 46 shows experimental data demonstrating the higher stability of circular RNA in a dividing cell compared to linear controls.
[0126] [0126] Figure 47 shows experimental data demonstrating the expression of the protein from exemplary circular RNAs with a plurality of expression sequences and the rolling circle translation of
[0127] [0127] Figure 48 shows experimental data demonstrating reduced toxicity to transfected cells from an exemplary circular RNA compared to linear control.
[0128] [0128] Figure 49 shows that the exemplary circular RNA has been translated to a higher level compared to linear RNA under stress.
[0129] [0129] Figure 50 shows the generation of circular RNAs with a riboswitch.
[0130] [0130] Figures 51A, 51B and 51C show that the modified circular RNAs have been translated into cells.
[0131] [0131] Figures 52A-52C show that the modified circular RNAs have reduced immunogenicity compared to unmodified circular RNAs to cells as assessed by MDA5, OAS and IFN-beta expression in the transfected cells.
[0132] [0132] Figure 53 shows that, after injection into mice, circular RNA was detected at higher levels than linear RNA in mouse livers at 3, 4 and 7 days post-injection.
[0133] [0133] Figures 54A and 54B show that, after injection of circular RNA or linear RNA expressing Gaussia Luciferase in mice, Gaussia Luciferase activity was detected in plasma at 1, 2, 7, 11, 16 and 23 days post-dosing of circular RNA, while its activity was only detected in plasma at 1 and 2 days after dosing of modified linear RNA.
[0134] [0134] Figure 55 shows that, after RNA injection, circular RNA, but not linear RNA, was detected in the liver and spleen at 16 days post RNA administration.
[0135] [0135] Figure 56 shows that, after RNA injection, linear RNA, but not circular RNA, showed immunogenicity as assessed by RIG-I, MDA-5, IFN-B and OEA. DETAILED DESCRIPTION
[0136] [0136] This invention relates generally to pharmaceutical compositions and preparations of circular polyribonucleotides and their uses. Circular Polyribonucleotides
[0137] [0137] In some respects, the invention described here comprises compositions and methods of use and preparation of circular polyribonucleotides and administration of circular polyribonucleotides. In some embodiments, the circular polyribonucleotide is non-immunogenic in a mammal, eg, a human. In some embodiments, the circular polyribonucleotide is capable of replicating or replicating itself in a cell of an aquaculture animal (fish, crabs, shrimp, oysters, etc.), a mammalian cell, eg, a cell of a pet or zoo animal (cats, dog lizards, birds, lions, tigers and bears, etc.), a farm cell or work animal (horses, cows, pigs, chickens, etc.), a human cell , cultured cells, primary cells or cell lines, stem cells, progenitor cells, differentiated cells, germ cells, cancer cells (e.g.,
[0138] [0138] In some embodiments, the circular polyribonucleotide includes sequences or expression products.
[0139] [0139] In some embodiments, the circular polyribonucleotide has a half-life of at least that of a linear counterpart, eg, linear expression sequence, or linear circular polyribonucleotide. In some embodiments, the circular polyribonucleotide has a half-life that is increased over that of a linear counterpart.
[0140] [0140] In some embodiments, the circular polyribonucleotide modulates a cellular function, eg, transiently or long term. In certain embodiments, cell function is stably altered, such as a modulation that persists for at least about 1 h to about 30 days or at least about 2 h, 6 h, 12 h, 18 h, 24 h, 2 days , 3, days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 22 days, 23 days, 24 days, 25 days, 26 days, 27 days, 28 days, 29 days, 30 days, 60 days or more or any intermediate time. In certain embodiments, cell function is transiently altered, eg, as a modulation that persists for no more than about 30 mins to about 7 days or no more than about 1 h, 2 h, 3 h, 4 h, 5 h, 6 h, 7 h, 8 h, 9 h, 10 h, 11 h, 12 h, 13 h, 14 h, 15 h, 16 h, 17 h, 18 h, 19 h, 20 h, 21 h, 22 h, 24 h, 36 h, 48 h, 60 h, 72 h, 4 days, 5 days, 6 days, 7 days or any other intermediate time.
[0141] [0141] In some embodiments, the circular polyribonucleotide has at least about 20 nucleotides, at least about 30 nucleotides, at least about 40 nucleotides, at least about 50 nucleotides, at least about 75 nucleotides, at least about 100 nucleotides, at least about 200 nucleotides, at least about 300 nucleotides, at least about 400 nucleotides, at least about 500 nucleotides, at least about 1,000 nucleotides, at least about 2,000 nucleotides, at least about 5,000 nucleotides, at least about 6,000 nucleotides, at least about 7,000 nucleotides, at least about 8,000 nucleotides, at least about 9,000 nucleotides, at least about 10,000 nucleotides, at least about 12,000 nucleotides, at least about 14,000 nucleotides , at least about 15,000 nucleotides, at least about 16,000 nucleotides, at least about 17,000 nucleotides, at least about 18,000 nucleotides otids, at least about 19,000 nucleotides or at least about 20,000 nucleotides.
[0142] [0142] In some embodiments, the circular polyribonucleotide comprises one or more elements described elsewhere here. In some embodiments, the elements may be separated from each other by a spacer or linker sequence. In some embodiments, the elements may be separated from each other by 1 ribonucleotide, 2 nucleotides, about 5 nucleotides, about 10 nucleotides, about 15 nucleotides, about 20 nucleotides, about 30 nucleotides, about 40 nucleotides, about of 50 nucleotides, about 60 nucleotides, about 80 nucleotides, about 100 nucleotides, about 150 nucleotides, about 200 nucleotides, about 250 nucleotides, about 300 nucleotides, about 400 nucleotides, about 500 nucleotides, about of 600 nucleotides, about 700 nucleotides, about 800 nucleotides, about 900 nucleotides, about 1000 nucleotides, up to about 1 kb, at least about 1000 nucleotides, any number of intermediate nucleotides. In some embodiments, one or more elements are contiguous to each other, eg, without a spacer element. In some embodiments, one or more elements in the circular polyribonucleotide are conformationally flexible. In some embodiments, conformational flexibility is due to the sequence being substantially free of a secondary structure. In some embodiments, the circular polyribonucleotide comprises a secondary or tertiary structure that accommodates one or more desired functions or characteristics described here, e.g., accommodating a binding site for a ribosome, e.g., translation, e.g. , translation of rolling circle.
[0143] [0143] In some embodiments, the circular polyribonucleotide comprises characteristics of particular sequences. For example, the circular polyribonucleotide may comprise a specific nucleotide composition. In some such embodiments, the circular polyribonucleotide may include one or more regions rich in purine (adenine or guanosine). In some such embodiments, the circular polyribonucleotide may include one or more regions rich in purine (adenine or guanosine). In some embodiments, the circular polyribonucleotide may include one or more AU-rich regions or elements (AREs). In some embodiments, the circular polyribonucleotide may include one or more regions rich in adenine.
[0144] [0144] In some embodiments, the circular polyribonucleotide may include one or more repetitive elements described elsewhere here.
[0145] [0145] In some embodiments, the circular polyribonucleotide comprises one or more modifications described elsewhere here.
[0146] [0146] In some embodiments, the circular polyribonucleotide comprises one or more expression sequences and is configured for persistent expression in a subject's cell in vivo. In some embodiments, the circular polyribonucleotide is configured so that the expression of one or more expression sequences in the cell at a later time is equal to or higher than an earlier time. In such embodiments, the expression of one or more expression sequences can be maintained at a relatively stable level or can increase over time. The expression of the expression sequences can be relatively stable over an extended period of time. For example, in some cases, the expression of one or more expression sequences in the cell over a period of time of at least 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 23 or more days does not decrease by 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10% or 5%. In some cases, the expression of one or more expression sequences in the cell is maintained at a level that does not vary by more than 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15% , 10% or 5% for at least 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 23 or more days. Expression sequences Peptides or polypeptides
[0147] [0147] In some embodiments, the circular polyribonucleotide comprises at least one expression sequence that encodes a peptide or polypeptide. Such a peptide includes, but is not limited to, small peptide, peptidomimetic (e.g., peptide), amino acids and amino acid analogs. The peptide can be linear or branched. Such a peptide can have a molecular weight less than about 5,000 grams per mole, a molecular weight less than about 2,000 grams per mole, a molecular weight less than about 1,000 grams per mole, a molecular weight less than about 500 grams per mole and salts, esters and other pharmaceutically acceptable forms of such compounds. Such a peptide can include, but is not limited to, a neurotransmitter, a hormone, a drug, a toxin, a viral or microbial particle, a synthetic molecule and its agonists or antagonists.
[0148] [0148] The polypeptide can be linear or branched. The polypeptide can be about 5 to about 40,000 amino acids in length, about 15 to about 35,000 amino acids, about 20 to about 30,000 amino acids, about 25 to about 25,000 amino acids, about 50 to about 20,000 amino acids, about 100 to about 15,000 amino acids, about 200 to about 10,000 amino acids, about 500 to about 5,000 amino acids, about 1,000 to about 2,500 amino acids or any intermediate range.
[0149] [0149] Some examples of a peptide or polypeptide include, but are not limited to, fluorescent tag or label, antigen, therapeutic peptide, synthetic peptide or the like from naturally bioactive peptide, agonist or antagonist peptide, antimicrobial peptide, peptide-forming peptide pores, a bicyclic peptide, a targeting or cytotoxic peptide, a degradation or self-destruction peptide and degradation or self-destruction peptides. Peptides useful in the invention described here also include antigen-binding peptides, e.g., antigen-binding antibody or antibody-like fragments, such as single chain antibodies, nanobodies (see, e.g., Steeland et al. 2016 Nanobodies as therapeutics: big opportunities for small antibodies Drug Discov Today: 21 (7): 1076-113). Such antigen-binding peptides can bind to a cytosolic antigen, a nuclear antigen, an intra-organellar antigen.
[0150] [0150] In some embodiments, the circular polyribonucleotide comprises one or more RNA expression sequences, each of which can encode a polypeptide. The polypeptide can be produced in substantial amounts. As such, the polypeptide can be any proteinaceous molecule that can be produced. A polypeptide can be a polypeptide that can be secreted from a cell or located in the cytoplasm, nucleus or membrane compartment of a cell. Some polypeptides include, but are not limited to, at least a portion of a viral envelope protein, metabolic regulatory enzymes (eg, which regulate the production of lipids or steroids), an antigen, a toleragen, a cytokine, a toxin, enzymes whose absence is associated with a disease, and polypeptides that are not active in an animal until they are cleaved (eg, in an animal's intestines) and a hormone.
[0151] [0151] In some embodiments, the circular polyribonucleotide includes an expression sequence encoding a protein, e.g., a therapeutic protein. In some embodiments, therapeutic proteins that can be expressed from the circular polyribonucleotide disclosed here have antioxidant activity, binding, charge receptor activity, catalytic activity, molecular carrier activity, molecular function regulator, molecular transducer activity, reservoir activity nutrients, protein tag, structural molecule activity, toxin activity, transcription regulatory activity, translation regulatory activity, or carrier activity. Some examples of therapeutic proteins may include, but are not limited to, an enzyme replacement protein, a protein for supplementation, a protein vaccination, antigens (eg, tumor, viral, bacterial antigens), hormones, cytokines, antibodies, immunotherapy (eg, cancer), reprogramming factor / cell transdifferentiation, transcription factors, chimeric antigen receptor, transposase or nuclease, immune effector (eg, influences susceptibility to an immune response / signal) , a regulated death-effecting protein (eg, an apoptosis or necrosis inducer), a non-lytic tumor inhibitor (eg, an oncoprotein inhibitor), an epigenetic modifying agent, epigenetic enzyme, a transcription factor, a DNA or protein modifying enzyme, a DNA intercalating agent, an efflux bomb inhibitor, a nuclear receptor activator or inhibitor, a proteasome inhibitor, a competitive enzyme inhibitor, an effect a protein synthesis inhibitor or inhibitor, a nuclease, a protein fragment or domain, a ligand or a receptor, and a CRISPR system or its component.
[0152] [0152] In some embodiments, exemplary proteins that can be expressed from the circular polyribonucleotide disclosed here include human proteins, for example, receptor-binding protein, hormone, growth factor, growth factor receptor modulator and regenerative protein ( eg proteins involved in proliferation and differentiation, eg therapeutic protein, for wound healing). In some embodiments, exemplary proteins that can be expressed from the circular polyribonucleotide disclosed here include EGF (epithelial growth factor). In some combinations, exemplary proteins that can be expressed from the circular polyribonucleotide disclosed here include enzymes, for example, oxidoreductase enzymes, metabolic enzymes, mitochondrial enzymes, oxygenases, dehydrogenases, ATP-independent enzymes and desaturases.
[0153] [0153] In some embodiments, the circular polyribonucleotide expresses an antibody, e.g., an antibody fragment or a portion thereof. In some embodiments, the antibody expressed by the circular polyribonucleotide can be of any isotype, such as IgA, IgD, IgE, IgG, IgM. In some embodiments, the circular polyribonucleotide expresses a portion of an antibody, such as a light chain, a heavy chain, an Fc fragment, a CDR (complementarity determining region), an Fv fragment or an Fab fragment, an additional portion thereof. In some embodiments, the circular polyribonucleotide expresses one or more portions of an antibody. For example, the circular polyribonucleotide can comprise more than one expression sequence, each of which expresses a portion of an antibody, and the sum of which can constitute the antibody. In some cases, the circular polyribonucleotide comprises an expression sequence encoding the heavy chain of an antibody and another expression sequence encoding the light chain of the antibody. In some cases, when the circular polyribonucleotide is expressed in a cell or in a cell-free environment, the light chain and heavy chain may be subject to modification, folding or other appropriate post-translational modifications to form a functional antibody. Regulatory elements
[0154] [0154] In some embodiments, the circular polyribonucleotide comprises a regulatory element, e.g., a sequence that modifies the expression of an expression sequence within the circular polyribonucleotide.
[0155] [0155] A regulatory element can include a sequence that is located adjacent to an expression sequence that encodes an expression product. A regulatory element can be operationally connected to the adjacent sequence. A regulatory element can increase an amount of product expressed compared to an amount of product expressed when there is no regulatory element. In addition, a regular element can increase an amount of products expressed for multiple expression sequences attached in tandem. Consequently, a regulatory element can enhance the expression of one or more expression sequences. Multiple regulatory elements are well known to those skilled in the art.
[0156] [0156] A regulatory element as provided here can include a selective translation sequence. As used here, the term "selective translation sequence" can refer to a nucleic acid sequence that selectively initiates or activates the translation of an expression sequence in the circular polyribonucleotide, for example, certain riboswtich aptazomes. A regulatory element can also include a selective degradation sequence. As used here, the term "selective degradation sequence" can refer to a nucleic acid sequence that initiates degradation of the circular polyribonucleotide or an expression product of the circular polyribonucleotide. Exemplary selective degradation sequences can include riboswitch aptzymes and miRNA binding sites.
[0157] [0157] In some modalities, the regulatory element is a modulator of translation. A translation modulator can modulate the translation of the expression sequence in the circular polyribonucleotide. A translation modulator can be a translation enhancer or suppressor. In some embodiments, the circular polyribonucleotide includes at least one translation modulator adjacent to at least one expression sequence. In some embodiments, the circular polyribonucleotide includes a translation modulator adjacent to each expression sequence. In some embodiments, the translation modulator is present on one or both sides of each expression sequence, leading to the separation of expression products, eg, peptide (s) and / or polypeptide (s).
[0158] [0158] In some modalities, a translation initiation sequence can act as a regulatory element. In some embodiments, a translation initiation sequence comprises an AUG codon. In some embodiments, a translation initiation sequence comprises any eukaryotic start codon such as AUG, CUG, GUG, UUG, ACG, AUC, AUU, AAG, AUA or AGG. In some embodiments, a translation initiation sequence comprises a Kozak sequence. In some modalities, the translation begins in an alternative translation initiation sequence, eg, translation initiation sequence other than the AUG codon, under selective conditions, eg, stress-induced conditions. As a non-limiting example, the translation of the circular polyribonucleotide can begin in the sequence of initiation of the alternative translation, such as ACG. As another non-limiting example, the translation of the circular polyribonucleotide can begin in the sequence of initiation of the alternative translation, CTG / CUG. As yet another non-limiting example, the translation of the circular polyribonucleotide can begin in the sequence of initiation of the alternative translation, GTG / GUG. As yet another non-limiting example, the circular polyribonucleotide can begin translation into a sequence other than the AUG (RAN) associated with the repetition, such as an alternate translation initiation sequence that includes short stretches of repetitive RNA, eg CGG , GGGGCC, CAG, CTG.
[0159] [0159] It is known that nucleotides flanking a codon that initiates translation, such as, but not limited to, a starting codon or an alternative starting codon, affect the efficiency of the translation, the length and / or the structure of the circular polyribonucleotide. (See, eg, Matsuda and Mauro PLoS ONE, 2010 5:11; the contents of which are incorporated herein by reference in their entirety). The masking of any of the nucleotides flanking a codon that initiates the translation can be used to change the position of the translation initiation, translation efficiency, length and / or structure of the circular polyribonucleotide.
[0160] [0160] In one embodiment, a masking agent can be used close to the departure codon or alternate start codon in order to mask or hide the codon to reduce the likelihood of translation initiation at the masked start codon or alternate start codon . Non-limiting examples of masking agents include antisense blocked nucleic acid (LNA) oligonucleotides and exon junction complexes (EJCs). (See, eg, Matsuda and Mauro describing oligonucleotide masking agents LNA and EJCs (PLoS ONE, 2010 5: 11); the contents of which are incorporated herein by reference in their entirety). In another embodiment, a masking agent can be used to mask a starting codon from the circular polyribonucleotide in order to increase the likelihood that the translation will start at an alternate starting codon.
[0161] [0161] In some embodiments, translation is initiated under selective conditions, such as but not limited to viral induced selection in the presence of GRSF-1 and the circular polyribonucleotide includes GRSF-1 binding sites, see for example http: / /jvi.asm.org/content/76/20/10417.full. Translation initiation sequence
[0162] [0162] In some embodiments, the circular polyribonucleotide encodes a polypeptide and may comprise a translation initiation sequence, eg, a start codon. In some embodiments, the translation initiation sequence includes a Kozak or Shine-Dalgarno sequence. In some embodiments, the circular polyribonucleotide includes the translation initiation sequence, e.g., Kozak sequence, adjacent to an expression sequence. In some embodiments, the translation initiation sequence is a non-coding start codon. In some embodiments, the translation initiation sequence, eg, Kozak sequence, is present on one or both sides of each expression sequence, leading to the separation of the expression products. In some embodiments, the circular polyribonucleotide includes at least one translation initiation sequence adjacent to an expression sequence. In some embodiments, the translation initiation sequence provides conformational flexibility to the circular polyribonucleotide. In some embodiments, the translation initiation sequence is within a substantially unique ribbon region of the circular polyribonucleotide.
[0163] [0163] The circular polyribonucleotide may include more than 1 starting codon such as, but not limited to, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 25, at least 30, at least 35, at least 40, at least 50, at least 60 or more than 60 starting codons. The translation can start at the first start codon or it can start downstream of the first start codon.
[0164] [0164] In some embodiments, the circular polyribonucleotide may start at a codon that is not the first starting codon, eg, AUG. The translation of the circular polyribonucleotide can begin in an alternative translation initiation sequence, such as, but not limited to, ACG, AGG, AAG, CTG / CUG, GTG / GUG, ATA / AUA, ATT / AUU, TTG / UUG (see Touriol et al. Biology of the Cell 95 (2003) 169-178 and Matsuda and Mauro PLoS ONE, 2010 5: 11; the contents of each of which are incorporated by reference in their entirety). In some modalities, translation begins in an initiation sequence of alternative translation under selective conditions, eg, stress-induced conditions. As a non-limiting example, the translation of the circular polyribonucleotide can begin in the sequence of initiation of the alternative translation, such as ACG. As another non-limiting example, the translation of the circular polyribonucleotide can begin in sequence of initiation of the alternative translation, CTG / CUG. As yet another non-limiting example, the translation of the circular polyribonucleotide can begin in the sequence of initiation of the alternative translation, GTG / GUG. As yet another non-limiting example, the circular polyribonucleotide can begin translation into a sequence other than the AUG (RAN) associated with the repetition, such as an alternate translation initiation sequence that includes short stretches of repetitive RNA, eg CGG , GGGGCC, CAG, CTG.
[0165] [0165] In some modalities, translation is initiated by treating eukaryotic initiation factor 4A (eIF4A) with Rocaglates (translation is suppressed by blocking the 43S scan, leading to initiation of translation upstream, premature and reduced protein expression from transcripts carrying the target sequence RocA – eIF4A, see, for example, www.nature.com/articles/nature17978). IRES
[0166] [0166] In some embodiments, the circular polyribonucleotide described here comprises an element of internal ribosomal entry site (IRES). An IRES element suitable for inclusion in a circular polyribonucleotide comprises an RNA sequence capable of enveloping a eukaryotic ribosome. In some modalities, the element
[0167] [0167] In some embodiments, the IRES element is at least partially derived from a virus, for example, it can be derived from a viral IRES element, such as ABPV_IGRpred, AEV, ALPV_IGRpred, BQCV_IGRpred, BVDV1_1-385, BVDV1_29-391, CrPV_5R , CrPV_IGR, crTMV_IREScp, crTMV_IRESmp75, crTMV_IRESmp228, crTMV_IREScp, crTMV_IREScp, CSFV, CVB3, DCV_IGR, EMCV-R, EoPV_5NTR, ERAV_245-961, -VV_245-961, ERV_245-961, ERV_2, , GBV-C, gypsy_env, gypsyD5, gypsyD2, HAV_HM175, HCV_type_1a, HiPV_IGRpred, HIV-1, HoCV1_IGRpred, HRV-2, IAPV_IGRpred, idefix, KBV_IGRpred, 1-LINE_-1__1F1, LINE-1_1 -
[0168] [0168] In some embodiments, the circular polyribonucleotide includes at least one IRES flanking at least one (eg, 2, 3, 4, 5 or more) expression sequence. In some embodiments, the IRES flanks both sides of at least one (eg, 2, 3, 4, 5 or more) expression sequence. In some embodiments, the circular polyribonucleotide includes one or more IRES sequences on one or both sides of each expression sequence, leading to the separation of the resulting peptide (s) and / or polypeptide (s). Terminating element
[0169] [0169] In some embodiments, the circular polyribonucleotide includes one or more expression sequences and each expression sequence may or may not have a terminating element. In some embodiments, the circular polyribonucleotide includes one or more expression sequences and the expression sequences do not have a terminating element, so that the circular polyribonucleotide is continuously translated. The exclusion of a terminating element can result in a rolling circle translation or continuous expression of expression product, eg, peptides or polypeptides, due to the lack of interruption or fall of the ribosome. In such an embodiment, the rolling circle translation expresses a product of continuous expression through each expression sequence. In some other embodiments, an ending element of an expression sequence can be part of a scaled element. In some embodiments, one or more expression sequences in the circular polyribonucleotide comprise a terminating element. However, translation of a rolling circle or expression of a subsequent expression sequence (eg, second, third, fourth, fifth, etc.) is performed on the circular polyribonucleotide. In such cases, the expression product may fall from the ribosome when the ribosome encounters the terminating element, e.g., a stop codon, and terminates the translation. In some embodiments, the translation is completed while the ribosome, eg, at least one subunit of the ribosome, remains in contact with the circular polyribonucleotide.
[0170] [0170] In some embodiments, the circular polyribonucleotide includes a terminating element at the end of one or more expression sequences. In some embodiments, one or more expression sequences comprise two or more terminating elements in succession. In such modalities, the translation is terminated and the rolling circle translation is terminated. In some modalities, the ribosome disengages completely with the circular polyribonucleotide. In some such embodiments, the production of a subsequent expression sequence (eg, second, third, fourth, fifth, etc.) in the circular polyribonucleotide may require the ribosome to re-engage with the circular polyribonucleotide before initiation of Translation. The termination elements generally include a triplet of grid nucleotides that signals the termination of the translation, eg UAA, UGA, UAG. In some embodiments, one or more terminating elements in the circular polyribonucleotide are terminating elements with grid offset, such as, but not limited to, off-grid reading frames or with -1 and +1 offset (e.g. , hidden stop) that can finish the translation. The grid-shifted termination elements include nucleotide triplets, TAA, TAG and TGA, which appear in the second and third reading frames of an expression sequence. Terminating elements with grid deviation can be important in preventing mRNA readings, which are often harmful to the cell. Stepped element
[0171] [0171] In some embodiments, the circular polyribonucleotide includes at least one staggered element adjacent to an expression sequence. In some embodiments, the circular polyribonucleotide includes a stepped element adjacent to each expression sequence. In some embodiments, the scaled element is present on one or both sides of each expression sequence, leading to the separation of expression products, eg, peptide (s) and / or polypeptide (s). In some embodiments, the scaled element is a portion of one or more expression sequences. In some embodiments, the circular polyribonucleotide comprises one or more expression sequences, and each of the one or more expression sequences is separated from a subsequent expression sequence by a stepped element in the circular polyribonucleotide. In some embodiments, the scaled element prevents the generation of a single polypeptide (a) from two translation rounds of a single expression sequence or (b) from one or more translation rounds of two or more expression sequences . In some embodiments, the scaled element is a sequence separate from one or more expression sequences. In some embodiments, the scaled element comprises a portion of an expression sequence from one or more expression sequences.
[0172] [0172] In some embodiments, the circular polyribonucleotide includes a stepped element. To prevent the production of a continuous expression product, eg, peptide or polypeptide, while the circle translation is maintained, a stepped element can be included to induce ribosomal pause during translation. In some embodiments, the scaled element is at the 3 'end of at least a portion of one or more expression sequences. The staggered element can be configured to interrupt a ribosome during the rolling circle translation of the circular polyribonucleotide. The stepped element may include, but is not limited to, a type 2A or CHYSEL sequence (cis-acting hydrolase element). In some embodiments, the scaled element encodes a sequence with a C-terminal consensus sequence that is X1X2X3EX5NPGP, where X1 is absent or is G or H, X2 is absent or is D or G, X3 is D or V or I or S or M, and X5 is any amino acid. In some embodiments, this sequence comprises a non-conserved amino acid sequence with a strong alpha-helical propensity followed by the consensus sequence -D (V / I) ExNPG P, where x = any amino acid. Some non-limiting examples of scaled elements include GDVESNPGP, GDIEENPGP, VEPNPGP, IETNPGP, GDIESNPGP, GDVELNPGP, GDIETNPGP, GDVENPGP, GDVEENPGP, GDVEQNPGP,
[0173] [0173] In some embodiments, the stepped element described here cleaves an expression product, such as between G and P of the consensus sequence described here. As a non-limiting example, the circular polyribonucleotide includes at least one stepped element to cleave the expression product. In some embodiments, the circular polyribonucleotide includes a stepped element adjacent to at least one expression sequence. In some embodiments, the circular polyribonucleotide includes a stepped element after each expression sequence. In some embodiments, the circular polyribonucleotide includes a stepped element present on one or both sides of each expression sequence, leading to the translation of individual peptide (s) and / or polypeptide (s) from each sequence of expression.
[0174] [0174] In some embodiments, a stepped element comprises one or more modified nucleotides or unnatural nucleotides that induce ribosomal pause during translation. Unnatural nucleotides can include peptide nucleic acid (PNA), Morpholino and blocked nucleic acid (LNA), as well as glycol nucleic acid (GNA) and threose nucleic acid (TNA). Examples such as these are distinguished from DNA or RNA occurring naturally by changes to the molecule's skeleton. Exemplary modifications may include any modification to sugar, nucleobase, internucleoside bonding (eg, a phosphate binding / phosphodiester bond / phosphodiester backbone) and any combination that may induce ribosomal pause during translation . Some of the exemplary modifications provided here are described elsewhere here.
[0175] [0175] In some modalities, the staggered element is present in the circular polyribonucleotide in other forms. For example, in some exemplary circular polyribonucleotides, a stepped element comprises a terminating element for a first expression sequence in the circular polyribonucleotide and a nucleotide spacer sequence that separates the terminating element for a first translation initiation sequence from a successive expression to the first expression string. In some examples, the first stepped element of the first expression sequence is upstream of (5 'with respect to) a first expression translation initiation sequence following the first expression sequence in the circular polyribonucleotide. In some cases, the first expression sequence and the expression sequence following the first expression sequence are two separate expression sequences in the circular polyribonucleotide. The distance between the first stepped element and the first translation initiation sequence can allow for continuous translation of the first expression sequence and its subsequent expression sequence. In some embodiments, the first stepped element comprises a terminating element and separates an expression product from the first expression sequence of an expression product from its subsequent expression sequences, thereby creating discrete expression products.
[0176] [0176] In some embodiments, the circular polyribonucleotide comprises one or more expression sequences that encode regulatory nucleic acid, eg, which modifies the expression of an endogenous gene and / or an exogenous gene. In some embodiments, the expression sequence of a circular polyribonucleotide as provided herein may comprise a sequence that is antisense to a regulatory nucleic acid such as a non-coding RNA, such as, but not limited to, tRNA, lncRNA, miRNA, rRNA, snRNA, microRNA, siRNA, piRNA, snoRNA, snRNA, exRNA, scaRNA, Y RNA and hnRNA.
[0177] [0177] In one embodiment, the regulatory nucleic acid targets a host gene. Regulatory nucleic acids may include, but are not limited to, a nucleic acid that hybridizes to an endogenous gene (eg, miRNA, siRNA, mRNA, lncRNA, RNA, DNA, an antisense RNA, gRNA as described here elsewhere place), nucleic acid that hybridizes to an exogenous nucleic acid such as viral DNA or RNA, nucleic acid that hybridizes to an RNA, nucleic acid that interferes with gene transcription, nucleic acid that interferes with RNA translation, nucleic acid that stabilizes RNA or destabilizes RNA such as by targeting degradation and nucleic acid that modulates a DNA or RNA binding factor. In one embodiment, the sequence is a miRNA. In some embodiments, the regulatory nucleic acid targets a sense strand of a host gene. In some embodiments, the regulatory nucleic acid targets an antisense strand of a host gene.
[0178] [0178] In some embodiments, the circular polyribonucleotide comprises a regulatory nucleic acid, such as a guide RNA (gRNA). In some embodiments, the circular polyribonucleotide comprises a guide RNA or encodes the guide RNA. A short synthetic RNA gRNA composed of a "template" sequence required for binding to the incomplete effector fraction and a definida 20 nucleotide targeting sequence defined by the user to a genomic target. In practice, guide RNA sequences are generally designed to be between 17 - 24 nucleotides (e.g., 19, 20 or 21 nucleotides) in length and complementary to the target nucleic acid sequence. Customized gRNA generators and algorithms are commercially available for use in effective guide RNA design. Genetic editing has also been achieved using a chimeric "simple guide RNA" ("sgRNA"), a simple manipulated (synthetic) RNA molecule that mimics a naturally occurring crRNA-tracrRNA complex and contains both a tracrRNA (for nuclease binding) and by minus one crRNA (to guide the nuclease to the target sequence for editing). Chemically modified sgRNAs have also been shown to be effective in editing the genome; see, for example, Hendel et al. (2015) Nature Biotechnol., 985 - 991.
[0179] [0179] The gRNA can recognize specific DNA sequences (eg, sequences adjacent to or within a gene promoter, enhancer, silencer or repressor).
[0180] [0180] In one embodiment, gRNA is used as part of a CRISPR system for editing genes. For the purposes of genetic editing, the circular polyribonucleotide can be designed to include one or multiple guide RNA sequences corresponding to a desired target DNA sequence; see, for example, Cong et al. (2013) Science, 339: 819–823; Ran et al. (2013) Nature Protocols, 8: 2281 - 2308. At least about 16 or 17 nucleotides of the gRNA sequence are required by Cas9 for DNA cleavage to occur; for Cpf1, at least about 16 nucleotides of the gRNA sequence are required to achieve detectable DNA cleavage.
[0181] [0181] Certain regulatory nucleic acids can inhibit gene expression through the biological process of RNA interference (RNAi). RNAi molecules comprise RNA or RNA-like structures typically containing 15-50 base pairs (such as about 18-25 base pairs) and having an identical (complementary) or almost identical (substantially complementary) nucleobase sequence to a sequence encoding a target gene expressed within the cell. RNAi molecules include, but are not limited to: short interfering RNAs (siRNAs), double-stranded RNA (dsRNAs), microRNA (miRNAs), short-clip RNAs (shRNAs), meroduplexes and Dicer substrates (U.S. Pat. Nos. 8,084,599, 8,349,809 and 8,513,207).
[0182] [0182] In some embodiments, the circular polyribonucleotide comprises regulatory nucleic acids that are RNA or RNA-like structures typically between about 5-500 base pairs (depending on the specific structure of the RNA, eg, miRNA 5-30 pbs, lncRNA 200-500 pbs) and may have an identical (complementary) or almost identical (substantially complementary) nucleobase sequence to a coding sequence in a target gene expressed within the cell.
[0183] [0183] Long non-coding RNAs (lncRNA) are defined as non-coding protein transcripts longer than 100 nucleotides. This somewhat arbitrary limit distinguishes lncRNAs from small regulatory RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs) and other short RNAs. In general, the majority (~ 78%) of lncRNAs are characterized as tissue specific. Divergent lncRNAs that are transcribed in the opposite direction to genes encoding nearby proteins (comprising a significant ~ 20% proportion of total lncRNAs in mammalian genomes) may possibly regulate transcription of the nearby gene. In one embodiment, the circular polyribonucleotide provided here comprises a sense strand of an lncRNA. In one embodiment, the circular polyribonucleotide provided here comprises an antisense strand of an lncRNA.
[0184] [0184] The circular polyribonucleotide can encode a regulatory nucleic acid substantially complementary, or fully complementary, to all or a fragment of an endogenous gene or gene product (e.g., mRNA). Regulatory nucleic acids can complement sequences at the border between introns and exons, between exons or adjacent to exons, to prevent the maturation of newly generated nuclear RNA transcripts from specific genes in mRNA for transcription. Regulatory nucleic acids that are complementary to specific genes can hybridize with the mRNA for that gene and prevent its translation. The antisense regulatory nucleic acid can be DNA, RNA or a derivative or hybrid thereof. In some embodiments, the regulatory nucleic acid comprises a protein-binding site that can bind to a protein that participates in regulating the expression of an endogenous gene or an exogenous gene.
[0185] [0185] The length of the circular polyribonucleotide can encode a regulatory nucleic acid that hybridizes to a transcript of interest that is between 5 and 30 nucleotides, between about 10 and 30 nucleotides or about 11, 12, 13, 14, 15, 16 , 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more nucleotides. The degree of identity of the regulatory nucleic acid to the target transcript must be at least 75%, at least 80%, at least 85%, at least 90% or at least 95%.
[0186] [0186] The circular polyribonucleotide can encode a micro-RNA (miRNA) molecule identical to about 5 to about 25 contiguous nucleotides of a target gene. In some embodiments, the miRNA sequence targets an mRNA and begins with the dinucleotide AA, comprises a GC content of about 30-70% (about 30-60%, about 40-60% or about 45% - 55%) and does not have a high percentage of identity with any nucleotide sequence other than the target in the mammalian genome into which it is to be introduced, for example as determined by standard BLAST screening.
[0187] [0187] In some embodiments, the circular polyribonucleotide comprises at least one miRNA, eg, 2, 3, 4, 5, 6 or more. In some embodiments, the circular polyribonucleotide comprises a sequence that encodes a miRNA at least about 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identity nucleotide sequences with any of the nucleotide sequences or a sequence that is complementary to a target sequence.
[0188] [0188] siRNA and shRNA resemble intermediates in the processing pathway of endogenous microRNA (miRNA) genes (Bartel, Cell 116: 281-297, 2004). In some modalities, siRNAs can function as miRNAs and vice versa (Zeng et al., Mol Cell 9: 1327-1333, 2002; Doench et al., Genes Dev 17: 438-442, 2003). MicroRNAs, like siRNAs, use RISC to subregulate target genes, but unlike siRNAs, most animal miRNAs do not cleave mRNA. Instead, miRNAs reduce protein production through translational suppression or removal of polyA and degradation of mRNA (Wu et al., Proc Natl Acad Sci USA 103: 4034-4039, 2006). The known miRNA binding sites are within the 3 'mRNA RTU; miRNAs appear to target sites with almost perfect complementarity with nucleotides 2-8 from the 5 'end of miRNA (Rajewsky, Nat Genet 38 Supl: S8-13, 2006; Lim et al., Nature 433: 769-773, 2005 ). This region is known as the seed region. Since siRNAs and miRNAs are interchangeable, exogenous siRNAs subregulate mRNAs with seed complementarity in siRNA (Birmingham et al., Nat Methods 3: 199- 204, 2006). Multiple target sites within a 3 'RTU give stronger sub-regulation (Doench et al., Genes Dev 17: 438- 442, 2003).
[0189] [0189] Lists of known miRNA sequences can be found in databases maintained by research organizations, such as Wellcome Trust Sanger Institute, Penn Center for Bioinformatics, Memorial Sloan Kettering Cancer
[0190] [0190] The circular polyribonucleotide can modulate the expression of RNA encoded by a gene. Since multiple genes can share some degree of sequence homology with each other, in some embodiments, the circular polyribonucleotide can be designed to target a class of genes with sufficient sequence homology. In some embodiments, the circular polyribonucleotide may contain a sequence that is complementary to sequences that are shared between different gene targets or are unique to a specific gene target. In some embodiments, the circular polyribonucleotide can be designed to target conserved regions of an RNA sequence having homology between several genes, thereby targeting several genes in a family of genes (eg, isoforms of different genes, splice variants, genes mutants, etc.). In some embodiments, the circular polyribonucleotide can be designed to target a sequence that is unique to a single gene-specific RNA sequence.
[0191] [0191] In some embodiments, the expression sequence is less than 5000 pbs in length (eg less than about 5000 pbs, 4000 pbs, 3000 pbs, 2000 pbs, 1000 pbs, 900 pbs, 800 pbs , 700 pbs, 600 pbs, 500 pbs, 400 pbs, 300 pbs, 200 pbs, 100 pbs, 50 pbs, 40 pbs, 30 pbs, 20 pbs, 10 pbs or less). In some embodiments, the expression sequence has, independently or in addition to, a length greater than 10 pbs (eg, at least about 10 pbs, 20 pbs, 30 pbs, 40 pbs, 50 pbs, 60 pbs, 70 pbs, 80 pbs, 90 pbs, 100 pbs, 200 pbs, 300 pbs, 400 pbs, 500 pbs, 600 pbs, 700 pbs, 800 pbs, 900 pbs, 1000 kb, 1.1 kb, 1.2 kb, 1 , 3 kb, 1.4 kb, 1.5 kb, 1.6 kb, 1.7 kb, 1.8 kb, 1.9 kb, 2 kb, 2.1 kb, 2.2 kb, 2.3 kb, 2.4 kb, 2.5 kb, 2.6 kb, 2.7 kb, 2.8 kb, 2.9 kb, 3 kb, 3.1 kb, 3.2 kb, 3.3 kb, 3.4 kb, 3.5 kb, 3.6 kb, 3.7 kb, 3.8 kb, 3.9 kb, 4 kb, 4.1 kb, 4.2 kb, 4.3 kb, 4, 4 kb, 4.5 kb, 4.6 kb, 4.7 kb, 4.8 kb, 4.9 kb, 5 kb or greater).
[0192] [0192] In some embodiments, the expression sequence comprises one or more of the characteristics described here, e.g., a sequence encoding one or more peptides or proteins, one or more regulatory elements, one or more regulatory nucleic acids, e.g. , one or more non-coding RNAs, other expression sequences and any combination thereof. Translation Efficiency
[0193] [0193] In some embodiments, the translation efficiency of a circular polyribonucleotide as provided here is greater than a reference, e.g., a linear counterpart, a linear expression sequence, or a linear circular polyribonucleotide. In some embodiments, a circular polyribonucleotide as provided here has a translation efficiency that is at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50% , 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 125%, 150%, 175%, 200%, 250%, 300%, 350 %, 400%, 450%, 500%, 600%, 70%, 800%, 900%, 1000%, 2000%, 5000%, 10000%, 100000% or greater than that of a reference. In some embodiments, a circular polyribonucleotide has a translation efficiency 10% greater than that of a linear counterpart. In some embodiments, a circular polyribonucleotide has a translation efficiency 300% greater than that of a linear counterpart.
[0194] [0194] In some embodiments, the circular polyribonucleotide produces stoichiometric ratios of expression products. The rolling circle translation continuously produces expression products for substantially equivalent reasons. In some embodiments, the circular polyribonucleotide has a stoichiometric translation efficiency, so that the expression products are produced for substantially equivalent reasons. In some embodiments, the circular polyribonucleotide has a stoichiometric translation efficiency of multiple expression products, eg products from 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more expression strings.
[0195] [0195] In some embodiments, once translation of the circular polyribonucleotide has begun, the ribosome attached to the circular polyribonucleotide does not disengage from the circular polyribonucleotide before completing at least one round of translation of the circular polyribonucleotide. In some embodiments, the circular polyribonucleotide as described here is competent for translation of a rolling circle. In some modalities, during the translation of the rolling circle, once the translation of the circular polyribonucleotide has started, the ribosome attached to the circular polyribonucleotide does not disengage from the circular polyribonucleotide before finishing at least 2 rounds, at least 3 rounds, at least 4 rounds, in at least 5 rounds, at least 6 rounds, at least 7 rounds, at least 8 rounds, at least 9 rounds, at least 10 rounds, at least 12 rounds, at least 13 rounds, at least 14 rounds , in at least 15 rounds, at least 20 rounds, at least 30 rounds, at least 40 rounds, at least 50 rounds, at least 60 rounds, at least 80 rounds, at least 90 rounds, at least 100 rounds rounds, in at least 150 rounds, at least 200 rounds, at least 250 rounds, at least 1000 rounds, at least 1500 rounds, at least 2000 rounds, at least 5000 rounds, at least 10,000 rounds, at least 105 rounds or less s 106 rounds of translation of the circular polyribonucleotide.
[0196] [0196] In some embodiments, the rolling circle translation of the circular polyribonucleotide leads to the generation of the polypeptide product that is translated from more than one round of translation of the circular polyribonucleotide (product of “continuous” expression). In some embodiments, the circular polyribonucleotide comprises a stepped element, and the rolling circle translation of the circular polyribonucleotide leads to the generation of the polypeptide product that is generated from a single translation round or less than a single translation round of the polyribonucleotide circular (product of “discreet” expression). In some embodiments, the circular polyribonucleotide is configured so that at least 10%, 20%, 30%, 40%, 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% of the total polypeptides (molar / molar) generated during translation of circular polyribonucleotide are discrete polypeptides.
[0197] [0197] In some embodiments, the circular polyribonucleotide comprises untranslated regions (RTUs). RTUs from a genomic region comprising a gene can be transcribed, but not translated. In some embodiments, a RTU may be included upstream of the translation initiation sequence for an expression sequence described here. In some embodiments, a RTU can be included downstream of an expression sequence described here. In some cases, a RTU for the first expression sequence is equal to or continuous with or overlaid with another RTU for a second expression sequence. In some embodiments, the intron is a human intron. In some embodiments, the intron is a full-length human intron, eg, ZKSCAN1.
[0198] [0198] In some embodiments, the circular polyribonucleotide comprises an RTU with one or more stretches of Adenosines and Uridines embedded inside. These AU rich signatures can increase the renewal rates of the expression product.
[0199] [0199] The introduction, removal or modification of AU-rich elements of RTU (AREs) can be useful to modulate the stability or immunogenicity of the circular polyribonucleotide. When specific circular polyribonucleotides are manipulated, one or more copies of an ARE can be introduced into the circular polyribonucleotide and copies of an ARE can modulate the translation and / or production of an expression product. Likewise, AREs can be identified and removed or manipulated in the circular polyribonucleotide to modulate intracellular stability and thus affect the translation and production of the resulting protein.
[0200] [0200] It should be understood that any RTU of any gene can be incorporated into the respective flanking regions of the circular polyribonucleotide. As a non-limiting example, the RTU or a fragment thereof that can be incorporated is a RTU listed in US Provisional Orders Nos. US 61 / 775,509 and US 61 / 829,372 or in International Patent Application No. PCT / US2014 / 021522; the contents of each of which are incorporated herein by reference in their entirety. In addition, multiple wild-type RTUs of any known gene can be used. It is also within the scope of the present invention to provide artificial RTUs that are not variants of wild-type genes. These RTUs or their portions can be placed in the same orientation as in the transcript from which they were selected or can be changed in orientation or location. Consequently, a 5 'or 3' RTU can be inverted, shortened, elongated, made chimeric with one or more other 5 'RTUs or 3' RTUs. As used here, the term “changed” as it relates to a RTU sequence means that the RTU has been changed in some way from a reference sequence. For example, a 3 'or 5' RTU can be changed from a wild-type or native RTU by changing the orientation or location as taught above or it can be changed by adding additional nucleotides, deleting nucleotides, exchanging or transposing nucleotides. Any of these changes producing an “altered” RTU (3´ or 5´) comprises a variant RTU.
[0201] [0201] In one mode, a double, triple or quadruple RTU, such as a 5´ or 3´ RTU, can be used. As used here, a "double" RTU is one in which two copies of the same RTU are encoded serially or substantially serially. For example, a double 3-beta-globin RTU can be used as described in U.S. Patent Publication 20100129877, the contents of which are incorporated herein by reference in their entirety. PolyA string
[0202] [0202] In some embodiments, the circular polyribonucleotide may include a poly-A sequence. In some embodiments, the length of a poly-A sequence is greater than 10 nucleotides in length. In one embodiment, the poly-A sequence is more than 15 nucleotides in length (eg, at least or greater than about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1,000, 1,100, 1,200, 1,300, 1,400, 1,500, 1,600, 1,700, 1,800, 1,900, 2,000, 2,500 and 3,000 nucleotides). In some embodiments, the poly-A sequence has about 10 to about 3,000 nucleotides (e.g., 30 to 50, 30 to 100, 30 to 250, 30 to 500, 30 to 750, from 30 to 1,000,
[0203] [0203] In one embodiment, the poly-A sequence is drawn in relation to the length of the global circular polyribonucleotide. This design can be based on the length of the coding region, the length of a particular feature or region (such as the first or flanking regions) or based on the length of the final product expressed from the circular polyribonucleotide. In this context, the poly-A sequence can be 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100% longer in length than the circular polyribonucleotide or a characteristic thereof. The poly-A sequence can also be designed as a circular polyribonucleotide fraction to which it belongs. In this context, the poly-A sequence can be 10, 20, 30, 40, 50, 60, 70, 80 or 90% or more of the total construct length or the total construct length minus the poly-A sequence . In addition, the engineered binding sites and the conjugation of circular polyribonucleotide to the Poly-A binding protein can enhance expression.
[0204] [0204] In one embodiment, the circular polyribonucleotide is designed to include a quartet of polyA-G. The G quartet is an arrangement linked to cyclic hydrogen of four guanine nucleotides that can be formed by G-rich sequences in both DNA and RNA. In one embodiment, the G quartet is incorporated at the end of the poly-A sequence. The resulting circular polyribonucleotide construct is analyzed for stability, protein production and / or other parameters including half-life at various time points. In some embodiments, the polyA-G quartet results in protein production equivalent to at least 75% of that view using a 120 nucleotide poly-A sequence alone.
[0205] [0205] In some embodiments, the circular polyribonucleotide comprises a polyA, does not have a polyA, or has a polyA modified to modulate one or more characteristics of the circular polyribonucleotide. In some embodiments, the circular polyribonucleotide having no polyA or having modified polyA improves one or more functional characteristics, eg, immunogenicity, half-life, expression efficiency, etc. Binding to RNA
[0206] [0206] In some embodiments, the circular polyribonucleotide comprises one or more RNA binding sites. MicroRNAs (or miRNAs) are short, non-coding RNAs that bind to the 3'UTR of nucleic acid molecules and downregulate gene expression by reducing the stability of nucleic acid molecules or by inhibiting translation. The circular polyribonucleotide may comprise one or more microRNA target sequences, microRNA sequences or microRNA seeds. Such sequences can correspond to any known microRNA, such as those taught in US Publication US2005 / 0261218 and US Publication US2005 / 0059005, the contents of which are incorporated herein by reference in their entirety.
[0207] [0207] A microRNA sequence comprises a "seed" region, i.e., a sequence in the 2-8 position region of the mature microRNA, which sequence has Watson-Crick's perfect complementarity with the target miRNA sequence. A microRNA seed can comprise positions 2-8 or 2-7 of the mature microRNA. In some embodiments, a microRNA seed may comprise 7 nucleotides (eg, nucleotides 2-8 of the mature microRNA), where the complementary seed site on the corresponding miRNA target is flanked by an adenine (A) opposite the position 1 of microRNA. In some embodiments, a microRNA seed may comprise 6 nucleotides (eg, nucleotides 2-7 of the mature microRNA), where the complementary seed location on the corresponding miRNA target is flanked by an adenine (A) opposite the position 1 of microRNA. See, for example, Grimson A, Farh K, Johnston WK, Garrett-Engele P, Lim LP, Barrel DP; Mol Cell. Jul 6, 2007;
[0208] [0208] The microRNA seed bases are substantially complementary to the target sequence. By manipulating microRNA target sequences in the circular polyribonucleotide, the circular polyribonucleotide can escape or be detected by the host's immune system, have modulated degradation or modulated translation, as long as the microRNA in question is available. This process will reduce the danger of off-target effects after administration of circular polyribonucleotides. The identification of microRNA, microRNA target regions and their patterns of expression and role in biology have been reported (Bonauer et al., Curr Drug Targets 2010 11: 943-949; Anand and Cheresh Curr Opin Hematol 2011 18: 171-176; Contreras and Rao Leukemia 2012 26: 404-413 (20 Dec 2011. doi:
[0209] [0209] Conversely, microRNA binding sites can be manipulated outside (i.e., removed) of the circular polyribonucleotide to modulate protein expression in specific tissues. Regulation of expression in multiple tissues can be achieved by introducing or removing one or more microRNA binding sites.
[0210] [0210] Examples of tissues where microRNAs are known to regulate mRNA and thus protein expression,
[0211] [0211] The circular polyribonucleotide disclosed here may comprise a miRNA binding site that hybridizes to any miRNA, such as any of those disclosed in miRNA databases, such as miRBase, deepBase, miRBase, microRNA.org, miRGen 2, 0; miRNAMap, PMRD, TargetScan or VIRmiRNA. In some cases, the miRNA binding site can be any site that is complementary to a miRNA whose target gene is disclosed in microRNA target gene databases such as StarBase, StarScan, Cupid, TargetScan, TarBase, Diana-microT, miRecords, PicTar, PITA, RepTarm RNA22, miRTarBase, miRwalk or MBSTAR.
[0212] [0212] Through an understanding of microRNA expression patterns in different cell types, the circular polyribonucleotide described here can be manipulated for more targeted expression in specific cell types or only under specific biological conditions. By introducing tissue-specific microRNA binding sites, the circular polyribonucleotide can be designed for optimal expression of proteins in a tissue or in the context of a biological condition Examples of using microRNA to direct the expression of tissue-specific genes or diseases are listed (Getner and Naldini, Tissue Antigens. 2012, 80: 393-403; incorporated herein by reference in their entirety).
[0213] [0213] In addition, microRNA seed sites can be incorporated into the circular polyribonucleotide to modulate expression in certain cells which results in biological improvement. An example of this is the incorporation of miR-142 sites. The incorporation of miR-142 sites into the circular polyribonucleotide described here can modulate expression in hematopoietic cells, but also reduce or abolish immune responses to a protein encoded in the circular polyribonucleotide.
[0214] [0214] In some embodiments, the circular polyribonucleotide includes one or more binding sites to large intergenic non-coding RNAs (lincRNA). Large intergenic non-coding RNAs (lincRNAs) constitute the majority of long non-coding RNAs. LincRNAs are non-coding transcripts and, in some embodiments, are more than about 200 nucleotides in length. In some modalities they have an exon-intron-exon structure, similar to protein coding genes, but do not include open reading frames and do not encode proteins. More than 8,000 lincRNAs have been described recently and are thought to be the largest subclass of RNAs, originating from the non-coding transcriptome in humans. Thousands of lincRNAs are known and some appear to be key regulators of several cellular processes. Determining the function of individual lincRNAs remains a challenge. The expression of lincRNA is remarkably tissue-specific compared to coding genes, and that they are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of genes encoding neighboring proteins.
[0215] [0215] In some embodiments, the circular polyribonucleotide includes one or more lincRNAs, such as FIRRE, LINC00969, PVT1, LINC01608, JPX, LINC01572, LINC00355,
[0216] [0216] In some embodiments, the circular polyribonucleotide includes one or more protein-binding sites that allow a protein, eg, a ribosome, to bind to an internal site in the RNA sequence. By manipulating protein binding sites, eg ribosome binding sites, in the circular polyribonucleotide, the circular polyribonucleotide may escape or have reduced detection by the host's immune system, have modulated degradation or modulated translation, by masking the circular polyribonucleotide from components of the host's immune system.
[0217] [0217] In some embodiments, the circular polyribonucleotide comprises at least one immunoprotein-binding site, for example to escape immune responses, eg, CTL responses (cytotoxic T lymphocytes). In some embodiments, the immunoprotein binding site is a sequence of nucleotides that binds to an immunoprotein and assists in masking the circular polyribonucleotide as exogenous. In some embodiments, the immunoprotein binding site is a sequence of nucleotides that binds to an immunoprotein and helps to hide the circular polyribonucleotide as exogenous or foreign.
[0218] [0218] Traditional mechanisms of ribosome wrapping with linear RNA involve binding the ribosome to the 5 'capped end of an RNA. From the 5 'end, the ribosome migrates to an initiation codon, after which the first peptide bond is formed. According to the present invention, the internal (i.e., cap-independent) initiation of the translation of the circular polyribonucleotide does not require a free end or a capped end. Instead, a ribosome attaches to an internal, non-capped site, whereby the ribosome begins elongating the polypeptide in an initiation codon. In some embodiments, the circular polyribonucleotide includes one or more RNA sequences comprising a ribosome binding site, e.g., an initiation codon.
[0219] [0219] The natural 5'UTRs have characteristics that play roles in the initiation of translation. They house signatures like Kozak sequences that are commonly known to be involved in the process by which the ribosome initiates the translation of many genes. Kozak sequences have the CCR (A / G) CCAUGG consensus, where R is a purine (adenine or guanine) three bases upstream from the start codon (AUG), which is followed by another "G". It is also known that the 5´UTR form secondary structures that are involved in the connection of the elongation factor.
[0220] [0220] In some embodiments, the circular polyribonucleotide encodes a protein-binding sequence that binds to a protein. In some embodiments, the protein-binding sequence targets or localizes the circular polyribonucleotide to a specific target. In some embodiments, the protein-binding sequence specifically binds to an arginine-rich region of a protein.
[0221] [0221] In some embodiments, the protein binding site includes, but is not limited to, a protein binding site such as ACIN1, AGO, APOBEC3F, APOBEC3G, ATXN2, AUH, BCCIP, CAPRIN1, CELF2, CPSF1, CPSF2 , CPSF6, CPSF7, CSTF2, CSTF2T, CTCF, DDX21, DDX3, DDX3X, DDX42, DGCR8, EIF3A, EIF4A3, EIF4G2, ELAVL1, ELAVL3, FAM120A, FBL, FIP1L, FKBP4, FMR1, , HNRNPA1, HNRNPA2B1, HNRNPC, HNRNPK, HNRNPL, HNRNPM, HNRNPU, HNRNPUL1, IGF2BP1, IGF2BP2, IGF2BP3, ILF3, KHDRBS1, LN, LM, LM, NOP58, NPM1, NUDT21, PCBP2, POLR2A, PRPF8, PTBP1, RBFOX2, RBM10, RBM22, RBM27, RBM47, RNPS1, SAFB2, SBDS, SF3A3, SF3B4, SIRT7, SLBP, SLTM, SRM, SRT, SMNDC SRSF7, SRSF9, TAF15, TARDBP, TIA1, TNRC6A, TOP3B, TRA2A, TRA2B, U2AF1, U2AF2, UNK, UPF1, WDR33, XRN2, YBX1, YTHDC1, YTHDF1, YTHDF2, YWHAG, ZK3 and any other protein binds to RNA. Encryptogen
[0222] [0222] As described here, the circular polyribonucleotide comprises an encryptogen to reduce, escape or prevent a cell's innate immune response. In one aspect, circular polyribonucleotide is provided here which, when administered to cells, results in a reduced immune response from the host compared to the response elicited by a reference compound, e.g., a linear polynucleotide corresponding to the described circular polyribonucleotide or a circular polyribonucleotide having no encryptogen. In some embodiments, the circular polyribonucleotide has less immunogenicity than a counterpart without an encryptogen.
[0223] [0223] In some embodiments, an encryptogen enhances stability. There is a growing body of evidence about the regulatory roles played by RTUs in terms of the stability of a nucleic acid molecule and translation. The regulatory characteristics of an RTU can be included in the encryptogen to enhance the stability of the circular polyribonucleotide.
[0224] [0224] In some embodiments, the 5 'or 3'UTRs may constitute encryptogens in a circular polyribonucleotide. For example, the removal or modification of AU-rich UTR elements (AREs) can be useful to modulate the stability or immunogenicity of the circular polyribonucleotide.
[0225] [0225] In some embodiments, the removal or modification of AU-rich elements (AREs) in the expression sequence, eg, translatable regions, can be useful to modulate the stability or immunogenicity of the circular polyribonucleotide.
[0226] [0226] In some embodiments, an encryptogen comprises the miRNA binding site or the binding site to any other non-coding RNAs. For example, the incorporation of miR-142 sites in the circular polyribonucleotide described here can not only modulate expression in hematopoietic cells, but also reduce or abolish immune responses to a protein encoded in the circular polyribonucleotide.
[0227] [0227] In some embodiments, an encryptogen comprises one or more protein-binding sites that allow a protein, eg, an immunoprotein, to bind to the RNA sequence. By manipulating protein-binding sites in the circular polyribonucleotide, the circular polyribonucleotide may escape or have reduced detection by the host's immune system, have modulated degradation or modulated translation, by masking the circular polyribonucleotide from components of the host's immune system. In some embodiments, the circular polyribonucleotide comprises at least one immunoprotein binding site, for example to escape immune responses, e.g., CTL responses. In some embodiments, the immunoprotein binding site is a sequence of nucleotides that binds to an immunoprotein and assists in masking the circular polyribonucleotide as exogenous.
[0228] [0228] In some embodiments, an encryptogen comprises one or more modified nucleotides. Exemplary modifications may include any modification to sugar, nucleobase, internucleoside binding (e.g., a phosphate binding / phosphodiester bond / phosphodiester backbone) and any combination thereof that may prevent or reduce the immune response against the circular polyribonucleotide. Some of the exemplary modifications provided here are described in detail below.
[0229] [0229] In some embodiments, the circular polyribonucleotide includes one or more modifications as described elsewhere here to reduce an immune response from the host compared to the response triggered by a reference compound, e.g., a circular polyribonucleotide not having the modifications. In particular, it has been shown that the addition of one or more inosines discriminates RNA as endogenous versus viral. See, for example, Yu, Z. et al. (2015) RNA editing by ADAR1 marks dsRNA as “self”. Cell Res. 25, 1283–1284, which is incorporated by reference in its entirety.
[0230] [0230] In some embodiments, the circular polyribonucleotide includes one or more expression sequences for shRNA or an RNA sequence that can be processed into siRNA, and the shRNA or siRNA targets RIG-1 and reduces RIG-1 expression. RIG-1 can detect foreign circular RNA and leads to the degradation of foreign circular RNA. Therefore, a circular polynucleotide harboring sequences for shRNA targeting RIG-1, siRNA or any other regulatory nucleic acids can reduce the immunity, e.g., host cell immunity, against the circular polyribonucleotide.
[0231] [0231] In some embodiments, the circular polyribonucleotide does not have a sequence, element or structure that assists the circular polyribonucleotide in reducing, escaping or preventing an innate immune response in a cell. In some such embodiments, the circular polyribonucleotide may lack a polyA sequence, a 5 'end, a 3' end, a phosphate group, a hydroxyl group or any combination thereof. Riboswitches
[0232] [0232] In some embodiments, the circular polyribonucleotide comprises one or more riboswitches.
[0233] [0233] A riboswitch is typically considered to be a part of the circular polyribonucleotide that can bind directly to a small target molecule and whose binding to the target affects RNA translation, expression product stability and activity (Tucker BJ, Breaker RR (2005 ), Curr Opin Struct Biol 15 (3): 342-8). Thus, the circular polyribonucleotide that includes a riboswitch is directly involved in the regulation of its own activity, depending on the presence or absence of its target molecule. In some embodiments, a riboswitch has an aptamer-like affinity region for a separate molecule. Thus, in the broader context of the present invention, any aptamer included within a non-coding nucleic acid can be used for sequestering molecules from large volumes. Reporting downstream of the event through the “(ribo) switch” activity can be especially advantageous.
[0234] [0234] In some embodiments, the riboswitch may have an effect on gene expression including, but not limited to, transcriptional termination, inhibition of translation initiation, mRNA autocleaving and, in eukaryotes, alteration of splicing pathways. The riboswitch can work to control gene expression by attaching or removing a trigger molecule. Thus, subjecting a circular polyribonucleotide that includes the riboswitch to conditions that activate, deactivate or block the riboswitch to alter expression. Expression can be altered as a result of, for example, terminating transcription or blocking ribosome binding to RNA. The binding of a trigger molecule or an analogue thereof can, depending on the nature of the riboswitch, reduce or prevent the expression of the RNA molecule or promote or increase the expression of the RNA molecule. Some examples of riboswitches are described here.
[0235] [0235] In some modalities, the riboswitch is a Cobalamin riboswitch (also a B12 element), which binds to adenosylcobalamin (the coenzyme form of vitamin B12) to regulate the biosynthesis and transport of cobalamin and similar metabolites.
[0236] [0236] In some embodiments, the riboswitch is a cyclic di-GMP riboswitch, which binds to the cyclic di-GMP to regulate a variety of genes. There are two classes that are not structurally related - cyclic di-GMP-1 and cyclic di-GMP-11.
[0237] [0237] In some embodiments, the riboswitch is an FMN riboswitch (also an RFN element) that binds to the flavin mononucleotide (FMN) to regulate riboflavin biosynthesis and transport.
[0238] [0238] In some embodiments, the riboswitch is a glmS riboswitch, which cleaves when there is a sufficient concentration of glucosamine-6-phosphate.
[0239] [0239] In some modalities, the riboswitch is a Glutamine riboswitch, which binds to glutamine to regulate genes involved in the metabolism of glutamine and nitrogen. They also bind to short peptides of unknown function. Such riboswitches fall into two classes, which are structurally related: the motif of the glnA RNA and the motif of the downstream peptide.
[0240] [0240] In some modalities, the riboswitch is a Glycine riboswitch, which binds to glycine to regulate glycine metabolism genes. It comprises two domains of adjacent aptamers in the same mRNA and is the only known natural RNA that exhibits cooperative binding.
[0241] [0241] In some modalities, the riboswitch is a lysine riboswitch (also box L), which binds to lysine to regulate lysine biosynthesis, catabolism and transport.
[0242] [0242] In some embodiments, the riboswitch is a PreQ1 riboswitch, which binds to the pre-queuosin to regulate genes involved in the synthesis or transport of this precursor to the queuosin. Two entirely distinct classes of PreGI riboswitches are known: PreQ1-l riboswitches and PreQ1-ll riboswitches. The binding domain of the PreQ1-1 riboswitches is unusually small among naturally occurring riboswitches. The PreGI-II riboswitches, which are only found in certain species in the genera Streptococcus and Lactococcus, have a completely different structure and are larger.
[0243] [0243] In some embodiments, the riboswitch is a Purine riboswitch, which binds purines to regulate genes for purine metabolism and transport. Different forms of the purine riboswitch bind to guanine (a form originally known as the G box) or adenine. The specificity for guanine or adenine depends completely on Watson-Crick interactions with a single pyrimidine in the riboswitch at position Y74. In the guanine riboswitch, this residue is a cytosine (i.e., C74), in the adenine residue it is always a uracil (i.e., U74). The homologous types of purine riboswitches bind to deoxyganosine, but have more significant differences than a single nucleotide mutation.
[0244] [0244] In some embodiments, the riboswitch is a SAH riboswitch, which binds to S-adenosylhomocysteine to regulate genes involved in recycling this metabolite that is produced when S-adenosylmethionine is used in methylation reactions.
[0245] [0245] In some embodiments, the riboswitch is a SAM riboswitch, which binds to S-adenosyl methionine (SAM) to regulate methionine and SAM biosynthesis and transport. Three distinct SAM riboswitches are known: SAM-I (originally called box S), SAM-II and the SMK box riboswitch. SAM-I is disseminated in bacteria, in SAM-II it is found only in α-, β- and some γ-proteobacteria. The SMK box riboswitch is found only in the order Lactobacillales. These three varieties of riboswitch have no obvious similarities in terms of sequence or structure. A fourth variety, SAM-IV, appears to have a ligand-binding nucleus similar to that of SAM-I, but in the context of a different template.
[0246] [0246] In some modalities, the riboswitch is a SAM-SAH riboswitch, which links both SAM and SAH with similar affinities. Since they are always found in a position to regulate genes encoding methionine adenosyltransferase, it has been proposed that only their binding to SAM is physiologically relevant.
[0247] [0247] In some embodiments, the riboswitch is a riboswitch of Tetrahydrofolate, which binds to tetrahydrofolate to regulate transport synthesis genes.
[0248] [0248] In some embodiments, the riboswitch is a theophylline-binding riboswitch or a thymine pyrophosphate-binding riboswitch.
[0249] [0249] In some embodiments, the riboswitch is a T. tengcongensis glmS catalytic riboswitch, which detects glucosamine-6-phosphate (Klein and Ferre-D'Amare 2006).
[0250] [0250] In some modalities, the riboswitch is a TPP riboswitch (also THI box), which binds to thiamine pyrophosphate (TPP) to regulate thiosin biosynthesis and transport, as well as transport of similar metabolites. It is the only riboswitch found so far in eukaryotes.
[0251] [0251] In some modalities, the riboswitch is a Moco riboswitch, which connects to the molybdenum cofactor, to regulate genes involved in the biosynthesis and transport of this coenzyme, as well as enzymes that use it or its derivatives as a cofactor.
[0252] [0252] In some embodiments, the riboswitch is an Adenine detection add-A riboswitch, found in the 5 'RTU of the gene encoding Vibrio vulnificus adenine deaminase. Aptazima
[0253] [0253] In some embodiments, the circular polyribonucleotide comprises an aptazyme. Aptazyme is a switch for conditional expression in which an aptamer region is used as an allosteric control element and coupled to a catalytic RNA region (a "ribozyme" as described below). In some embodiments, aptazyme is active in the specific translation of cell types. In some embodiments, aptazime is active under specific translation of the cell state, eg, viral infected cells or in the presence of nucleic acids or viral proteins.
[0254] [0254] A ribozyme (from the ribonucleic acid enzyme, also called an RNA or catalytic RNA enzyme) is an RNA molecule that catalyzes a chemical reaction. Many natural ribozymes catalyze the hydrolysis of one of their own phosphodiester bonds, or the hydrolysis of bonds in other RNAs, but it has also been found to catalyze the ribosome's aminotransferase activity. More recently it has been shown that catalytic RNAs can be "evolved" by in vitro methods [1. Agresti J J, Kelly B T, Jaschke A, Griffiths A D: Selection of ribozymes that catalyse multiple- turnover Diels-Alder cycloadditions by using in vitro compartmentalization. Proc Natl Acad Sci USA 2005, 102: 16170-16175; 2. Sooter L J, Riedel T, Davidson EA, Levy M, Cox J C, Ellington A D: Toward automated nucleic acid enzyme selection. Biological Chemistry 2001, 382 (9): 1327-1334.]. Winkler et al. showed [Winkler W C, Nahvi A, Roth A, Collins J A, Breaker R R: Control of gene expression by a natural metabolite-responsive ribozyme. Nature 2004, 428: 281-286.] That, similar to the riboswitch activity discussed above, ribozymes and their reaction products can regulate gene expression. In the context of the present invention, it may be particularly advantageous to place a catalytic RNA or ribozyme within a larger non-coding RNA so that the ribozyme is present in many copies within the cell for the purposes of chemical transformation of a molecule from a total volume . Furthermore, encoding both aptamers and ribozymes in the same noncoding RNA can be particularly advantageous.
[0255] [0255] Some non-limiting examples of ribozymes include hammerhead ribozyme, VL ribozyme, leadzyme, hairpin ribozyme.
[0256] [0256] In some embodiments, aptazyme is a ribozyme that can cleave RNA sequences and that can be regulated as a result of ligand / modulator binding. The ribozyme can also be a self-cleaving ribozyme. As such they combine the properties of ribozymes and aptamers. Aptazymes offer advantages over conventional aptamers due to their potential for trans activity, the fact that they act catalytically to inactivate expression and that inactivation, due to the cleavage of their own heterologous transcript or transcript, is irreversible.
[0257] [0257] In some embodiments, aptazime is included in an untranslated region of the circular polyribonucleotide and in the absence of ligand / modulator it is inactive, allowing expression of the transgene. The expression can be turned off (or sub-regulated) by adding the ligand. It should be noted that aptazymes that are unregulated in response to the presence of a particular modulator can be used in control systems where overregulation of gene expression in response to the modulator is desired.
[0258] [0258] Aptazymes may also allow the development of systems for self-regulation of the expression of circular polyribonucleotides. For example, the circular polyribonucleotide protein product is the rate-determining enzyme in the synthesis of a particular small molecule that could be modified to include a selected aptazyme to have increased catalytic activity in the presence of that molecule, thereby providing a self-regulatory feedback loop for your synthesis. Alternatively, aptazime activity can be selected to be sensitive to the accumulation of the protein product from the circular polyribonucleotide or any other cellular macromolecule.
[0259] [0259] In some embodiments, the circular polyribonucleotide may include an aptamer sequence. Some non-limiting examples include a RNA aptamer-binding lysozyme, a Toggle-25t which is an RNA aptamer that includes 2′fluoropyrimidine nucleotides that binds to thrombin with high specificity and affinity, RNATat that binds to the element responsive to human immunodeficiency virus (HIV TAR) trans action, RNA aptamer-binding hemin, RNA aptamer-binding interferon, vascular endothelial growth factor (VEGF) binding to RNA aptamer, prostate-specific antigen (PSA ) binding to the RNA aptamer, dopamine binding to the RNA aptamer and RNA aptamer binding to the non-classical oncogene, thermal shock factor 1 (HSF1).
[0260] [0260] In one embodiment, a linear circular polyribonucleotide can be cyclized or concatemerized. In some embodiments, the linear circular polyribonucleotide can be cyclized in vitro before formulation and / or administration. In some embodiments, the linear circular polyribonucleotide can be cyclized within a cell. Extracellular circularization
[0261] [0261] In some embodiments, the linear circular polyribonucleotide is cyclized or concatemerized using a chemical method to form a circular polyribonucleotide. In some chemical methods, the 5 'end and the 3' end of the nucleic acid (eg, a linear circular polyribonucleotide) include chemically reactive groups that, when close, can form a new covalent bond between the 5 'end and the 3´ end of the molecule. The 5 'end can contain an NHS-ester reactive group and the 3' end can contain a 3'-amino-terminated nucleotide so that in an organic solvent the 3'-amino-terminated nucleotide at the 3 'end of a molecule of Linear RNA will undergo a nucleophilic attack in the 5´- NHS-ester portion forming a new 5´- / 3´-amide bond.
[0262] [0262] In one embodiment, a DNA or RNA ligase can be used to enzymatically link a 5'-phosphorylated nucleic acid molecule (eg, a linear circular polyribonucleotide) to the 3'-hydroxyl group of a nucleic acid
[0263] [0263] In one embodiment, a DNA or RNA ligase can be used in the synthesis of circular polynucleotides. As a non-limiting example, the ligase can be a circ ligase or a circular ligase.
[0264] [0264] In one embodiment, the 5 'or 3' end of the linear circular polyribonucleotide can encode a ligase ribozyme sequence so that, during in vitro transcription, the resulting linear circular polyribonucleotide includes an active ribozyme sequence capable of binding the 5 'end of the linear circular polyribonucleotide to the 3' end of the linear circular polyribonucleotide. The ligase ribozyme can be derived from Group I Intron, Hepatitis Delta Virus, Hairpin Ribozyme or can be selected by SELEX (systematic evolution of ligands by exponential enrichment). The ligase ribozyme reaction can take 1 to 24 hours at temperatures between 0 and 37 ºC.
[0265] [0265] In one embodiment, a linear circular polyribonucleotide can be cyclized or concatermerized by using at least a different fraction of nucleic acid. In one aspect, at least a different fraction of nucleic acid can react with regions or characteristics close to the 5 'terminal and / or close to the 3' terminal of the linear circular polyribonucleotide in order to cyclize or concatermerize the linear circular polyribonucleotide. In another aspect, at least a different fraction of nucleic acid may be located at or linked to or near the 5 'and / or 3' terminal of the linear circular polyribonucleotide. The different nucleic acid fractions contemplated can be homologous or heterologous. As a non-limiting example, the different nucleic acid fraction can be a bond such as a hydrophobic bond, an ionic bond, a biodegradable bond and / or a cleavable bond. As another non-limiting example, the fraction other than nucleic acid is a binding fraction. As yet another non-limiting example, the different nucleic acid fraction can be an oligonucleotide or peptide fraction, such as an apatamer or a different nucleic acid linker as described herein.
[0266] [0266] In one embodiment, a linear circular polyribonucleotide can be cyclized or concatermerized due to a different fraction of nucleic acid that causes an attraction between atoms, molecular surfaces on, near or attached to the 5 'and 3' ends of the linear circular polyribonucleotide . As a non-limiting example, one or more linear circular polyribonucleotides can be cyclized or matched by intermolecular forces or intramolecular forces. Non-limiting examples of intermolecular forces include dipole-dipole forces, dipole-induced dipole forces, induced dipole-induced dipole forces, Van der Waals forces and London dispersion forces. Non-limiting examples of intramolecular forces include covalent bonds, metal bonds, ionic bonds, resonant bonds, agnostic bonds, dipolar bonds, conjugation, hyperconjugation and antiligation.
[0267] [0267] In one embodiment, the linear circular polyribonucleotide may comprise a ribozyme RNA sequence near the 5 'terminal and close to the 3' terminal. The ribozyme RNA sequence can covalently bind to a peptide when the sequence is exposed to the rest of the ribozyme. In one respect, peptides covalently linked to the sequence of
[0268] [0268] In some embodiments, the linear circular polyribonucleotide may include a 5 'nucleic acid triphosphate converted to a 5' monophosphate, eg by contact of the 5 'triphosphate with 5' pyrophospho-hydrolase (RppH) RNA or a ATP diphosphohydrolase (apyrase). Alternatively, conversion of the 5 'linear circular polyribonucleotide triphosphate to a 5' monophosphate can occur by a two-step reaction comprising: (a) contact of the 5 'linear nucleotide of the linear circular polyribonucleotide with a phosphatase (eg, Antarctic phosphatase , Shrimp Alkaline Phosphatase or Calf Intestinal Phosphatase) to remove all three phosphates; and (b) contact of the 5 'nucleotide after step (a) with a kinase (eg, Polynucleotide Kinase) that adds a single phosphate.
[0269] [0269] In some embodiments, the circularization efficiency of the circularization methods provided here is at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 60%, at least about 70%, at least about 80 %, at least about 90%, at least about 95% or 100%. In some embodiments, the circularization efficiency of the circularization methods provided here is at least about 40%. Splicing element
[0270] [0270] In some embodiment, the circular polyribonucleotide includes at least one splicing element. In a circular polyribonucleotide as provided herein, a splicing element can be a complete splicing element that can mediate the splicing of the circular polyribonucleotide. Alternatively, the splicing element can also be a residual splicing element from a completed splicing event. For example, in some cases, a splicing element of a linear polyribonucleotide can mediate a splicing event that results in the circularization of the linear polyribonucleotide, thus the resulting circular polyribonucleotide comprises a residual splicing element from such a circularization event mediated by splicing. In some cases, the residual splicing element is unable to mediate any splicing. In other cases, the residual splicing element can also mediate splicing under certain circumstances. In some embodiments, the splicing element is adjacent to at least one expression sequence. In some embodiments, the circular polyribonucleotide includes a splicing element adjacent to each expression sequence. In some embodiments, the splicing element is on one or both sides of each expression sequence, leading to the separation of the expression products, eg, peptide (s) and / or polypeptide (s).
[0271] [0271] In some embodiments, the circular polyribonucleotide includes an internal splicing element that when replicated the spliced ends are joined. Some examples may include miniature introns (<100 nt) with sequences of splice locations and short inverted repetitions (30–40 nt) such as AluSq2, AluJr and AluSz, inverted sequences in flanking introns, Alu elements in flanking introns and motifs found in (motifs enriched in suptable4) cis sequence elements close to backsplice events such as 200 bp sequences preceding (upstream of) or after (downstream of) a backsplice location with flanking exons. In some embodiments, the circular polyribonucleotide includes at least one repetitive nucleotide sequence described elsewhere here as an internal splicing element. In such embodiments, the repetitive nucleotide sequence may include repeated sequences from the Alu family of introns. In some embodiments, a splicing-related ribosome-binding protein can regulate the biogenesis of circular polyribonucleotides (eg, Muscleblind and Quaking (QKI) splicing factors).
[0272] [0272] In some embodiments, the circular polyribonucleotide may include canonical splice sites that flank the head-to-tail junctions of the circular polyribonucleotide.
[0273] [0273] In some embodiments, the circular polyribonucleotide may include a protuberance-helix-protuberance motif, comprising a 4-base pair stem flanked by two 3-nucleotide protuberances. Cleavage occurs at a location in the protuberance region, generating characteristic fragments with a terminal 5'-hydroxyl group and 2 ', 3'-cyclic phosphate. The circularization proceeds by nucleophilic attack of the 5'-OH group on the 2 ', 3'-cyclic phosphate of the same molecule forming a 3', 5'-phosphodiester bridge.
[0274] [0274] In some embodiments, the circular polyribonucleotide may include a repetitive multimeric RNA sequence that houses an HPR element. The HPR comprises a 2 ′, 3′-cyclic phosphate and a 5′-OH terminal. The HPR element self-processes the 5 'and 3' ends of the linear circular polyribonucleotide, thus connecting the ends together.
[0275] [0275] In some embodiments, the circular polyribonucleotide may include a sequence that mediates self-ligation. In one embodiment, the circular polyribonucleotide may include an HDV sequence (eg, sequence conserved in the HDV replication domain,
[0276] [0276] In some embodiments, linear circular polyribonucleotides may include complementary sequences, including repetitive or non-repetitive nucleic acid sequences within individual introns or through flanking introns. Repetitive nucleic acid sequences are sequences that occur within a circular polyribonucleotide segment. In some embodiments, the circular polyribonucleotide includes a repetitive nucleic acid sequence. In some embodiments, the repetitive nucleotide sequence includes poly CA or poly UG sequences. In some embodiments, the circular polyribonucleotide includes at least one repetitive nucleic acid sequence that hybridizes to a complementary repetitive nucleic acid sequence in another segment of the circular polyribonucleotide, with the hybridized segment forming an internal double strand. In some embodiments, the repetitive nucleic acid sequences and the complementary repetitive nucleic acid sequences of two separate circular polyribonucleotides hybridize to generate a single circularized polyribonucleotide, with the hybridized segments forming internal double strands. In some embodiments, the complementary sequences are found at the 5 'and 3' ends of the linear circular polyribonucleotides. In some embodiments, the complementary sequences include about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more paired nucleotides.
[0277] [0277] In some embodiments, chemical circularization methods can be used to generate the circular polyribonucleotide. Such methods may include, but are not limited to, click chemistry (eg, alkaline and azide-based methods or clickable bases), olefin metathesis, phosphoramidate bonding, hemiaminalimine crosslinking, base modification and any combination thereof .
[0278] [0278] In some embodiments, enzymatic circularization methods can be used to generate the circular polyribonucleotide. In some embodiments, a binding enzyme, e.g., DNA or RNA ligase, can be used to generate a circular or complementary polyribonuclease model, a complementary circular polyribonuclease strand or circular polyribonuclease.
[0279] [0279] Circular polyribonucleotide circularization can be achieved by methods known in the art, for example, those described in “RNA circularization strategies in vivo and in vitro” by Petkovic and Muller from Nucleic Acids Res, 2015, 43 (4) : 2454-2465 and “In vitro circularization of RNA” by Muller and Appel, from RNA Biol, 2017, 14 (8): 1018-1027. Replication element
[0280] [0280] The circular polyribonucleotide can encode a sequence and / or motifs useful for replication. The replication of a circular polyribonucleotide can occur by generating a complement circular polyribonucleotide. In some embodiments, the circular polyribonucleotide includes a reason to initiate transcription, where the transcription is directed by endogenous cellular machines (DNA-dependent RNA polymerase) or an RNA-dependent RNA polymerase encoded by the circular polyribonucleotide. The product of the rolling circle transcriptional event can be cut by a ribozyme to generate complementary circular polyribonucleotide or propagated in unit length. Ribozymes can be encoded by the circular polyribonucleotide, its complement or by a trans RNA sequence. In some embodiments, the encoded ribozymes may include a sequence or motif that regulates (inhibits or promotes) the activity of the ribozyme to control the spread of circular RNA. In some embodiments, the unit-length sequences can be linked in a circular form by a cellular RNA ligase. In some embodiments, the circular polyribonucleotide includes a replication element that assists in self-amplification. Examples of such replication elements include, but are not limited to, HDV replication domains described elsewhere here, Potato Bundle Tuber Viroid RNA promoter (see for example Kolonko 2005 Virology) and sense and / or ribozymes replication-competent circular RNA antisense such as 5'-
[0281] [0281] In some embodiments, the circular polyribonucleotide includes at least one staggered element as described here to aid replication. A stepped element within the circular polyribonucleotide can cleave replicated long transcripts from the circular polyribonucleotide to a specific length that could subsequently circularize to form a complement to the circular polyribonucleotide.
[0282] [0282] In another embodiment, the circular polyribonucleotide includes at least one ribozyme sequence to cleave long replicates transcribed from the circular polyribonucleotide to a specific length, where another encoded ribozyme cuts the transcripts in the ribozyme sequence. Circularization forms a complement to circular polyribonucleotide.
[0283] [0283] In some embodiments, the circular polyribonucleotide is substantially resistant to degradation, eg by exonucleases.
[0284] [0284] In some embodiments, the circular polyribonucleotide replicates within a cell. In some embodiments, the circular polyribonucleotide replicates within a cell at a rate of between about 10% -20%, 20% -30%, 30% -40%, 40% -50%, 50% -60%, 60% -70%, 70% -75%, 75% - 80%, 80% -85%, 85% -90%, 90% -95%, 95% -99% or any intermediate percentage. In some embodiments, the circular polyribonucleotide is replicated within a cell and is passed on to the daughter cells. In some embodiments, a cell passes at least one circular polyribonucleotide to daughter cells with an efficiency of at least 25%, 50%, 60%, 70%, 80%, 85%, 90%, 95% or 99%. In some embodiments, the cell undergoing meiosis passes the circular polyribonucleotide to daughter cells with an efficiency of at least 25%, 50%, 60%, 70%, 80%, 85%, 90%, 95% or 99%. In some embodiments, a cell suffering from mitosis passes the circular polyribonucleotide to daughter cells with an efficiency of at least 25%, 50%, 60%, 70%, 80%, 85%, 90%, 95% or 99%.
[0285] [0285] In some embodiments, the circular polyribonucleotide replicates within the host cell. In one embodiment, the circular polyribonucleotide is able to replicate in a mammalian cell, e.g., human cell.
[0286] [0286] While in some embodiments the circular polyribonucleotide replicates in the host cell, the circular polyribonucleotide does not integrate into the host's genome, eg, with the host's chromosomes. In some embodiments, the circular polyribonucleotide has a negligible frequency of recombination, e.g., with the host's chromosomes. In some embodiments, the circular polyribonucleotide has a frequency of recombination, e.g., less than about 1.0 cM / Mb, 0.9 cM / Mb, 0.8 cM / Mb, 0.7 cM / Mb , 0.6 cM / Mb, 0.5 cM / Mb, 0.4 cM / Mb, 0.3 cM / Mb, 0.2 cM / Mb, 0.1 cM / Mb or less, e.g. with the host's chromosomes. Other strings
[0287] [0287] In some embodiments, the circular polyribonucleotide additionally includes another nucleic acid sequence. In some embodiments, the circular polyribonucleotide may comprise other sequences that include DNA, RNA or artificial nucleic acids. The other sequences may include, but are not limited to, genomic DNA, cDNA or sequences that encode tRNA, mRNA, rRNA, miRNA, gRNA, siRNA or other RNAi molecules. In one embodiment, the circular polyribonucleotide includes a sequence encoding a siRNA to target a loci other than the same gene expression product as the circular polyribonucleotide. In one embodiment, the circular polyribonucleotide includes a sequence encoding a siRNA to target a different gene expression product than the circular polyribonucleotide.
[0288] [0288] In some modalities, the circular polyribonucleotide does not have a 5´-RTU. In some embodiments, the circular polyribonucleotide does not have a 3´-RTU. In some embodiments, the circular polyribonucleotide does not have a poly-A sequence. In some embodiments, the circular polyribonucleotide does not have a termination sequence. In some embodiments, the circular polyribonucleotide does not have an internal ribosomal entry site. In some embodiments, the circular polyribonucleotide is not susceptible to degradation by exonucleases. In some embodiments, the fact that the circular polyribonucleotide is not susceptible to degradation may mean that the circular polyribonucleotide is not degraded by an exonuclease or only degraded in the presence of an exonuclease to a limited extent that is comparable to or similar to the absence of exonuclease. In some embodiments, the circular polyribonucleotide has no degradation by exonucleases. In some embodiments, the circular polyribonucleotide has reduced degradation when exposed to exonuclease. In some embodiments, the circular polyribonucleotide has no binding to a cap binding protein. In some embodiments, the circular polyribonucleotide does not have a 5 'cap.
[0289] [0289] In some embodiments, the circular polyribonucleotide does not have a 5'-RTU and is competent for expression of proteins from its one or more expression sequences. In some embodiments, the circular polyribonucleotide does not have a 3'-UTR and is competent for expression of proteins from its one or more expression sequences. In some embodiments, the circular polyribonucleotide does not have a poly-A sequence and is competent for expressing proteins from its one or more expression sequences. In some embodiments, the circular polyribonucleotide does not have a terminating element and is competent for expressing proteins from its one or more expression sequences. In some embodiments, the circular polyribonucleotide does not have an internal ribosomal entry site and is competent for protein expression from its one or more expression sequences. In some embodiments, the circular polyribonucleotide does not have a cap and is competent for expressing proteins from its one or more expression sequences. In some embodiments, the circular polyribonucleotide does not have a 5'-UTR, a 3'-UTR and an IRES and is competent for the expression of proteins from its one or more expression sequences. In some embodiments, the circular polyribonucleotide comprises one or more of the following sequences: a sequence that encodes one or more miRNAs, a sequence that encodes one or more replication proteins, a sequence that encodes an exogenous gene, a sequence that encodes a therapeutic, a regulatory element (eg, translation modulator, eg translation enhancer or suppressor), a translation initiation sequence, one or more regulatory nucleic acids that target endogenous genes (siRNA, lncRNAs, shRNA) and a sequence that encodes a therapeutic mRNA or protein.
[0290] [0290] The other sequence can be about 2 to about 10,000 nts in length, about 2 to about 5000 nts, about 10 to about 100 nts, about 50 to about 150 nts, about 100 about 200 nts, about 150 to about 250 nts about 200 to about 300 nts, about 250 to about 350 nts, about 300 to about 500 nts, about 10 to about 1000 nts, about 50 to about 1000 nts, about 100 to about 1000 nts, about 1000 to about 2000 nts, about 2000 to about 3000 nts, about 3000 to about 4000 nts, about 4000 to about 5000 nts or any intermediate range.
[0291] [0291] As a result of its circularization, the circular polyribonucleotide may include certain characteristics that distinguish it from linear RNA. For example, circular polyribonucleotide is less susceptible to exonuclease degradation compared to linear RNA. As such, the circular polyribonucleotide is more stable than linear RNA, especially when incubated in the presence of an exonuclease. The increased stability of the circular polyribonucleotide compared to linear RNA makes the circular polyribonucleotide more useful as a cell transformation reagent to produce polypeptides and can be stored more easily and for longer than linear RNA. The stability of the circular exonuclease-treated polyribonucleotide can be tested using standard methods in the art that determine whether RNA degradation has occurred (eg, by gel electrophoresis).
[0292] [0292] Furthermore, unlike linear RNA, circular polyribonucleotide is less susceptible to dephosphorylation when circular polyribonucleotide is incubated with phosphatase, such as calf intestine phosphatase. Nucleotide spacer sequences
[0293] [0293] In some embodiments, the circular polyribonucleotide comprises a spacer sequence.
[0294] [0294] In some embodiments, the circular polyribonucleotide comprises at least one spacer sequence. In some embodiments, the circular polyribonucleotide comprises 1, 2, 3, 4, 5, 6, 7 or more spacer sequences.
[0295] [0295] In some embodiments, the circular polyribonucleotide comprises a ratio of the spacer to the non-spacer sequence of the circular polyribonucleotide, e.g., expression sequences, of about 0.05: 1, about 0.06: 1, about 0.07: 1, about 0.08: 1, about 0.09: 1, about 0.1: 1, about 0.12: 1, about 0.125: 1, about 0.15 : 1, about 0.175: 1, about 0.2: 1, about 0.225: 1, about 0.25: 1, about 0.3: 1, about 0.35: 1, about 0 , 4: 1, about 0.45: 1, about 0.5: 1, about 0.55: 1, about 0.6: 1, about 0.65: 1, about 0.7 : 1, about 0.75: 1, about 0.8: 1, about 0.85: 1, about 0.9: 1, about 0.95: 1, about 0.98: 1 , about 1: 1, about 1.02: 1, about 1.05: 1, about 1.1: 1, about 1.15: 1, about 1.2: 1, about 1 , 25: 1, about 1.3: 1, about 1.35: 1, about 1.4: 1, about 1.45: 1, about 1.5: 1, about 1.55 : 1, about 1.6: 1, about 1.65: 1, about 1.7: 1, about 1.75: 1, about 1.8: 1, about 1.85: 1 , about 1.9: 1 , about 1.95: 1, about 1.975: 1, about 1.98: 1 or about 2: 1.
[0296] [0296] In some embodiments, the spacer sequence comprises a ratio between the spacer sequence and a downstream non-spacer element (eg, 3 'of the spacer sequence) of the circular polyribonucleotide of about 0.5: 1, about 0 , 06: 1, about 0.07: 1, about 0.08: 1, about 0.09: 1, about 0.1: 1, about 0.12: 1, about 0.125: 1 , about 0.15: 1, about 0.175: 1, about 0.2: 1, about 0.225: 1, about 0.25: 1, about 0.3: 1, about 0.35 : 1, about
[0297] [0297] In some embodiments, the spacer sequence comprises a sequence of at least 3 ribonucleotides, at least 4 ribonucleotides, at least 5 ribonucleotides, at least about 8 ribonucleotides, at least about 10 ribonucleotides, at least about 12 ribonucleotides, at least about 15 ribonucleotides, at least about 20 ribonucleotides, at least about 25 ribonucleotides, at least about 30 ribonucleotides, at least about 40 ribonucleotides, at least about 50 ribonucleotides, at least about 60 ribonucleotides, at least at least about 70 ribonucleotides, at least about 80 ribonucleotides, at least about 90 ribonucleotides, at least about 100 ribonucleotides, at least about 120 ribonucleotides, at least about 150 ribonucleotides, at least about 200 ribonucleotides, at least about 250 ribonucleotides, at least about 300 ribonucleotides, at least about 400 ribonucleotides, at least about 500 ribonucleotides, at least about 600 ribonucleotides, at least about 700 ribonucleotides, at least about 800 ribonucleotides, at least about 900 ribonucleotides or at least about 100 ribonucleotides.
[0298] [0298] In some embodiments, the spacer sequence may be a nucleic acid sequence or molecule having low GC content, for example less than 65%, 60%, 55%, 50%, 55%, 50%, 45% , 40%, 39%, 38%, 37%, 36%, 35%, 34%, 33%, 32%, 31%, 30%, 29%, 28%, 27%, 26%, 25%, 24 %, 23%, 22%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1%, over the total length of the spacer, or over at least 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% of contiguous spacer nucleic acid residues. In some embodiments, the spacer sequence may comprise at least 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 55%, 50%, 45%, 40%, 35%, 30%, 20% or any intermediate percentage of adenine ribonucleotides. In some embodiments, the spacer sequence comprises at least 5 or more adenine ribonucleotides in a row. In some embodiments, the spacer sequence comprises at least 6 adenine ribonucleotides in sequence, at least 7 adenine ribonucleotides in sequence, at least 8 ribonucleotides in at least about 10 adenine ribonucleotides in sequence, at least about 12 adenine ribonucleotides next, at least about 15 adenine ribonucleotides then, at least about 20 adenine ribonucleotides next, at least about 25 adenine ribonucleotides next, at least about 30 adenine ribonucleotides next, at least about of 40 adenine ribonucleotides next, at least about 50 adenine ribonucleotides next, at least about 60 adenine ribonucleotides next, at least about 70 adenine ribonucleotides next, at least about 80 adenine ribonucleotides next then at least about 90 adenine ribonucleotides then at least about 95 adenine ribonucleotides next, at least about 100 adenine ribonucleotides then, at least about 150 adenine ribonucleotides next, at least about 200 adenine ribonucleotides next, at least about 250 adenine ribonucleotides next, at least about 300 adenine ribonucleotides next, at least about 350 adenine ribonucleotides next, at least about 400 adenine ribonucleotides next, at least about 450 adenine ribonucleotides next, at least about 500 adenine ribonucleotides then, at least about 550 adenine ribonucleotides then, at least about 600 adenine ribonucleotides then, at least about 700 adenine ribonucleotides then, at least about 800 adenine ribonucleotides then, at least about 900 adenine ribonucleotides in a row or at least about 1000 adenine ribonucleotides in a row.
[0299] [0299] In some embodiments, the spacer sequence is located between one or more elements. In some embodiments, the spacer sequence provides conformational flexibility between the elements. In some embodiments, conformational flexibility is due to the spacer sequence being substantially free of a secondary structure. In some embodiments, the spacer sequence is substantially free of a secondary structure, such as less than 40 kcal / mol, less than -39, -38, -37, -36, - 35, -34, -33, - 32, -31, -30, -29, -28, -27, -26, -25, -24, -23, -22, -20, -19, -18, -17, -16, -15, -14, -13, - 12, -11, -10, -9, -8, -7, -6, -5, -4, -3, -2 or -1 kcal / mol. The spacer can include a nucleic acid, such as DNA or RNA.
[0300] [0300] In some embodiments, the spacer sequence may encode an RNA sequence and preferably a protein or peptide sequence, including a secretion signal peptide.
[0301] [0301] In some embodiments, the spacer sequence may be noncoding. Where the spacer is a non-coding sequence, a translation initiation sequence can be provided in the coding sequence of an adjacent sequence. In some embodiments, it is envisaged that the first nucleic acid residue of the coding sequence may be residue A of a translation initiation sequence, such as AUG. Where the spacer encodes an RNA or protein or peptide sequence, a translation initiation sequence can be provided in the spacer sequence.
[0302] [0302] In some embodiments, the spacer is operationally linked to another sequence described here. Different nucleic acid ligands
[0303] [0303] The circular polyribonucleotide described here may also comprise a linker other than nucleic acid. In some embodiments, the circular polyribonucleotide described here has a different nucleic acid linker between one or more of the sequences or elements described here. In one embodiment, one or more sequences or elements described here are linked with the linker. The linker other than nucleic acid can be a chemical bond, e.g., one or more covalent bonds or non-covalent bonds. In some embodiments, the linker other than nucleic acid is a peptide or protein linker. Such a linker can have between 2-30 amino acids or more. The binder includes any flexible, rigid or cleavable binders described here.
[0304] [0304] The most commonly used flexible ligands have sequences consisting mainly of stretches of Gly and Ser residues ("GS" ligand). Flexible ligands can be useful for joining domains that require a certain degree of movement or interaction and can include small, non-polar (e.g., Gly) or polar (e.g., Ser or
[0305] [0305] Rigid ligands are useful for maintaining a fixed distance between domains and for maintaining their independent functions. Rigid ligands can also be useful when a spatial separation of domains is critical to preserve the stability or bioactivity of one or more components in the fusion. The rigid ligands can have an alpha helix structure or a sequence rich in Pro, (XP) n, with X designating any amino acid, preferably Ala, Lys or Glu.
[0306] [0306] Cleavable ligands can release free functional domains in vivo. In some embodiments, the ligands can be cleaved under specific conditions, such as the presence of reducing reagents or proteases. In vivo cleavable linkers can utilize the reversible nature of a disulfide bond. An example includes a thrombin-sensitive sequence (eg, PRS) between the two Cys residues. In vitro thrombin treatment of CPRSC results in cleavage of the thrombin-sensitive sequence, while the reversible disulfide bond remains intact. Such binders are known and described, for example, in Chen et al. 2013. Fusion Protein Linkers: Property, Design and Functionality. Adv Drug Deliv Rev. 65 (10): 1357-1369.
[0307] [0307] Examples of binding molecules include a hydrophobic linker, such as a negatively charged sulfonate group; lipids, such as a poly (--CH2--) hydrocarbon chain, such as polyethylene glycol (PEG) group, its unsaturated variants, its hydroxylated variants, its amidated or otherwise containing N, non-carbon ligands; carbohydrate binders; phosphodiester linkers or another molecule capable of covalently linking two or more polypeptides. Non-covalent linkers are also included, such as hydrophobic lipid globules to which the polypeptide is attached, for example through a hydrophobic region of the polypeptide or a hydrophobic extension of the polypeptide, such as a series of residues rich in leucine, isoleucine, valine or maybe also alanine, phenylalanine or even tyrosine, methionine, glycine or other hydrophobic residue. The polypeptide can be linked using charge-based chemistry, so that a positively charged fraction of the polypeptide is linked to a negative charge of another polypeptide or nucleic acid.
[0308] [0308] In some embodiments, the circular polyribonucleotide provided here has an increased half-life over a reference, e.g., a linear polyribonucleotide having the same nucleotide sequence but not being circularized (linear counterpart). In some embodiments, the circular polyribonucleotide is substantially resistant to degradation, e.g., exonuclease. In some embodiments, the circular polyribonucleotide is resistant to self-degradation. In some embodiments, the circular polyribonucleotide does not have an enzymatic cleavage site, eg, a dicer cleavage site. In some embodiments, the circular polyribonucleotide has a half-life of at least about 5%, at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 120%, at least about 140%, at least about 150%, at least about 160%, at least about 180%, at least about 200%, at least about 300%, at least about 400%, at least about 500 %, at least about 600%, at least about 700% at least about 800%, at least about 900%, at least about 1000% or at least about 10000%, greater than a reference, p eg, a linear counterpart.
[0309] [0309] In some embodiments, the circular polyribonucleotide persists in a cell during cell division.
[0310] [0310] The circular polyribonucleotide may include one or more substitutions, insertions and / or additions, deletions and covalent modifications with respect to the reference sequences, in particular, the parent polyribonucleotide, are included within the scope of this invention.
[0311] [0311] In some embodiments, the circular polyribonucleotide includes one or more post-transcriptional modifications (eg, capping, cleavage, polyadenylation, splicing, poly-A sequence, methylation, acylation, phosphorylation, methylation of lysine residues and arginine, acetylation and nitrosylation of thiol groups and tyrosine residues, etc.). The one or more post-transcriptional modifications can be any post-transcriptional modification, such as any of the more than one hundred different nucleoside modifications that have been identified in RNA (Rozenski, J, Crain, P and McCloskey, J. (1999) The RNA Modification Database: 1999 update. Nucl Acids Res 27: 196-197). In some embodiments, the first isolated nucleic acid comprises messenger RNA (mRNA). In some embodiments, the mRNA comprises at least one nucleoside selected from the group consisting of pyridin-4-one ribonucleoside, 5-aza-uridine, 2-thio-5-aza-uridine, 2-thiouridine, 4-thiopseudouridine, 2-thio-pseudouridine, 5-hydroxyuridine, 3-methyluridine, 5-carboxymethyl-uridine, 1-carboxymethyl-pseudouridine, 5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyluridine, 1-taurinomethyl, 5-taurinomethane taurinomethyl-2-thio-uridine, 1-taurinomethyl-4-thio-uridine, 5-methyl-uridine, 1-methyl-pseudouridine, 4-thio-1-methyl-pseudouridine, 2-thio-1-methyl-pseudouridine, 1- methyl-1-deaza-pseudouridine, 2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine, dihydropseudouridine, 2-thio-dihydrouridine, 2-thio-dihydropseudouridine, 2- methoxyuridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine and 4-methoxy-2-thio-pseudouridine.
[0312] [0312] The circular polyribonucleotide may include any useful modification, such as sugar, nucleobase or internucleoside bonding (eg, to a phosphate binding / phosphodiester bond / phosphodiester backbone). One or more atoms of a pyrimidine nucleobase can be repositioned or replaced with an optionally substituted amino, optionally substituted thiol, optionally substituted alkyl (e.g., methyl or ethyl) or halo (e.g., chlorine or fluorine). In certain embodiments, modifications (eg, one or more modifications) are present in each of the sugar and the internucleoside bond. The modifications may be modifications of ribonucleic acids (RNAs) to deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), blocked nucleic acids (LNAs) or theirs hybrids. Additional modifications are described here.
[0313] [0313] In some embodiments, the circular polyribonucleotide includes at least one modification of N (6) methyladenosine (m6A) to increase translation efficiency. In some embodiments, modification of N (6) methyladenosine (m6A) can reduce the immunogenicity of the circular polyribonucleotide.
[0314] [0314] In some embodiments, the modification may include a chemical or cellular induced modification. For example, some non-limiting examples of intracellular RNA modifications are described by Lewis and Pan in “RNA modifications and structures cooperate to guide RNA-protein interactions” from Nat Reviews Mol Cell Biol, 2017, 18: 202-210.
[0315] [0315] In some embodiments, chemical modifications to the circular polyribonucleotide ribonucleotides can enhance immune escape. The circular polyribonucleotide can be synthesized and / or modified by methods well established in the art, such as those described in “Current protocols in nucleic acid chemistry”, Beaucage, S.L. et al. (Eds.), John Wiley & Sons, Inc., New York, NY, USA, which is hereby incorporated by reference. Modifications include, for example, end modifications, e.g., 5 'end modifications ( phosphorylation (mono-, di- and tri-), conjugation, inverted bonds, etc.), modifications of the 3 'end (conjugation, DNA nucleotides, inverted bonds, etc.), base modifications (eg, substitution by stabilizing bases, destabilizing bases or bases that pair in terms of bases with an expanded repertoire of partners), removal of bases (abasic nucleotides) or conjugated bases. Modified ribonucleotide bases can also include 5-methylcytidine and pseudouridine. In some embodiments, base modifications can modulate the expression, immune response, stability, subcellular location, to name some functional effects, of the circular polyribonucleotide. In some embodiments, the modification includes bi-orthogonal nucleotides, e.g., an unnatural base. See, for example, Kimoto et al., Chem Commun (Camb), 2017, 53: 12309, DOI: 10.1039 / c7cc06661a, which is hereby incorporated by reference.
[0316] [0316] In some embodiments, sugar modifications (eg, in the 2´ or 4´ position) or sugar substitution of one or more ribonucleotides of the circular polyribonucleotide may, as well as skeleton modifications, include modification or substitution of the phosphodiester bonds. Specific examples of circular polyribonucleotide include, but are not limited to, circular polyribonucleotide including modified backbones or no natural internucleoside bonds such as internucleoside modifications, including modification or replacement of phosphodiester bonds. Circular polyribonucleotides having modified skeletons include, among others, those that do not have a phosphorus atom in the skeleton. For the purposes of this application, and as sometimes referred to in the art, modified RNAs that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides. In particular embodiments, the circular polyribonucleotide will include ribonucleotides with a phosphorus atom in its internucleoside skeleton.
[0317] [0317] Modified circular polyribonucleotide skeletons may include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl phosphates and other alkyls such as 3'-alkylene phosphorates and phosphoramides, such as phosphonates, phosphonates and phosphonates of 3'-amino and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters and boranophosphates having bonds
[0318] [0318] The modified nucleotides, which can be incorporated into the circular polyribonucleotide, can be modified in the internucleoside bond (eg, phosphate backbone). Here, in the context of the polynucleotide skeleton, the phrases "phosphate" and "phosphodiester" are used interchangeably. The phosphate groups on the skeleton can be modified by replacing one or more of the oxygen atoms with a different substituent. In addition, the modified nucleosides and nucleotides may include the total replacement of an unmodified phosphate fraction with another internucleoside bond as described herein. Examples of modified phosphate groups include, but are not limited to, phosphorothioate, phosphoroselenates, boranophosphates, boranophosphate esters, hydrogen phosphonates, phosphoramidates, phosphorodiamidates, alkyl or aryl phosphonates and phosphotriesters. Phosphorodithioates have both unbound oxygen replaced by sulfur. The phosphate binder can also be modified by replacing a bonding oxygen with nitrogen (bridged phosphoramidates), sulfur
[0319] [0319] A-thio-substituted phosphate fraction is provided to provide stability to RNA and DNA polymers through unnatural phosphorothioate backbone bonds. Phosphorothioate DNA and RNA have increased nuclease resistance and subsequently a longer half-life in a cellular environment. Circular polyribonucleotide-bound phosphorothioate is expected to reduce the innate immune response through weaker binding / activation of the innate cellular immune molecules.
[0320] [0320] In specific embodiments, a modified nucleoside includes an alpha-thio-nucleoside (eg, 5'-0- (1-thiophosphate) -adenosine, 5'-0- (1-thiophosphate) -cytidine (a -thio-cytidine), 5'-0- (1-thiophosphate) -guanosine, 5'-0- (1-thiophosphate) -uridine or 5'-0- (1-thiophosphate) -pseudouridine).
[0321] [0321] Other internucleoside bonds that can be employed in accordance with the present invention, including internucleoside bonds that do not contain a phosphorus atom, are described here.
[0322] [0322] In some embodiments, the circular polyribonucleotide may include one or more cytotoxic nucleosides. For example, cytotoxic nucleosides can be incorporated into the circular polyribonucleotide, such as bifunctional modification. Cytotoxic nucleosides may include, but are not limited to, adenosine arabinoside, 5-azacitidine, 4'-thio-aracitidine,
[0323] [0323] The circular polyribonucleotide may or may not be uniformly modified along the entire length of the molecule. For example, one or more of or all types of nucleotides (eg, naturally occurring nucleotides, purine or pyrimidine or any one or more of or all A, G, U, C, I, pU) may or may not be uniformly modified in the circular polyribonucleotide or in a given region of predetermined sequence. In some embodiments, the circular polyribonucleotide includes a pseudouridine. In some embodiments, the circular polyribonucleotide includes an inosine, which can assist the immune system by characterizing the circular polyribonucleotide as endogenous versus viral RNAs. Inosine incorporation can also mediate improved RNA stability / reduced degradation. See, for example, Yu, Z. et al. (2015) RNA editing by ADAR1 marks dsRNA as “self”. Cell Res. 25, 1283–1284, which is incorporated by reference in its entirety.
[0324] [0324] In some embodiments, all nucleotides in the circular polyribonucleotide (or in a given sequence region) are modified. In some embodiments, the modification may include an m6A, which may increase expression; an inosine, which can attenuate an immune response; pseudouridine, which can increase the stability of RNA or translational reading (staggered element), a m5C, which can increase stability; and a 2,2,7-trimethylguanosine, which helps subcellular translocation (eg, nuclear localization).
[0325] [0325] Different sugar modifications, nucleotide modifications and / or internucleoside bonds (eg, skeletal structures) can exist at various positions in the circular polyribonucleotide. One skilled in the art will appreciate that nucleotide analogs or other modification (s) can be located in any (any) position (s) of the circular polyribonucleotide, so that the function of the circular polyribonucleotide is not substantially diminished. A modification can also be a modification in a non-coding region. The circular polyribonucleotide can include from about 1% to about 100% of modified nucleotides (in relation to the overall nucleotide content or in relation to one or more types of nucleotides, ie, any one or more of A, G, U or C) or any intermediate percentage (eg, from 1% to 20%>, from 1% to 25%, from 1% to 50%, from 1% to 60%, from 1% to 70%, from 1% to 80%, 1% to 90%, 1% to 95%, 10% to 20%, 10% to 25%, 10% to 50%, 10% to 60%, 10 % to 70%, 10% to 80%, 10% to 90%, 10% to 95%, 10% to 100%, 20% to 25%, 20% to 50%, 20% 60%, 20% to 70%, 20% to 80%, 20% to 90%, 20% to 95%, 20% to 100%, 50% to 60%, 50% to 70%, 50% to 80%, 50% to 90%, 50% to 95%, 50% to 100%, 70% to 80%, 70% to 90%, 70% to 95 %, 70% to 100%, 80% to 90%, 80% to 95%, 80% to 100%, 90% to 95%, 90% to 100% and 95% to 100% ). Structure
[0326] [0326] In some embodiments, the circular polyribonucleotide comprises a higher order structure, eg a secondary or tertiary structure. In some embodiments, complementary segments of the circular polyribonucleotide fold into a double-stranded segment, held together with hydrogen bonds between pairs, eg, A-U and C-G. In some embodiments, the propellers, also known as rods, are formed intramolecularly, having a double ribbon segment connected to a final loop. In some embodiments, the circular polyribonucleotide has at least one segment with a secondary, almost double-stranded structure. In some embodiments, a segment having an almost double secondary tape structure has at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 , 20, 21, 22, 23, 24, 25, 26,
[0327] [0327] In some embodiments, one or more circular polyribonucleotide sequences include substantially single-stranded vs. single-stranded regions. double ribbon. In some embodiments, the ratio between single and double strands may influence the functionality of the circular polyribonucleotide
[0328] [0328] In some embodiments, one or more sequences of the circular polyribonucleotide is substantially single-stranded. In some embodiments, one or more circular polyribonucleotide sequences that are substantially single-stranded may include a protein or RNA binding site. In some embodiments, circular polyribonucleotide sequences that are substantially single-stranded can be conformationally flexible to allow for increased interactions. In some embodiments, the circular polyribonucleotide sequence is purposely designed to include such secondary structures to bind or enhance binding to proteins or nucleic acids.
[0329] [0329] In some embodiments, the circular polyribonucleotide sequences are substantially double-stranded. In some embodiments, one or more circular polyribonucleotide sequences that are substantially double-stranded may include a conformational recognition site, e.g., a riboswitch or aptazyme. In some embodiments, circular polyribonucleotide sequences that are substantially double-stranded may be conformationally rigid. In some such cases, the conformationally rigid sequence can sterically prevent the circular polyribonucleotide from binding to a protein or nucleic acid. In some embodiments, the circular polyribonucleotide sequence is purposely designed to include such secondary structures to prevent or reduce binding to proteins or nucleic acids.
[0330] [0330] There are 16 possible base pairings, however, of these, six (AU, GU, GC, UA, UG, CG) can form real base pairs. The rest is called incompatibility and occurs at very low frequencies in propellers. In some embodiments, the structure of the circular polyribonucleotide cannot be easily interrupted without impacting its function and lethal consequences, which provides a selection to maintain the secondary structure. In some embodiments, the primary structure of the stems (i.e., their nucleotide sequence) may still vary, while maintaining the helical regions.
[0331] [0331] In some embodiments, the circular polyribonucleotide has two quasi-helical structures (eg, separated by a phosphodiester bond), so that their terminal base pairs stack, and the quasi-helical structures become collinear, resulting in in a “coaxially stacked” substructure.
[0332] [0332] In some embodiments, the circular polyribonucleotide comprises a tertiary structure with one or more motifs, eg, a pseudonó, a f quadruplex, a helix and coaxial stacking.
[0333] [0333] In some embodiments, the circular polyribonucleotide has at least one binding site, eg at least one protein binding site, at least one miRNA binding site, at least one lncRNA binding site, at least at least one tRNA-binding site, at least one rRNA-binding site, at least one snRNA-binding site, at least one siRNA-binding site, at least one piRNA-binding site, at least one piRNA-binding site snoRNA, at least one snRNA binding site, at least one exRNA binding site, at least one scaRNA binding site, at least one Y RNA binding site, at least one hnRNA binding site and / or at least one tRNA motif. Administration
[0334] [0334] The circular polyribonucleotide described here can also be included in pharmaceutical compositions with an administration carrier.
[0335] [0335] The pharmaceutical compositions described herein can be formulated, for example including a carrier, such as a pharmaceutical carrier and / or a polymeric carrier, e.g., a liposome, and administered by methods known to a subject in need ( eg a human or a non-human agricultural or domestic animal, eg cattle, dog, cat, horse, poultry). Such methods include, but are not limited to, transfection (eg, lipid-mediated, cationic polymers, calcium phosphate, dendrimers); electroporation or other methods of membrane disruption (eg, nucleofection), viral administration (eg, lentivirus, retrovirus, adenovirus, AAV), microinjection, bombardment of microprojectiles (“gene gun”), fugene, charge direct sonication, cell compression, optical transfection, protoplast fusion, impalefection, magnetofection, exosome-mediated transfer, lipid nanoparticle-mediated transfer and any combination thereof. Administration methods are also described, eg, in Gori et al., Delivery and Specificity of CRISPR / Cas9 Genome Editing Technologies for Human Gene Therapy. Human Gene Therapy. July 2015, 26 (7): 443-451. doi: 10.1089 / hum.2015.074; and Zuris et al. Cationic lipid- mediated delivery of proteins enables efficient protein- based genome editing in vitro and in vivo. Nat Biotechnol. Oct 30, 2014; 33 (1): 73–80.
[0336] [0336] The invention is further directed to a host or host cell comprising the circular polyribonucleotide described herein. In some embodiments, the host or host cell is a plant, insect, bacterium, fungus, vertebrate, mammal (eg, human) or another organism or cell.
[0337] [0337] In some embodiments, the circular polyribonucleotide is non-immunogenic in the host. In some embodiments, the circular polyribonucleotide has a diminished response or fails to produce a response by the host's immune system compared to the response triggered by a reference compound, eg, a linear polynucleotide corresponding to the described circular polyribonucleotide or a polyribonucleotide circular not having an encryptogen. Some immune responses include, but are not limited to, humoral immune responses (eg, production of antigen-specific antibodies) and cell-mediated immune responses (eg, lymphocyte proliferation).
[0338] [0338] In some embodiments, a host or host cell is contacted with (eg, delivered to or administered to) circular polyribonucleotide. In some embodiments, the host is a mammal, just like a human. The amount of the circular polyribonucleotide, expression product, or both in the host can be measured at any time after administration. In certain embodiments, a time course of host growth in a culture is determined. If growth is increased or reduced in the presence of the circular polyribonucleotide, the circular polyribonucleotide or expression product or both are identified as being effective in increasing or reducing host growth. Production Methods
[0339] [0339] In some embodiments, the circular polyribonucleotide includes a naturally occurring deoxyribonucleic acid sequence that can be produced using recombinant technology (methods described in detail below; eg, derived in vitro using a DNA plasmid) or chemical synthesis.
[0340] [0340] It is within the scope of the invention that a DNA molecule used to produce a circle of RNA can comprise a DNA sequence from a naturally occurring original nucleic acid sequence, a modified version or a DNA sequence encoding a synthetic polypeptide not normally found in nature (eg, chimeric molecules or fusion proteins). DNA and RNA molecules can be modified using a variety of techniques including, but not limited to, classic mutagenesis techniques and recombinant techniques, such as site-directed mutagenesis, chemical treatment of a nucleic acid molecule to induce mutations, cleavage with restriction enzymes of a nucleic acid fragment, binding of nucleic acid fragments, amplification by polymerase chain reaction (PCR) and / or mutagenesis of selected regions of a nucleic acid sequence, synthesis of oligonucleotide mixtures and binding of mixing groups to “build” a mixture of nucleic acid molecules and their combinations.
[0341] [0341] The circular polyribonucleotide can be prepared according to any available technique including, but not limited to, chemical synthesis and enzymatic synthesis. In some embodiments, a primary linear construct or linear mRNA can be cyclized or concatemerized to create a circular polyribonucleotide described here. The cyclization or concatemerization mechanism can occur through methods such as, but not limited to, chemical, enzymatic, splint bonding or ribozyme catalyzed methods. The newly formed 5 '/ 3' bond can be an intramolecular bond or an intermolecular bond.
[0342] [0342] The methods for preparing the circular polyribonucleotides described here are described in, for example, Khudyakov & Fields, Artificial DNA: Methods and
[0343] [0343] Various methods of synthesizing circular polyribonucleotides are also described in the art (see, eg, U.S. Patent No. US6210931, US Patent No. US5773244, US Patent No. US5766903, US Patent No. US5712128 , US Patent No. US5426180, US Publication US20100137407, International Publication No. WO1992001813 and International Publication No. WO2010084371; the contents of each of which are incorporated herein by reference in their entirety).
[0344] [0344] In some embodiments, circular polyribonucleotides can be cleaned after production to remove production impurities, e.g., free ribonucleic acids, linear or cut RNA, DNA, proteins, etc. In some embodiments, circular polyribonucleotides can be purified by any known method commonly used in the art. Examples of non-limiting purification methods include column chromatography, gel excision, size exclusion, etc. Pharmaceutical Compositions
[0345] [0345] The present invention includes compositions in combination with one or more pharmaceutically acceptable excipients. The pharmaceutical compositions can optionally comprise one or more additional active substances, e.g., therapeutically and / or prophylactically active substances. The pharmaceutical compositions of the present invention can be sterile and / or free of pyrogens. General considerations in the formulation and / or manufacture of pharmaceutical agents can be found, for example, in Remington: The Science and Practice of Pharmacy 21st ed., Lippincott Williams & Wilkins, 2005 (incorporated by reference).
[0346] [0346] Although the descriptions of pharmaceutical compositions provided herein are primarily directed to pharmaceutical compositions that are suitable for administration to humans it will be understood by the skilled person that such compositions are generally suitable for administration to any other animal, e.g., to non-human animals , e.g., non-human mammals. The modification of pharmaceutical compositions suitable for administration to humans in order to make the compositions suitable for administration to various animals is well understood, and the skilled veterinary pharmacologist can design and / or perform such modification with merely ordinary experimentation, if any. Subjects for whom administration of the pharmaceutical compositions is contemplated include, but are not limited to, humans and / or other primates; mammals, including commercially relevant mammals such as cattle, pigs, horses, sheep, cats, dogs, mice and / or mice; and / or birds,
[0347] [0347] The formulations of the pharmaceutical compositions described here can be prepared by any method known or henceforth developed in the pharmacology technique. In general, such preparatory methods include the step of placing the active ingredient in association with an excipient and / or one or more other accessory ingredients and then, if necessary and / or desirable, dividing, shaping and / or packaging the product. Expression Methods
[0348] [0348] The present invention includes a method for expressing proteins, comprising translating at least one region of the circular polyribonucleotide provided herein.
[0349] [0349] In some embodiments, methods for protein expression include translation of at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70% at least 80%, at least 90% or at least 95% of the total length of the circular polyribonucleotide in polypeptides. In some embodiments, methods for protein expression comprise translation of the circular polyribonucleotide into polypeptides of at least 5 amino acids, at least 10 amino acids, at least 15 amino acids, at least 20 amino acids, at least 50 amino acids, at least 100 amino acids, at least 150 amino acids, at least 200 amino acids, at least 250 amino acids, at least 300 amino acids, at least 400 amino acids, at least 500 amino acids, at least 600 amino acids, at least 700 amino acids, at least 800 amino acids, at least 900 amino acids or at least minus 1000 amino acids. In some embodiments, methods for protein expression include translation of the circular polyribonucleotide into polypeptides of about 5 amino acids, about 10 amino acids, about 15 amino acids, about 20 amino acids, about 50 amino acids, about 100 amino acids, about 150 amino acids, about 200 amino acids, about 250 amino acids, about 300 amino acids, about 400 amino acids, about 500 amino acids, about 600 amino acids, about 700 amino acids, about 800 amino acids, about 900 amino acids, or about 1000 amino acids. In some embodiments, the methods comprise translating the circular polyribonucleotide into continuous polypeptides as provided herein, discrete polypeptides as provided here or both.
[0350] [0350] In some embodiments, translation of at least one region of the circular polyribonucleotide takes place in vitro, such as rabbit reticulocyte lysate. In some embodiments, translation of at least one region of the circular polyribonucleotide takes place in vivo, for example, after transfection of a eukaryotic cell, or transformation of a prokaryotic cell such as a bacterium.
[0351] [0351] In some respects, the present disclosure provides methods of in vivo expression of one or more expression sequences in a subject, comprising: administration of a circular polyribonucleotide to a subject cell in which the circular polyribonucleotide comprises one or more sequences of expression; and expressing one or more expression sequences from the circular polyribonucleotide in the cell. In some embodiments, the circular polyribonucleotide is configured so that the expression of one or more expression sequences in the cell at a later time is equal to or higher than an earlier time. In some embodiments, the circular polyribonucleotide is configured so that the expression of one or more expression sequences in the cell over a period of time of at least 7, 8, 9, 10, 12, 14, 16, 18, 20 , 22, 23 or more days do not decrease by more than about 40%. In some embodiments, the circular polyribonucleotide is configured so that the expression of one or more expression sequences in the cell is maintained at a level that does not vary by more than about 40% for at least 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 23 or more days. In some embodiments, administration of the circular polyribonucleotide is conducted using any method of administration described herein. In some embodiments, the circular polyribonucleotide is administered to the subject through an intravenous injection. In some embodiments, administration of the circular polyribonucleotide includes, but is not limited to, prenatal administration, neonatal administration, postnatal administration, oral, by injection (eg, intravenous, intraarterial, intraperitoneal, intradermal, subcutaneous and intramuscular), by ophthalmic administration and intranasal administration.
[0352] [0352] In some embodiments, methods for protein expression comprise modification, folding or other post-translation modification of the translation product. In some embodiments, methods for protein expression comprise post-translational modification in vivo, eg, via cellular machinery.
[0353] [0353] All references and publications and references cited here are hereby incorporated by reference.
[0354] [0354] The modalities described above can be combined to achieve the functional characteristics mentioned above. This is also illustrated by the examples below that show exemplary combinations and functional characteristics achieved. Table 1 provides an exemplary overview that shows how the different elements described above can be combined and the functional characteristics observed. Table 1. Exemplary elements in the EXAMPLES Elements (eg, start codon, stepped effect element, encryptogen, IRES, etc.) of
[0355] [0355] The following examples are provided to further illustrate some embodiments of the present invention, but are not intended to limit the scope of the invention; it will be understood by its exemplary nature that other procedures, methodologies or techniques known to those skilled in the art may alternatively be used. Example 1: Circular RNA production in vitro
[0356] [0356] This example demonstrates the in vitro production of a circular RNA.
[0357] [0357] A circular RNA is designed with a start codon (SEQ ID NO: 1), ORF (s) (SEQ ID NO: 2), stepped element (s) (SEQ ID NO: 3), encryptogen (s) (SEQ ID NO: 4) and an IRES (SEQ ID NO: 5), shown in Figure 2. Circularization allows the translation of a rolling circle, multiple open reading grids (ORFs) with alternating stepped elements for discrete expression of ORF and controlled protein stoichiometry, encryptogen (s) to attenuate or mitigate the immunogenicity of RNA and an optional IRES that targets the RNA for ribosomal entry without poly-A sequence.
[0358] [0358] In this Example, circular RNA is generated as follows. Unmodified linear RNA is synthesized by in vitro transcription using T7 RNA polymerase from a DNA segment having 5'- and 3'-ZKSCAN1 introns and an ORF encoding GFP linked to 2A sequences. The transcribed RNA is purified with an RNA purification system (QIAGEN), treated with alkaline phosphatase (ThermoFisher Scientific, EF0652) following the manufacturer's instructions and purified again with the RNA purification system.
[0359] [0359] Circular RNA with splint binding is generated by treatment of the transcribed linear RNA and DNA splint using T4 DNA ligase (New England Bio, Inc., M0202M), and circular RNA is isolated after enrichment with treatment with RNase R. The quality of the RNA is assessed by agarose gel or by automated electrophoresis (Agilent). Example 2: Production of circular RNA in vivo, cell culture
[0360] [0360] This example demonstrates the in vivo production of a circular RNA.
[0361] [0361] GFP (SEQ ID NO: 2) is cloned into an expression vector, eg, pcDNA3,1 (+) (Addgene) (SEQ ID NO: 6). This vector is mutagenized to induce the production of circular RNA in cells (SEQ ID NO: 6 and described by Kramer et al. 2015), shown in Figure 3.
[0362] [0362] HeLa cells are cultured at 37 ºC and 5% CO2 in Eagle's medium modified by Dulbecco (DMEM) with high glucose level (Life Technologies), supplemented with penicillin-streptomycin and 10% fetal bovine serum. One microgram of the expression plasmid described above is transfected using lipid transfection reagent (Life Technologies), and the total RNA of the transfected cells is isolated using a phenol-based RNA isolation reagent (Life Technologies) according to the manufacturer's instructions between 1 hour and 20 days after transfection.
[0363] [0363] qPCR reverse transcription using random hexamers is performed to measure the levels of circular RNA and GFP mRNA. In summary, for RT-qPCR, total RNA from Hela cells and RNA digested by RNase R from the same source are used as templates for RT – PCR. To prepare the GFP mRNA cDNAs and GFP circular RNAs, reverse transcription reactions are performed with a reverse transcriptase (Super-Script II: RNase H; Invitrogen) and random hexamers according to the manufacturer's instructions. The amplified PCR products are analyzed using a 6% PAGE and visualized by ethidium bromide staining. In order to estimate the enrichment factor, PCR products are quantified by densitometry (ImageQuant; Molecular Dynamics) and the concentrations of total RNA samples are measured by UV absorbance.
[0364] [0364] An additional RNA measurement is performed with Northern blot analysis. Briefly, the whole cell extract was obtained using a phenol-based reagent (TRIzol) or the extracts of nuclear and cytoplasmic proteins are obtained by fractionation of the cells with a commercial kit (CelLytic NuCLEAR Extraction Kit, Sigma). To inhibit RNA polymerase II transcription, cells are treated with flavopyridol (final concentration of 1 mM; Sigma) for 0-6 h at 37 ºC. For RNase R treatments, 10 mg of total RNA is treated with 20 U of RNase R (Epicenter) for 1 h at 37 ° C.
[0365] [0365] Northern blots using oligonucleotide probes are performed as follows. Oligonucleotide probes, PCR primers are designed using standard primer design tools. The sequence of the T7 promoter is added to the reverse primer to obtain an antisense probe in the in vitro transcription reaction. In vitro transcription is performed using T7 RNA polymerase with a DIG-RNA labeling mixture according to the manufacturer's instructions. The DNA models are removed by digestion by DNAs I and the RNA probes purified by extraction with phenol and chloroform and subsequent precipitation. The probes are used at 50 ng / ml. The total RNA (2 μg - 10 μg) is denatured using glyoxal loading dye (Ambion) and resolved on a 1.2% agarose gel in MOPS buffer. The gel is soaked in 1 × TBE for 20 min and transferred to a Hybond-N + membrane (GE Healthcare) for 1 h (15 V) using a semi-dry transfer system (Bio-Rad). The membranes are dried and cross-linked with UV (at 265 nm) 1 × at 120,000 μJ cm-2. Pre-hybridization is done at 68 ° C for 1 h and the RNA probes transcribed in vitro with DIG labeling are hybridized overnight. The membranes are washed three times in 2 × SSC, 0.1% SDS at 68 ° C for 30 min, followed by three 30 min washes in 0.2 × SSC, 0.1% SDS at 68 ° C. Immunodetection is performed with anti-DIG directly conjugated to antibodies against alkaline phosphatase. The immunoreactive bands are visualized using chemiluminescent alkaline phosphatase substrate (CDP star reagent) and an image detection and quantification system (LAS-4000 detection system). Example 3: Preparation of circular RNA and in vitro translation
[0366] [0366] This example demonstrates gene expression and detection of the gene product from a circular RNA.
[0367] [0367] In this example, the circular RNA is designed with a start codon (SEQ ID NO: 1), a GFP ORF (SEQ ID NO: 2), stepped element (s) (SEQ ID NO: 3), human-derived encryptogen (s) (SEQ ID NO: 4) and with or without an IRES (SEQ ID NO: 5), see Figure 4. In this example, circular RNA is generated in vitro or in cells as described in Examples 1 and 2.
[0368] [0368] The circular RNA is incubated for 5 h or overnight in rabbit reticulocyte lysate (Promega, Fitchburg, WI, USA) at 30 ° C. The final composition of the reaction mixture includes 70% rabbit reticulocyte lysate, 10 μM methionine and leucine, non-methionine and 20 μM leucine amino acids and 0.8 U / μL RNase inhibitor (Toyobo, Osaka, Japan) . Aliquots are removed from the mixture and separated into polyacrylamide / sodium dodecyl sulfate (SDS) gels with a 10-20% gradient (Atto, Tokyo, Japan). The supernatant is removed and the pellet is dissolved in 2 × SDS sample buffer (0.125 M Tris-HCl, pH 6.8, 4% SDS, 30% glycerol, 5% 2-mercaptoethanol, bromophenol blue 0.01%) at 70 ° C for 15 min. Hemoglobin protein is removed during this process while proteins other than hemoglobin are concentrated.
[0369] [0369] After centrifugation at 1,400 × g for 5 min, the supernatant is analyzed in polyacrylamide / SDS gels with a 10–20% gradient. A commercially available standard (BioRad) is used as the size marker. After being electrotransferred to a polyvinylidene fluoride (PVDF) membrane (Millipore) using a semi-dry method, the transfer is visualized using a chemiluminescent case (Rockland).
[0370] [0370] The GFP protein is expected to be visualized in cell lysates and to be detected in higher amounts in circular RNA than linear RNA as a result of the translation of the rolling circle. Example 4: Stoichiometric expression of proteins from circular RNA
[0371] [0371] This example demonstrates the ability of circular RNA to express stoichiometrically proteins.
[0372] [0372] In this Example, a circular RNA is designed to include encryptogens (SEQ ID NO: 4) and an ORF encoding GFP (SEQ ID NO: 2) and an ORF encoding RFP (SEQ ID NO: 8) with staggered elements ( SEQ ID NO: 3) flanking the GFP and RFP ORFs, see Figure 5. Another circular RNA is similarly designed, however, instead of flanking the 2A sequences, it will have a Stop and Start codon between the GFP ORFs and RFP. Circular RNAs are generated in vitro or in cells as described in Examples 1 and 2.
[0373] [0373] Circular RNAs are incubated for 5 h or overnight in rabbit reticulocyte lysate (Promega, Fitchburg, WI, USA) at 30 ° C. The final composition of the reaction mixture includes 70% rabbit reticulocyte lysate, 10 μM methionine and leucine, non-methionine and 20 μM leucine amino acids and 0.8 U / μL RNase inhibitor (Toyobo, Osaka, Japan) . Aliquots are removed from the mixture and separated into polyacrylamide / sodium dodecyl sulfate (SDS) gels with a 10-20% gradient (Atto, Tokyo, Japan). The supernatant is removed and the pellet is dissolved in 2 × SDS sample buffer (0.125 M Tris-HCl, pH 6.8, 4% SDS, 30% glycerol, 5% 2-mercaptoethanol, bromophenol blue 0.01%) at 70 ° C for 15 min. Hemoglobin protein is removed during this process while proteins other than hemoglobin are concentrated.
[0374] [0374] After centrifugation at 1,400 × g for 5 min, the supernatant is analyzed on polyacrylamide / SDS gels with a 10–20% gradient. A commercially available standard (BioRad) is used as the size marker. After being electrotransferred to a polyvinylidene fluoride (PVDF) membrane (Millipore) using a semi-dry method, the transfer is visualized using a chemiluminescent case (Rockland).
[0375] [0375] It is expected that the circular RNA with GFP and RFP ORFs not separated by a Stop and start codon will have equal amounts of any of the proteins, whereas cells treated with a circular RNA including the start and stop codon between ORFs will have different amounts of any of the proteins. Example 5: Non-immunogenicity in cell culture
[0376] [0376] This example demonstrates the in vivo evaluation of the immunogenicity of circular RNA after infection of cells.
[0377] [0377] In this Examples, circular RNAs are designed to include an encryptogen, eg, a ZKSCAN1 intron and a GFP ORF. In addition, circular control RNA is designed to include a GFP ORF with and without introns, see Figure 6. The circular RNA is generated in vitro or in cells as described in Examples 1 and 2. HeLa cells are transfected with 500 ng of RNAs circular.
[0378] [0378] Transfection of circular RNA includes the following conditions: (1) naked circular RNA in cell culture media (Lingor et al. 2004); (2) electroporation (Muller et al. 2015); (3) cationic lipids (SNALP, Vaxfectin) (Chesnoy and Huang, 2000); (3) cationic polymers (PEI, polybene, DEAE-dextran) (Turbofect); (4) virus-like particles (HPV L1, polyomavirus VP1) (Tonges et al. 2006); (5) exosomes (Exo-Fect from SBI); (6) nanostructured calcium phosphate (nanoCaP) (Olton et al. 2006); (6) peptide transduction domains (TAT, polyR, SP, pVEC, SynB1, etc.) (Zhang et al. 2009); (7) vesicles (VSV-G, TAMEL) (Liu et al. 2017); (8)
[0379] [0379] After 2-48 h post-transfection, the medium is removed and the relative expression of the indicated RNA and transfected RNA is measured by qRT-PCR.
[0380] [0380] For qRT-PCR analysis, total RNA is isolated from the cells using a phenol-based RNA isolation solution (TRIzol) and an RNA isolation kit (QIAGEN) following the manufacturer's instructions. QRT-PCR analysis is performed in triplicate using a PCR master mix (Brilliant II SYBR Green qRT-PCR Master Mix) and a PCR cycler (LightCycler 480). The mRNA levels for well-known innate immunity regulators such as RIG-I, MDA5, OEA, OASL and PKR are quantified and normalized to actin, GAPDH or HPRT values. The relative expression of RNA genes indicated for circular RNA transfection is normalized by the level of transfected RNA and compared with the level of expression of cells with circular RNA transfection that does not contain encryptogen (s).
[0381] [0381] In addition to qRT-PCR analysis, Western blot analysis and immunohistochemistry, as described above in Example 4, are used to evaluate the efficiency of GFP expression.
[0382] [0382] GFP positive cells containing encryptogen (s) are expected to show an attenuated immunogenicity response.
[0383] [0383] Additionally, (1) primary murine dendritic cells; (2) Human embryonic kidney 293 cells stably expressing TLR-7, 8 or 9 (InvivoGen); (3) monocyte-derived dendritic cells (AllCells) or (4) crude 264.7 cells are transfected with a DNA plasmid including ZKSCAN1 or td introns that produce a circular RF encoding GFP as described above. After 6-48 h post-transfection, the cell culture supernatant is collected and the expression of cytokines is measured using ELISA. When the cell culture supernatant is collected, the cells are collected for Northern transfer, gene expression arrangement and FACS analysis.
[0384] [0384] ELISA kits are used for ELISA for interferon-β (IFN-β), chemokine ligand (motif C – C) 5 (CCL5), IL-12 (BD Biosciences), IFN-α, TNF-α and IL-8 (Biosource International). ELISAs are performed according to the manufacturer's recommendations. Cytokine expression indicated for cells transfected with circular RNA is compared with the level of cells transfected with control RNA. It is expected that cells transfected with circular RNA with an encryptogen will have reduced cytokine expression compared to control transfected cells.
[0385] [0385] For Northern transfer analysis. The samples are processed and analyzed as previously described. The probes are derived from plasmids and are specific to the coding regions of human IFN-alpha 13, IFN-beta (Open Biosystems), TNF-alpha or GAPDH (ATCC). It is expected that cells transfected with circular RNA with an encryptogen will have reduced cytokine expression compared to control transfected cells.
[0386] [0386] For the gene expression array, RNA is isolated using a phenol-based solution (TRIzol) and / or an RNA isolation kit (RNeasy Qiagen). The RNA is amplified and analyzed (eg, Illumina Human HT12v4 chip in an Illumina BeadStation 500GX). Levels in cells treated with simulated control are used as the baseline for calculating the dimension of variation. It is expected that cells transfected with circular RNA with an encryptogen will have reduced cytokine expression compared to control transfected cells.
[0387] [0387] For FACS analysis, cells are stained with an antibody directly conjugated against CD83 (Research Diagnostics Inc), HLA-DR, CD80 or CD86 and analyzed on a flow cytometer. It is expected that cells transfected with circular RNA with an encryptogen will show reduced expression of these markers compared to control transfected cells. Example 6: Riboswitches for selective expression
[0388] [0388] This example demonstrates the ability to control protein expression from circular RNA in vivo.
[0389] [0389] For this Example, circular RNAs are designed to include encryptogen (s) (SEQ ID NO: 4), a synthetic riboswitch (SEQ ID NO: 9) regulating the expression of the ORF encoding GFP (SEQ ID NO: 2) with scaled elements (2A sequences) (SEQ ID NO: 3) flanking GFP ORF, see Figure 7. Circular RNA is generated in vitro or in cells as described in Examples 1 and 2.
[0390] [0390] Theophylline induces activation of the riboswitch, resulting in an inactivation of gene expression (as described by Auslander et al. 2010). The riboswitch is expected to control GFP expression from circular RNA. In the presence of theophylline, GFP expression is not expected to be observed.
[0391] [0391] HeLa cells are transfected with 500 ng of circular RNA encoding GFP described under the control of theophylline-dependent synthetic riboswitch (SEQ ID NO: 9) to assess selective expression. Transfection methods are described in Example 5.
[0392] [0392] After 24 h of culture at 37 ° C and 5% CO2, cells are treated with and without theophylline with concentrations ranging from 1 nM-3 mM. After 24 h of continuous culture, the cells are fixed in 4% paraformaldehyde for 15 minutes at room temperature, blocked and permeabilized for 45 minutes with 10% FBS in 0.2% detergent PBS. The samples are then incubated with primary antibodies against GFP (Invitrogen) and secondary antibodies conjugated with Alexa 488 and DAPI (Invitrogen) in PBS with 10% FBS and 0.1% detergent for 2 h at room temperature or overnight at 4 ° C. The cells are then washed with PBS and subsequently analyzed using a fluorescent microscope for GFP expression. Example 7: In vivo expression
[0393] [0393] This example demonstrates the ability to express protein from a circular RNA in vivo.
[0394] [0394] For this Example, circular RNAs are designed to include including encryptogen (s) (SEQ ID NO: 4) and an ORF encoding GFP (SEQ ID NO: 2) or RFP (SEQ ID NO: 8) or Luciferase ( SEQ ID NO: 10) with staggered elements (SEQ ID NO: 3) flanking the GFP, RFP or Luciferase ORF, see Figure 8. Circular RNA is generated in vitro or in cells as described in Examples 1 and 2.
[0395] [0395] Male BALB / c mice 6-8 weeks of age receive circular RNA at 300 mg / kg (6 mg) (50 uL vol) with GFP, RFP or luciferase ORFs, as described here, or linear RNA as a control, through intradermal (ID), intramuscular (IM), oral (PO), intraperitoneal (IP) or intravenous (IV) administration. The animals receive a single dose or three injections (day 1, day 3, day 5).
[0396] [0396] Blood, heart, lung, spleen, kidney, liver and skin injection sites are collected from unmeasured control mice and at 2, 4, 8, 24, 48,
[0397] [0397] Quantification of circular RNA for both serum and tissues is performed using quantification of branched DNA (bDNA) (Panomics / Affymetrix). A standard curve on each plate of known amounts of RNA (added to samples of untreated tissue) is used to quantify RNA in treated tissues. The amount calculated in picograms (pg) is normalized to the amount of heavy tissue in the lysate applied to the plate. Protein expression (RFP or GFP) is assessed by FACS or Western blot in each tissue as described in a previous Example.
[0398] [0398] A separate group of mice dosed with circular luciferase RNA is injected with 3 mg luciferin at 6, 24, 48, 72 and 96 h post-dosing and the animals are visualized in an in vivo visualization system (IVIS Spectrum , PerkinElmer). At 6 h post-dosing, three animals are sacrificed and dissected, and the muscle, skin, draining lymph nodes, liver and spleen are visualized ex vivo.
[0399] [0399] Mice are expected to express GFP, RFP or luciferase in treated tissues. Example 8: Biodistribution in vivo
[0400] [0400] This example demonstrates the ability to control and measure circular RNA biodistribution in vivo.
[0401] [0401] In this Example, mice are treated with circular RNA encoding luciferase as described in
[0402] [0402] The mice are dosed with circular luciferase RNA by injection with 3 mg luciferin at 6, 24, 48, 72 and 96 h post-dosing and the animals are visualized in an in vivo visualization system (IVIS Spectrum, PerkinElmer ). At 6 h post-dosing, three animals are sacrificed and dissected, and the muscle, skin, draining lymph nodes, liver and spleen are visualized ex vivo.
[0403] [0403] The quantification of circular RNA for both serum and tissues is performed using the quantification of branched DNA (bDNA) (Panomics / Affymetrix). A standard curve on each plate of known amounts of RNA (added to samples of untreated tissue) is used to quantify RNA in treated tissues. The amount calculated in picograms (pg) is normalized to the amount of heavy tissue in the lysate applied to the plate.
[0404] [0404] A separate group of male BALB / c mice 6-8 weeks of age is dosed with circular luciferase RNA via IM or ID administration at four dose levels: 10, 2, 0.4 and 0.08 mg (n = 6 per group). At 6, 24, 48, 72 and 96 h post-dosing, the animals are injected with 3 mg of luciferin and visualized in an in vivo visualization system (IVIS Spectrum, PerkinElmer). At 6 h post-dosing, three animals are sacrificed and dissected, and the muscle, skin, draining lymph nodes, liver and spleen are visualized ex vivo. The tissues of the mice are also evaluated for luciferase expression as described in Example 9 and the tissue distribution of this expression is analyzed.
[0405] [0405] Mice are expected to show luciferase expression in the treated tissues. Example 9: Non-immunogenicity in vivo
[0406] [0406] This example demonstrates the in vivo evaluation of the immunogenicity of circular RNA after infection of cells.
[0407] [0407] This example describes the quantification and comparison of the immune response after administrations of circular RNA harboring an encryptogen, see Figure 10. In one embodiment, any circular RNA with an encryptogen will have a reduced (e.g., reduced) immunogenic response. compared to administration of control RNA) after one or more administrations of circular RNA compared to control.
[0408] [0408] A measure of immunogenicity for circular RNA is serum cytokine levels.
[0409] [0409] In this Example, serum levels of cytokines are examined after one or more administrations of circular RNA. The circular RNA from any of the previous Examples is administered via intradermal (DI), intramuscular (IM), oral (PO), intraperitoneal (IP) or intravenous (IV) in 6-8 week old BALB / c mice. The serum is removed from the different cohorts: mice injected systemically and / or locally with injection (s) of circular RNA harboring an encryptogen and circular RNA without an encryptogen.
[0410] [0410] Serum samples collected are diluted 1-10x in PBS and analyzed for mouse IFN-α by enzyme-linked immunosorbent assay (PBL Biomedical Labs, Piscataway, NJ) and TNF-α (R&D, Minneapolis, MN) .
[0411] [0411] In addition to serum cytokine levels, the expression of inflammatory markers is another measure of immunogenicity. In this Example, spleen tissue from mice treated with vehicle (without circular RNA), linear RNA or circular RNA will be collected 1, 4 and 24 hours post-administration. The samples will be analyzed using the following analysis techniques by qRT-PCR, Northern transfer or FACS analysis.
[0412] [0412] For qRT-PCR analysis, mRNA levels for RIG-I, MDA5, OAS, OASL, TNF-alpha and PKR are quantified as previously described.
[0413] [0413] For Northern transfer analysis. The samples are processed and analyzed for IFN-alpha 13, IFN-beta (Open Biosystems), TNF-alpha or GAPDH (ATCC) as described above.
[0414] [0414] For FACS analysis, cells are stained with an antibody directly conjugated against CD83 (Research Diagnostics Inc), HLA-DR, CD80 or CD86 and analyzed on a flow cytometer.
[0415] [0415] In one embodiment, circular RNA with an encryptogen will have decreased cytokine levels (as measured by ELISA, Northern blot, FACS and / or qRT-PCR) after one or multiple administrations, compared to control RNA. Example 10: Circular RNA includes at least one double-stranded RNA segment
[0416] [0416] This example demonstrates that circular RNA includes at least one segment of double-stranded RNA.
[0417] [0417] In this example, circular RNA is synthesized using one of the methods previously described, to include a GFP ORF and an IRES, see Figure 11. Dot blot assays with monoclonal antibodies J2 and K1 will be used to measure structures of double-stranded RNA at least 40 bp in length. The circular RNA (200 ng) is transferred to a nylon membrane (Nytran supercharged), dried and blocked with 5% dry milk in TBS-T buffer (50 mM Tris-HCl, 150 mM NaCl, Tween- 20 to 0.05%, pH 7.4) and incubated with specific dsRNA mAb J2 or K1 (English & Scientific Consulting) for 60 min. The membranes are washed six times with TBS-T, then treated with donkey anti-mouse Ig conjugated to HRP (Jackson Immunology), then washed six times and the spots are visualized with an enhanced chemiluminescence Western transfer detection reagent (Amersham) .
[0418] [0418] A circular RNA is expected to create an internal almost double-stranded RNA segment.
[0419] [0419] Example 11: Circular RNA includes an almost double stranded structure
[0420] [0420] This example demonstrates that the circular RNA includes an almost double stranded structure.
[0421] [0421] In this example, circular RNA is synthesized using one of the methods previously described, with and without adding HDVmin expression (Griffin et al. 2014). This RNA sequence forms an almost helical structure, see Figure 12, and is used as a positive control (as shown by Griffin et al. 2014).
[0422] [0422] To test whether the circular RNA structure includes a functional almost double-stranded structure, we will determine the secondary structure using selective 2´OH acylation analyzed by primer extension (SHAPE). SHAPE assesses the flexibility of the local skeleton in RNA in single nucleotide resolution. The reactivity of the base positions with the SHAPE electrophile is related to the secondary structure: the positions paired with bases are weakly reactive, while the unpaired positions are more highly reactive.
[0423] [0423] SHAPE is performed on circular RNA, HDVmin and linear RNA containing. SHAPE is performed with N-methylisatoic anhydride (NMIA) or benzoyl cyanide (BzCN) essentially as reported by Wilkinson et al. 2006 and Griffin 2014 et al., Respectively. In summary for SHAPE with BzCN, 1 µL of 800 mM BzCN in dimethyl sulfoxide (DMSO) is added to a 20 µL reaction mixture containing
[0424] [0424] Crude electropherograms are analyzed using a primary fragment analysis tool (eg PeakScanner Applied Bio-systems). The peaks at each position on the electropherogram are then integrated. For each RNA analyzed, the y-axis scaling to correct for the load error is performed so that the background for each primer extension reaction is normalized to that of a negative control reaction performed on the RNA that is not treated with BzCN. A signal decay correction is applied to the data for each reaction. The peaks are aligned with a ladder created from two sequencing reactions. At each position, the peak area of the negative control is subtracted from the peak area in samples treated with BzCN; these values are then converted into normalized SHAPE reactivities by dividing the peak areas subtracted by the average of the highest 2% to 10% of the peak areas subtracted.
[0425] [0425] In addition to the SHAPE analysis, we will perform NMR (Marchanka et al. 2015); Probing with hydroxyl radicals (Ding et al. 2012); or a combination of DMS and CMTC and Cetoxal (Tijerina et al. 2007 and Ziehler et al. 2001).
[0426] [0426] It is expected that a circular RNA will have an almost double stranded structure. Example 12: The circular RNA includes a functional almost helical structure
[0427] [0427] This example demonstrates that the circular RNA includes an almost helical structural structure.
[0428] [0428] In this example, circular RNA is synthesized using one of the methods previously described, with the addition of the 395L expression (Defenbaugh et al. 2009). This RNA sequence forms an almost helical structure (as shown above, by the folding algorithm of the secondary structure of the RNA mfold and Defenbaugh et al. 2009), Figure 13. This structure is essential for the formation of complexes with the hepatitis D antigen. (HDAg).
[0429] [0429] Therefore, to test whether the circular RNA structure includes a quasi-functional structure, we will incubate the circular RNA and linear RNA with HDAg-160 or HDAg-195 and analyze the binding using EMSA assays. Binding reactions are carried out in 25 µL including 10 mM Tris-HCl (pH 7.0), 25 mM KCl, 10 mM NaCl, 0.1 g / L bovine serum albumin (New England Biolabs), 5% glycerol, 0.5 mM DTT, 0.2 U / L RNase inhibitor (Applied Biosystems) and 1 mM phenylmethylsulfonyl fluoride solution. The circular RNA is incubated with the HDAg protein (obtained as described by Defenbaugh et al. 2009) at concentrations ranging from 0-110 nM. The reaction mixtures are mounted on ice, incubated at 37 ° C for 1 h and subjected to electrophoresis in 6% native polyacrylamide gels in 0.5 to 240 V Tris-borate-EDTA for 2.5 h. Levels of free and bound RNA are determined using staining with nucleic acid (eg, gelred). The binding will be calculated as the intensity of the unbound RNA in relation to the intensity of the entire line minus the bottom.
[0430] [0430] It is expected that a circular RNA will have a functional almost helical structure. Example 13: Autotranscription / replication
[0431] [0431] In this example, circular RNA is synthesized using one of the methods described previously, with the addition of the expression of the HDV replication domain (s) (as described by Beeharry et al. 2014), the ribozyme competent for antigenic replication and a nuclear localization signal. These RNA sequences allow the circular RNA to be located in the nucleus where the host's RNA polymerase will bind to and transcribe the RNA. This RNA is then autocleaved using the ribozyme. The RNA is then switched on and self-replicated again, see Figure 14.
[0432] [0432] The circular RNA (1-5 microgram) will be transfected into HeLa cells using the techniques described above. HeLa cells are cultured at 37 ºC and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM) with high glucose level (Life Technologies), supplemented with penicillin-streptomycin and 10% fetal bovine serum. After transfection, HeLa cells are cultured for an additional 4-72 h, then the total RNA of the transfected cells is isolated using a phenol-based RNA isolation reagent (Life Technologies) according to the manufacturer's instructions between 1 hour and 20 days after transfection and the total amount of circular RNA encoding the HDV domains will be determined and compared to the control circular RNA using qPCR as described here. Example 14: Stability / half-life of circular RNA
[0433] [0433] In this example, circular RNA is synthesized using one of the methods described previously. A circular RNA is designed to include encryptogens (SEQ ID NO: 4) and an ORF encoding GFP (SEQ ID NO: 2) with staggered elements (SEQ ID NO: 3) flanking the GFP ORF, see Figure 15.
[0434] [0434] Human fibroblasts (eg, IMR-90) are cultured until confluence in Dulbecco's modified Eagle's medium (DMEM; Invitrogen) supplemented with 10% fetal bovine serum (FBS; Invitrogen) at 37 ° C under 5% CO2 in plates treated with tissue culture. When fibroblasts reach confluence, they stop dividing due to contact inhibition (Leontieva et al. 2014). Lipid transfection reagent (2 μL; Invitrogen) is added to a mixture of 1 μg of circular RNA or linear RNA (described above) and 145 μL of reduced serum medium (Opti-MEM I solution) in a well of a plate treated with 12 well tissue culture. After incubation at room temperature for 15 min, ~ 1 x 10 ^ 5 cells suspended in DMEM with 10% FBS are added to the circular RNA solution (described above).
[0435] [0435] The cells will be cultured and then collected on days 1, 2, 3, 4, 5, 10, 20 and 30 after circular RNA transfection. The cells will be isolated for q-rt-PCR and another subset for FACS analysis. To measure the levels of circular RNA and GFP mRNA, reverse transcription of qPCR is performed using random hexamers, as described in Example
[0436] [0436] It is expected that the circular RNA will persist in the cells for at least several days and that it will retain functional expression of the GFP protein.
[0437] [0437] In this example, circular RNA is synthesized using one of the methods previously described. A circular RNA is designed to include encryptogens (SEQ ID NO: 4) and an ORF encoding GFP (SEQ ID NO: 2) with staggered elements (SEQ ID NO: 3) flanking the GFP ORF, see Figure 16.
[0438] [0438] Human fibroblasts (eg, IMR-90) are grown in Dulbecco's modified Eagle's medium (DMEM; Invitrogen) supplemented with 10% fetal bovine serum (FBS; Invitrogen) at 37 ° C under CO2 at 5 % in plates treated with tissue culture. The cells are passed regularly to maintain exponential growth. Lipid transfection reagent (2 μL; Invitrogen) is added to a mixture of 1 μg of circular RNA or linear RNA (described above) and 145 μL of reduced serum medium (Opti-MEM I solution) in a well of a plate treated with 12 well tissue culture. After incubation at room temperature for 15 min, 1 x 10 ^ 5 HeLa cells suspended in DMEM with 10% FBS are added to the circular RNA solution (described above). After incubation for 24 h at 37 ° C and 5% CO2, the cells are pulsed with BrdU (e.g., Sigma-Aldrich). The duration of labeling with BrdU is optimized for each cell type according to its specific population doubling time, eg, human IMR-90 fibroblasts have a doubling time of 27 h and are pulsed for 8-9 h as described by Elabd et al. 2013.
[0439] [0439] The cells will be collected on days 1, 2, 3, 4, 5 and 10 after BrdU pulse. A subset of the cells will be isolated by q-rt-PCR and another subset for FACS analysis. To measure the levels of circular RNA and GFP mRNA, reverse transcription of qPCR is performed using random hexamers, as described in Example 2. The cells will be analyzed with FACS using antibodies against BrdU and GFP as described here.
[0440] [0440] It is expected that the circular RNA will persist in the daughter cells and that the daughter cells will express the GFP protein. Example 16: Circularization of circular RNA
[0441] [0441] This Example demonstrates the in vitro production of circular RNA using splint binding.
[0442] [0442] A non-naturally occurring circular RNA can be manipulated to include one or more desirable properties and can be produced using recombinant DNA technology. As shown in the following Example, linear RNA circularized by splint binding.
[0443] [0443] CircRNA1 was designed to encode EGF labeled with triple FLAG without stop codon (264 nts). There is a Kozak sequence (SEQ ID NO: 11) in the start codon for translation initiation. CirRNA2 has identical sequences with circular RNA1 except that it has a terminating element (triple stop codons) (273 nts, SEQ ID NO: 12). Circular RNA3 was designed to encode EGF labeled with triple FLAG flanked by a stepped element (sequence 2A, SEQ ID NO: 13), without a terminating element (stop codon) (330 nts). CircRNA4 has identical sequences with circular RNA3 except that it has a terminating element (triple stop codon) (339 nts).
[0444] [0444] In this example, circular RNA was generated as follows. DNA templates for in vitro transcription were amplified from a gBlocks gene fragment with corresponding sequences (IDT) with the direct primer harboring the T7 promoter and the 2-O-methylated nucleotide with a reverse primer. The amplified DNA templates were gel purified with a DNA gel purification kit (Qiagen). 250-500 ng of purified DNA template was subjected to in vitro transcription. Linear 5'-monophosphorylated in vitro transcripts were generated using T7 RNA polymerase from each DNA template having corresponding sequences in the presence of 7.5 mM GMP, 1.5 mM GTP, 7.5 mM UTP, CTP a 7.5 mM and 7.5 mM ATP. Around 40 µg of linear RNA were generated in each reaction. After incubation, each reaction was treated with DNase to remove the DNA template. The RNA transcribed in vitro was precipitated with ethanol in the presence of 2.5 M ammonium acetate to remove unincorporated monomers.
[0445] [0445] The transcribed linear RNA was circularized using T4 RNA ligase 2 in a 20 nt DNA splint oligomer (SEQ ID NO: 14) as a template. The DNA splint was designed to match 10 nt of each 5 'or 3' end of linear RNA. After pairing with DNA splint (3 µM), linear RNA at 1 µM was incubated with T4 RNA ligase 2 at 0.5 U / µL at 37 ºC or 4 h. The mixture without T4 RNA ligase 2 was used as the negative control.
[0446] [0446] The linearization of linear RNA was monitored by separation of RNA in 6% denaturing PAGE. The slower-moving RNA bands correspond to circular RNA instead of linear RNA in denaturing polyacrylamide gels due to their circular structure. As seen in Figure 17, the addition of ligase (+ lines) to the RNA mixtures generated new bands to appear above the linear RNA bands that were present in mixtures that did not have ligase (- lines). Slower migration bands appeared in all RNA mixtures indicating successful splint binding (eg, circularization) that occurred with multiple constructs compared to the negative control. Example 17: RNA Circularization Efficiency
[0447] [0447] This Example demonstrates circularization efficiencies of the RNA splint binding.
[0448] [0448] A circular RNA not occurring naturally manipulated to include one or more desirable properties can be produced using splint-mediated circularization. As shown in the following Example, the linear RNA is circularized by splint binding with higher efficiency than controls.
[0449] [0449] CircRNA1, CircRNA2, CircRNA3 and CircRNA4 as described in Example 1 were also used here. CircRNA5 was designed to encode FLAG-labeled EGF, flanked by a 2A sequence and followed by FLAG-labeled nano luciferase (873 nts, SEQ ID NO: 17). CircRNA6 has identical sequence to circular RNA5 except that it included a terminating element (triple stop codon) between the EGF and nano luciferase genes, and a terminating element (triple stop codon) at the end of the nano luciferase sequence (762 nts , SEQ ID NO: 18).
[0450] [0450] In this Example, to measure the efficiency of RNA circularization, 6 different sizes of linear RNA (264 nts, 273 nts, 330 nts, 339 nts, 873 nts and 762 nts) were generated and circularized as described in the Example 1. The circular RNAs were resolved by 6% denaturing PAGE and the corresponding RNA bands on the gel for linear or circular RNA were excised for purification. The excised RNA gel bands were crushed and the RNA was eluted with 800 µL of 300 mM NaCl overnight. The gel debris was removed by centrifugation filters and the RNA was precipitated with ethanol in the presence of 0.3 M sodium acetate.
[0451] [0451] The circularization efficiency was calculated as follows. The amount of eluted circular RNA was divided by the amount of total eluted RNA (circular + linear RNA) and the result was illustrated as a graph in Figure 18.
[0452] [0452] The binding of linear RNAs using T4 RNAse ligase 2 produced circular RNA at higher efficiency rates than the control. Trend data indicated that larger constructs circularized at higher rates.
[0453] [0453] This Example demonstrates that the susceptibility of circular RNA to degradation by RNAse R compared to linear RNA.
[0454] [0454] Circular RNA is more resistant to degradation by exonucleases than linear RNA due to the absence of 5 'and 3' ends. As shown in the following Example, circular RNA was less susceptible to degradation than its linear RNA counterpart.
[0455] [0455] CircRNA5 was generated and circularized as described in Example 2 for use in the assay described here.
[0456] [0456] To test the circularization of CircRNA5, 20 ng / µL of linear or CircRNA5 were incubated with 2 U / µL of RNAse R, a 5´ or 3´ exoribonuclease that digests linear RNAs, but does not digest linear or RNA structures circulate at 37 ° C for 30 min. After incubation, the reaction mixture was analyzed by 6% denaturing PAGE.
[0457] [0457] The linear RNA bands present in the lines having no exonuclease were absent in the CircRNA5 line (see Figure 19) indicating that CircRNA5 showed higher resistance to treatment with exonucleases compared to the linear RNA control. Example 19: Isolation and purification of circular RNA
[0458] [0458] This Example demonstrates the purification of circular RNA.
[0459] [0459] In certain embodiments, circular RNAs, as described in the previous Examples, can be isolated and purified before expression of the encoded protein products. This Example describes the isolation using UREA gel separation. As shown in the following Example, the circular RNA was isolated and purified.
[0460] [0460] CircRNA1, CircRNA2, CircRNA3, CircRNA4, CircRNA5 and CircRNA6, as described in Example 2, were isolated as described here.
[0461] [0461] In this Example, linear and circular RNA were generated as described. In order to purify the circular RNAs, the ligation mixtures were resolved in 6% denaturing PAGE and the RNA bands corresponding to each of the circular RNAs were excised. The excised RNA gel fragments were crushed and the RNA was eluted with 800 µL of 300 mM NaCl overnight. The gel debris was removed by centrifugation filters and the RNA was precipitated with ethanol in the presence of 0.3 M sodium acetate. The eluted circular RNA was analyzed by 6% denaturing PAGE, see Figure 20.
[0462] [0462] Unique bands were visualized by PAGE for circular RNAs having variable sizes. Example 20: Detection of protein expression
[0463] [0463] This Example demonstrates the expression of proteins in vitro from a circular RNA.
[0464] [0464] Protein expression is the process of generating a specific protein from mRNA. This process includes the transcription of DNA into messenger RNA (mRNA), followed by the translation of mRNA into polypeptide chains, which are ultimately folded into functional proteins and can be targeted to specific subcellular or extracellular sites.
[0465] [0465] As shown in the following Examples, a protein was expressed in vitro from a circular RNA sequence.
[0466] [0466] The circular RNA was designed to encode EGF tagged with triple FLAG flanked by a 2A sequence without a terminating element (stop codon) (330 nts, SEQ ID NO: 19).
[0467] [0467] Linear or circular RNA was incubated for 5 h in rabbit reticulocyte lysate at 30 ° C in a volume of 25 µL. The final composition of the reaction mixture contained lysate of rabbit reticulocytes at 70%, amino acids at 20 µM, RNase inhibitor at 0.8 U / µL and 1 µg of linear or circular RNA. After incubation, the hemoglobin protein was removed by adding acetic acid (0.32 µL) and water (300 µL) to the reaction mixture (16 µL) and centrifugation at 20.817xg for 10 min at 15 ° C. The supernatant was removed and the pellet was dissolved in 30 µL of 2x SDS sample buffer and incubated at 70 ° C for 15 min. After centrifugation at 1400xg for 5 min, the supernatant was analyzed on a polyacrylamide / SDS gel with a 10–20% gradient.
[0468] [0468] After being electrotransferred to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG and anti-mouse IgG peroxidase antibody. The transfer was visualized with an ECL kit (see Figure 21) and the intensity of the Western transfer band was measured by ImageJ.
[0469] [0469] Fluorescence was detected indicated that the expression product was present. Thus it was shown that circular RNA directed the expression of a protein. Example 21: IRES independent expression
[0470] [0470] This Example demonstrates circular RNA directing expression in the absence of an IRES.
[0471] [0471] An IRES, or internal ribosomal entry site, is an RNA element that allows translation to be initiated independently of the cap. Circular RNA has been shown to direct the expression of Flag protein in the absence of an IRES.
[0472] [0472] The circular RNA was designed to encode EGF labeled with triple FLAG flanked by a 2A sequence without a terminating element (stop codon) (330 nts, SEQ ID NO: 19).
[0473] [0473] Linear or circular RNA was incubated for 5 h in rabbit reticulocyte lysate at 30 ° C in a volume of 25 µL. The final composition of the reaction mixture included lysate of rabbit reticulocytes at 70%, amino acids at 20 µM, RNase inhibitor at 0.8 U / µL and 1 µg of linear or circular RNA. After incubation, the hemoglobin protein was removed by adding acetic acid (0.32 µL) and water (300 µL) to the reaction mixture (16 µL) and centrifugation at 20.817xg for 10 min at 15 ° C. The supernatant was removed and the pellet was dissolved in 30 µL of 2x SDS sample buffer and incubated at 70 ° C for 15 min. After centrifugation at 1400xg for 5 min, the supernatant was analyzed on a polyacrylamide / SDS gel with a 10–20% gradient.
[0474] [0474] After being electrotransferred to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG and anti-mouse IgG peroxidase antibody. The transfer was visualized with an enhanced chemiluminescence kit (ECL) (see Figure 21) and the intensity of the Western transfer band was measured by ImageJ.
[0475] [0475] The expression product was detected in the circular RNA reaction mixture even in the absence of an IRES. Example 22: Cap-independent expression
[0476] [0476] This Example demonstrates that circular RNA is capable of directing expression in the absence of a cap.
[0477] [0477] A cap is a nucleotide specially altered at the 5 'end of mRNA. The 5 'cap is useful for the stability, as well as the initiation of translation, of linear mRNA. Circular RNA directed product expression in the absence of a cap.
[0478] [0478] The circular RNA was designed to encode EGF tagged with triple FLAG flanked by a 2A sequence without a terminating element (stop codon) (330 nts, SEQ ID NO: 19).
[0479] [0479] Linear or circular RNA was incubated for 5 h in rabbit reticulocyte lysate at 30 ° C in a volume of 25 µL. The final composition of the reaction mixture included lysate of rabbit reticulocytes at 70%, amino acids at 20 µM, RNase inhibitor at 0.8 U / µL and 1 µg of linear or circular RNA. After incubation, the hemoglobin protein was removed by adding acetic acid (0.32 µL) and water (300 µL) to the reaction mixture (16 µL) and centrifugation at 20.817xg for 10 min at 15 ° C. The supernatant was removed and the pellet was dissolved in 30 µL of 2x SDS sample buffer at 70 ° C for 15 min. After centrifugation at 1400xg for 5 min, the supernatant was analyzed on polyacrylamide / SDS gel with a 10–20% gradient.
[0480] [0480] After being electrotransferred to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG antibody and anti-mouse IgG peroxidase. The transfer was visualized with an ECL kit (see Figure 21) and the intensity of the Western transfer band was measured by ImageJ.
[0481] [0481] The expression product was detected in the circular RNA reaction mixture even in the absence of a cap. Example 23: Expression without a 5'-RTU
[0482] [0482] This Example demonstrates the expression of proteins in vitro from a circular RNA without 5 'untranslated regions.
[0483] [0483] The 5 '(5' RTU) untranslated region is the region directly upstream of an initiation codon that assists in the translation of proteins downstream of an RNA transcript.
[0484] [0484] As shown in the following Example, a 5 'untranslated region in the circular RNA sequence was not required for protein expression in vitro.
[0485] [0485] The circular RNA was designed to encode EGF tagged with triple FLAG flanked by a 2A sequence without a terminating element (stop codon) (330 nts, SEQ ID NO: 19).
[0486] [0486] Linear or circular RNA was incubated for 5 h in rabbit reticulocyte lysate at 30 ° C in a volume of 25 µL. The final composition of the reaction mixture included lysate of rabbit reticulocytes at 70%, amino acids at 20 µM, RNase inhibitor at 0.8 U / µL and 1 µg of linear or circular RNA. After incubation, the hemoglobin protein was removed by adding acetic acid (0.32 µL) and water (300 µL) to the reaction mixture (16 µL) and centrifugation at 20.817xg for 10 min at 15 ° C. The supernatant was removed and the pellet was dissolved in 30 µL of 2x SDS sample buffer and incubated at 70 ° C for 15 min. After centrifugation at 1400xg for 5 min, the supernatant was analyzed on a polyacrylamide / SDS gel with a 10–20% gradient.
[0487] [0487] After being electrotransferred to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG antibody and anti-mouse IgG peroxidase. The transfer was visualized with an ECL kit (see Figure 21) and the intensity of the Western transfer band was measured by ImageJ.
[0488] [0488] The expression product was detected in the reaction mixture of circular RNA even in the absence of a 5´ RTU. Example 24: Expression without a 3'-RTU
[0489] [0489] This Example demonstrates the expression of proteins in vitro from a circular RNA not having a 3'-UTR.
[0490] [0490] The 3 '(3'-RTU) untranslated region is the region directly downstream of a translation termination codon and includes regulatory regions that can influence post-transcriptional gene expression. The 3 'untranslated region may also play a role in gene expression by influencing the location, stability, export and translation efficiency of an mRNA. In addition, the structural characteristics of 3'-UTR as well as its use of alternative polyadenylation may play a role in gene expression.
[0491] [0491] As shown in the following Example, a 3'-UTR in the circular RNA sequence was not required for protein expression in vitro.
[0492] [0492] The circular RNA was designed to encode EGF tagged with triple FLAG flanked by a 2A sequence without a terminating element (stop codon) (330 nts, SEQ ID NO: 19).
[0493] [0493] Linear or circular RNA was incubated for 5 h in rabbit reticulocyte lysate at 30 ° C in a volume of 25 µL. The final composition of the reaction mixture included lysate of rabbit reticulocytes at 70%, amino acids at 20 µM, RNase inhibitor at 0.8 U / µL and 1 µg of linear or circular RNA. After incubation, the hemoglobin protein was removed by adding acetic acid (0.32 µL) and water (300 µL) to the reaction mixture (16 µL) and centrifugation at 20.817xg for 10 min at 15 ° C. The supernatant was removed and the pellet was dissolved in 30 µL of 2x SDS sample buffer and incubated at 70 ° C for 15 min. After centrifugation at 1400xg for 5 min, the supernatant was analyzed on a polyacrylamide / SDS gel with a 10–20% gradient.
[0494] [0494] After being electrotransferred to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG and anti-mouse IgG peroxidase antibody. The transfer was visualized with an ECL kit (see Figure 21) and the intensity of the Western transfer band was measured by ImageJ.
[0495] [0495] The expression product was detected in the reaction mixture of circular RNA even in the absence of a 3´UTR. Example 25: Expression without a terminating codon
[0496] [0496] This Example demonstrates the generation of a polypeptide product after translation of a rolling circle from a circular RNA without a terminating codon.
[0497] [0497] Proteins are based on polypeptides, which are comprised of unique amino acid sequences. Each amino acid is encoded in mRNA by nucleotide triplets called codons. During protein translation, each codon in mRNA corresponds to the addition of an amino acid in a growing polypeptide chain. The terminating element or stop codons signal the termination of this process by binding to release factors, which cause the ribosomal subunits to disassociate, releasing the chain of amino acids.
[0498] [0498] As shown in the following Example, a circular RNA lacking a terminating codon generated a large polypeptide product comprising repeated polypeptide sequences through rolling circle translation.
[0499] [0499] The circular RNA was designed to encode EGF labeled with triple FLAG without a termination element (stop codon) (264 nts, SEQ ID NO: 20) and included a Kozak sequence in the start codon to favor initiation of Translation.
[0500] [0500] Linear or circular RNA was incubated for 5 h in rabbit reticulocyte lysate at 30 ° C in a volume of 25 µL. The final composition of the reaction mixture included lysate of rabbit reticulocytes at 70%, amino acids at 20 µM, RNase inhibitor at 0.8 U / µL and 1 µg of linear or circular RNA. After incubation, the hemoglobin protein was removed by adding acetic acid (0.32 µL) and water (300 µL) to the reaction mixture (16 µL) and centrifugation at 20.817xg for 10 min at 15 ° C. The supernatant was removed and the pellet was dissolved in 30 µL of 2x SDS sample buffer and incubated at 70 ° C for 15 min. After centrifugation at 1400xg for 5 min, the supernatant was analyzed on a polyacrylamide / SDS gel with a 10–20% gradient.
[0501] [0501] After being electrotransferred to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG and anti-mouse IgG peroxidase antibody. The transfer was visualized with an ECL kit (see Figure 22) and the intensity of the Western transfer band was measured by ImageJ.
[0502] [0502] The expression product was detected in the reaction mixture of circular RNA even in the absence of a stop codon. Example 26: Expression of discrete proteins without a terminating element (stop codon)
[0503] [0503] This Example demonstrates the generation of a discrete protein product translated from a circular RNA without a terminating element (stop codons).
[0504] [0504] Staggered elements, such as 2A peptides, can include short amino acid sequences, ~ 20 aa, which allow the production of equimolar levels of multiple genes from a single mRNA. The staggered element can work by causing the ribosome to prevent the synthesis of a peptide bond at the C-terminus of element 2A, leading to the separation between the end of the 2A sequence and the next downstream peptide. The separation occurs between the Glycine and Proline residues found at the C-terminus and the upstream cyst has some additional residues added to the end, while the downstream cyst begins with a proline.
[0505] [0505] As shown in the following Example, the circular RNA without a terminating element (stop codon) generated a large polypeptide polymer (panel to the left of Figure 23: no scaling - circular RNA range) and the inclusion of a 2A sequence at the 3 'end of the coding region resulted in the production of discrete protein at a size comparable to that generated by the linear construct of equivalent RNA (panel to the right of Figure 23: scaling - circular RNA line).
[0506] [0506] The circular RNA was designed to encode EGF labeled with triple FLAG without a termination element (stop codon) (264 nts, SEQ ID NO: 20) and without a stepped element. A second circular RNA was designed to encode EGF tagged with triple FLAG flanked by a 2A sequence without a termination element (stop codon) (330 nts, SEQ ID NO: 19).
[0507] [0507] Linear or circular RNA was incubated for 5 h in rabbit reticulocyte lysate at 30 ° C in a volume of 25 µL. The final composition of the reaction mixture included lysate of rabbit reticulocytes at 70%, amino acids at 20 µM, RNase inhibitor at 0.8 U / µL and 1 µg of linear or circular RNA. After incubation, the hemoglobin protein was removed by adding acetic acid (0.32 µL) and water (300 µL) to the reaction mixture (16 µL) and centrifugation at 20.817xg for 10 min at 15 ° C. The supernatant was removed and the pellet was dissolved in 30 µL of 2x SDS sample buffer and incubated at 70 ° C for 15 min. After centrifugation at 1400xg for
[0508] [0508] After being electrotransferred to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG and anti-mouse IgG peroxidase antibody. The transfer was visualized with an ECL kit (see Figure 23) and the intensity of the Western transfer band was measured by ImageJ.
[0509] [0509] The discrete expression products were detected indicating that the circular RNA comprising a staggered element directed the expression of the individual proteins even in the absence of a terminating element (stop codons). Example 27: Rolling Circle Translation
[0510] [0510] This Example demonstrates high in vitro biosynthesis of a protein from circular RNA using a stepped element.
[0511] [0511] A non-naturally occurring circular RNA was manipulated to include a stepped element to compare protein expression with the circular RNA without a stepped element. As shown in the following Example, a staggered element overexpressed protein compared to an otherwise identical circular RNA not having such a sequence.
[0512] [0512] The circular RNA was designed to encode EGF labeled with triple FLAG with a terminating element (eg, three tandem stop codons) (273 nts, SEQ ID
[0513] [0513] Linear or circular RNA was incubated for 5 h in rabbit reticulocyte lysate at 30 ° C in a volume of 25 µL. The final composition of the reaction mixture contained lysate of rabbit reticulocytes at 70%, amino acids at 20 µM, RNase inhibitor at 0.8 U / µL and 1 µg of linear or circular RNA. After incubation, the hemoglobin protein was removed by adding acetic acid (0.32 µL) and water (300 µL) to the reaction mixture (16 µL) and centrifugation at 20.817xg for 10 min at 15 ° C. The supernatant was removed and the pellet was dissolved in 30 µL of 2x SDS sample buffer and incubated at 70 ° C for 15 min. After centrifugation at 1400xg for 5 min, the supernatant was analyzed on a polyacrylamide / SDS gel with a 10–20% gradient.
[0514] [0514] After being electrotransferred to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG antibody and anti-mouse IgG peroxidase. The transfer was visualized with an ECL kit (see Figure 24) and the intensity of the Western transfer band was measured by ImageJ.
[0515] [0515] The discrete expression products were detected indicating that the circular RNA comprising a stepped element directed the expression of the individual proteins even in the absence of a terminating element (stop codons). Example 28: Expression of a biologically active protein in vitro
[0516] [0516] This Example demonstrates the in vitro biosynthesis of a biologically active protein from circular RNA.
[0517] [0517] A circular RNA not occurring naturally has been engineered to express a biologically active therapeutic protein. As shown in the following Example, a biologically active protein was expressed from the circular RNA in the reticulocyte lysate.
[0518] [0518] The circular RNA was designed to encode FLAG-labeled EGF, flanked by a 2A sequence and followed by FLAG-labeled nano-luciferase (873 nts, SEQ ID NO: 17).
[0519] [0519] Linear or circular RNA was incubated for 5 h in rabbit reticulocyte lysate at 30 ° C in a volume of 25 µL. The final composition of the reaction mixture contained 70% rabbit reticulocyte lysate, 20 µM amino acids, 0.8 U / µL RNase inhibitor. The luciferase activity in the translation mixture was monitored using a luciferase assay system according to the manufacturer's protocol (Promega).
[0520] [0520] As shown in Figure 25, much higher fluorescence was detected with both circular and linear RNA than control vehicle RNA, indicating that expression product was present. Thus it was shown that the circular RNA expressed a biologically active protein. Example 29: Circular RNA with a longer half-life than the linear RNA counterpart
[0521] [0521] This Example demonstrates circular RNA engineered to have an extended half-life compared to linear RNA.
[0522] [0522] Circular RNA encoding a therapeutic protein gave recipient cells the ability to produce higher levels of the encoded protein due to a prolonged biological half-life, eg, compared to linear RNA. As shown in the following Example, a circular RNA had a longer half-life than its linear RNA counterpart in the reticulocyte lysate.
[0523] [0523] A circular RNA was designed to encode FLAG-labeled EGF, flanked by a 2A sequence and followed by FLAG-labeled nano luciferase (873 nts, SEQ ID NO: 17).
[0524] [0524] In this example, a time-lapse experiment was performed to monitor RNA stability. 100 ng of linear or circular RNA was incubated with rabbit reticulocyte lysate and samples were collected at 1 h, 5 h, 18 h and 30 h. Total RNA was isolated from the lysate using a phenol-based reagent (Invitrogen) and the cDNA was generated by reverse transcription. The qRT-PCR analysis was performed using a quantitative dye-based PCR reaction mixture (BioRad).
[0525] [0525] As shown in Figure 26, higher concentrations of circular RNA were detected at the posterior temporal points than linear RNA. Thus, the circular RNA was more stable or had an increased half-life compared to its linear counterpart. Example 30: Circular RNA demonstrated a longer half-life than linear RNA in cells
[0526] [0526] This Example demonstrates the circular RNA administered to cells and has an increased half-life in cells compared to linear RNA.
[0527] [0527] A non-naturally occurring circular RNA has been engineered to express a biologically active therapeutic protein. As shown in the following Example, circular RNA was present at higher levels compared to its linear RNA counterpart, demonstrating a longer half-life for circular RNA.
[0528] [0528] In this example, circular RNA and linear RNA were designed to encode a Kozak, EGF, flanked by a 2A, a stop or non-stop sequence (SEQ ID NOs: 11, 19, 20, 21). To monitor the half-life of RNA in cells, 0.1 x 10 6 cells were plated in each well of a 12-well plate. After 1 day, 1 µg of linear or circular RNA was transfected in each well using a lipid-based transfection reagent (Invitrogen). Twenty-four hours after transfection, the total RNA was isolated from the cells using a phenol-based extraction reagent (Invitrogen). The total RNA (500 ng) was reverse transcribed to generate cDNA. The qRT-PCR analysis was performed using a quantitative dye-based PCR mixture (BioRad). The primer sequences were as follows: Primers for linear or circular RNA, F: ACGACGGTGTGTGCATGTAT, R: TTCCCACCACTTCAGGTCTC; primers for circular RNA, F: TACGCCTGCAACTGTGTTGT, R: TCGATGATCTTGTCGTCGTC.
[0529] [0529] Circular RNA was successfully transfected into 293T cells, as was its linear counterpart. After 24 hours, the remaining circular and linear RNA were measured using qPCR. As shown in Figures 27A and B, circular RNA was shown to have a longer half-life in cells compared to linear RNA. Example 31: Synthetic circular RNA has been translated into cells and synthetic circular RNA has been translated through rolling circle translation
[0530] [0530] This Example demonstrates the translation of synthetic circular RNA into cells.
[0531] [0531] As shown in the following Example, circular RNA and linear RNA were designed to encode a Kozak sequence, 3xFLAG-EGF without terminating element (SEQ ID NO: 11). The circular RNA was translated into polymeric EGF, while the linear RNA was not, demonstrating that the cells performed a rolling circle translation of a synthetic circular RNA.
[0532] [0532] In this Example, 0.1 x 10 6 cells were plated in each well of a 12-well plate to monitor the translation efficiency of linear or circular RNA in cells.
[0533] [0533] Circular RNA was successfully transfected into 293T cells, as was its linear counterpart. However, Figure 28 shows that, 24 hours after transfection, the EGF protein was detected in the cells transfected with circular RNA, while none was detected in the cells transfected with linear RNA. Thus, circular RNA was translated into cells by translating the rolling circle compared to linear RNA. Example 32: Synthetic circular RNA demonstrated reduced expression of immunogenic genes in cells
[0534] [0534] This Example demonstrates circular RNA engineered to have reduced immunogenicity compared to linear RNA.
[0535] [0535] The circular RNA that encoded a therapeutic protein provided a reduced induction of related immunogenic genes (RIG-I, MDA5, PKA and IFN-beta) in recipient cells, compared to linear RNA. RIG-I can recognize short double-stranded or single-stranded 5 'triphosphate RNA, while MDA5 can recognize longer dsRNAs. RIG-I and MDA5 can both be involved in the activation of MAVS and triggering antiviral responses. PKR can be activated by dsRNA and induced by interferons, such as IFN-beta. As shown in the following Example it was shown that the circular RNA had a reduced activation of an immunorelated gene in 293T cells than a linear analogue RNA, as assessed by expression of RIG-I, MDA5, PKR and IFN-beta by q-PCR.
[0536] [0536] Circular RNA and linear RNA were designed to encode (1) a Kozak sequence, 3xFLAG-EGF without terminator (SEQ ID NO: 11); (2) a Kozak, 3xFLAG-EGF, flanked by a terminating element (stop codon) (SEQ ID NO: 21); (3) a Kozak, 3xFLAG-EGF, flanked by a 2A sequence (SEQ ID NO: 19); or (4) a Kozak sequence, 3xFLAG-EGF, flanked by a 2A sequence followed by a terminating element (stop codon) (SEQ ID NO: 20).
[0537] [0537] In this Example, the level of innate immune response genes was monitored in the cells by plating 0.1 x 10 6 cells in each well of a 12-well plate. After 1 day, 1 µg of linear or circular RNA was transfected in each well using a lipid-based transfection reagent (Invitrogen). Twenty-four hours after transfection, the total RNA was isolated from the cells using a phenol-based extraction reagent (Invitrogen). The total RNA (500 ng) was reverse transcribed to generate cDNA. The qRT-PCR analysis was performed using a quantitative dye-based PCR mixture (BioRad).
[0538] [0538] Primer sequences used: Primers for GAPDH, F: AGGGCTGCTTTTAACTCTGGT, R: AcomACTTGATTTTGGAGGGA; RIG-I, F: TGTGGGCAATGTCATCAAAA, R: GAAGCACTTGCTACCTCTTGC; MDA5, F: GGCACCATGGGAAGTGATT, R: ATTTGGTAAGGCCTGAGCTG; PKR, F: TCGCTGGTATCACTCGTCTG, R: GATTCTGAAGACCGCCAGAG; IFN-beta, F: CTCTCCTGTTGTGCTTCTCC, R: GTCAAAGTTCATCCTGTCCTTG.
[0539] [0539] As shown in Figure 29, qRT-PCR levels of immunorelated genes from 293T cells transfected with circular RNA showed a reduction in RIG-I, MDA5, PKR and IFN-beta compared to cells transfected with linear RNA. Thus, the induction of immunogenic related genes in recipient cells was reduced in cells transfected with circular RNA, compared to cells transfected with linear RNA. Example 33: Increased expression from synthetic circular RNA through rolling circle translation in cells
[0540] [0540] This Example demonstrates enhanced expression from the translation of a circular circle of synthetic circular RNA into cells.
[0541] [0541] Circular RNAs were designed to include an IRES with a nanoluciferase gene or an EGF negative control gene without a terminating element (stop codon). The cells were transfected with negative EGF control (SEQ ID NO: 22); nLUC stop (SEQ ID NO: 23): EMCV IRES, stepped sequence (2A sequence), 3x FLAG-labeled nLUC sequences, stepped sequence (2A sequence) and a stop codon; or nLUC stepped (SEQ ID NO: 24): EMCV IRES, stepped sequence (2A sequence), 3x FLAG-labeled nLUC sequences and stepped sequence (2A sequence). As shown in Figure 30, both circular RNAs produced a translation product having functional luciferase activity.
[0542] [0542] In this Example, circular RNA translation was monitored in cells. Specifically, 0.1 x 10 6 cells were plated in each well of a 12-well plate. After 1 day, 300 ng of circular RNA was transfected in each well using a lipid-based transfection reagent (Invitrogen). After 24 h, cells were collected by adding 100 µL of RIPA buffer. Nanoluciferase activity in lysates was measured using a luciferase assay system according to its manufacturer's protocol (Promega).
[0543] [0543] As shown in Figure 30, both circular RNAs expressed protein in cells. However, circular RNA with a stepped element, eg, 2A sequence, which lacks a terminating element (stop codon), produced higher levels of protein product having functional luciferase activity than RNA circular with a terminating element (stop codon). Example 34: Synthetic circular RNA translated into cells
[0544] [0544] This Example demonstrates the translation of synthetic circular RNA into cells. In addition, this Example shows that the circular RNA produced more expression product than its linear counterpart.
[0545] [0545] Circular RNA was successfully transfected into 293T cells, as was its linear counterpart. The cells were transfected with circular RNA encoding EGF as a negative control (SEQ ID NO: 22): EMCV IRES, stepped sequence (2A sequence), EGF sequences labeled with 3x FLAG, stepped sequence (2A sequence); linear or circular nLUC (SEQ ID NO: 23): EMCV IRES, stepped sequence (2A sequence), 3x FLAG-labeled nLuc sequences, a stepped sequence (2A sequence) and stop codon. As shown in Figure 31, circular RNA was translated into nanoluciferase in cells.
[0546] [0546] Linear or circular RNA translation was monitored in cells. Specifically, 0.1 x 10 6 cells were plated in each well of a 12-well plate. After 1 day, 300 ng of linear or circular RNA was transfected in each well using a lipid-based transfection reagent (Invitrogen). After 24 h, cells were collected by adding 100 µL of RIPA buffer. Nanoluciferase activity in lysates was measured using a luciferase assay system according to its manufacturer's protocol (Promega).
[0547] [0547] As shown in Figure 31, the circular RNA translation product was detected in cells. In particular, circular RNA had higher levels of increased luciferase activity or produced protein compared to its linear RNA counterpart. Example 35: Rolling circle translation from synthetic circular RNA produced functional protein product in cells
[0548] [0548] This Example demonstrates the translation of a rolling circle of functional protein product from synthetic circular RNA without a terminating element (stop codon), e.g., having a stepped element without a terminating element ( stop codon) in cells. In addition, this Example shows that circular RNA with a stepped element expresses more functional protein product than its linear counterpart.
[0549] [0549] Circular RNA was successfully transfected into 293T cells, as was its linear counterpart. The cells were transfected with negative control of circular RNA EGF (SEQ ID NO: 22); linear and circular nLUC (SEQ ID NO: 24): EMCV IRES, stepped sequence (2A sequence), 3x FLAG-labeled nLuc sequences, a stepped sequence (2A sequence). As shown in Figure 32, circular RNA was translated into nanoluciferase in cells.
[0550] [0550] Linear or circular RNA translation was monitored in cells. Specifically, 0.1 x 10 6 cells were plated in each well of a 12-well plate. After 1 day, 300 ng of linear or circular RNA was transfected in each well using a lipid-based transfection reagent (Invitrogen). After 24 h, cells were collected by adding 100 µL of RIPA buffer. Nanoluciferase activity in lysates was measured using a luciferase assay system according to its manufacturer's protocol (Promega).
[0551] [0551] As shown in Figure 32, the circular RNA translation product was detected in cells. In particular, circular RNA without a terminating element (stop codon) produced higher levels of protein product having functional luciferase activity than its linear RNA counterpart. Example 36: Synthetic circular RNA through IRES initiation in cells
[0552] [0552] This Example demonstrates the initiation of translation of synthetic circular RNA with an IRES in cells.
[0553] [0553] Circular RNAs were designed to include a Kozak or IRES sequence with a nanoluciferase gene or an EGF negative control gene. The cells were transfected with negative control of EGF (SEQ ID NO: 22), Kozak of nLUC (SEQ ID NO: 25): Kozak sequence, EGF sequence labeled with 1x FLAG, a stepped sequence (T2A sequence), nLUC labeled with 1x FLAG, stepped sequence (P2A sequence) and a stop codon; or nLUC IRES (SEQ ID NO: 23): EMCV IRES, stepped sequence (2A sequence), 3x FLAG-labeled nLUC sequences, stepped sequence (2A sequence) and stop codon. As shown in Figure 33, circular RNA with an IRES demonstrated higher levels of luciferase activity, corresponding to higher protein levels, compared to circular RNA with a Kozak sequence.
[0554] [0554] In this Example, circular RNA translation was monitored in cells. Specifically, 0.1 x 10 6 cells were plated in each well of a 12-well plate. After 1 day, 300 ng of circular RNA was transfected in each well using a lipid-based transfection reagent (Invitrogen). After 24 h, cells were collected by adding 100 µL of RIPA buffer. Nanoluciferase activity in lysates was measured using a luciferase assay system according to its manufacturer's protocol (Promega).
[0555] [0555] As shown in Figure 33, circular RNA initiated protein expression with an IRES and produced higher levels of protein product having functional luciferase activity than circular RNA with protein expression initiated by Kozak. Example 37: Translation of synthetic circular RNA circular cell
[0556] [0556] This Example demonstrates increased protein production through circular circle translation of synthetic circular RNA in cells that initiated protein production with an IRES.
[0557] [0557] Circular RNAs were designed to include a Kozak or IRES sequence with a nanoluciferase gene or an EGF negative control with or without a termination element (stop codon). The cells were transfected with negative EGF control (SEQ ID NO: 22); nLUC IRES stop (SEQ ID NO: 23): EMCV IRES, stepped sequence (2A sequence), 3x FLAG-labeled nLUC sequences, stepped sequence (2A sequence) and a stop codon; or stepped nLUC IRES (SEQ ID NO: 24): EMCV IRES, stepped sequence (2A sequence), 3x FLAG-labeled nLUC sequences and stepped sequence (2A sequence). As shown in Figure 34, both circular RNAs produced expression product demonstrated rolling circle translation and the circular RNA without an initiated termination element an IRES (eg, without a Kozak sequence) initiated and produced higher levels of protein product with functional luciferase activity than circular RNA with a terminating element without an IRES (eg, with a Kozak sequence), demonstrating the translation of a rolling circle.
[0558] [0558] In this Example, circular RNA translation was monitored in cells. Specifically, 0.1 x 10 6 cells were plated in each well of a 12-well plate. After 1 day, 300 ng of circular RNA was transfected in each well using a lipid-based transfection reagent
[0559] [0559] As shown in Figure 34, the circular RNA was translated into protein in the cells using a rolling circle method given by both circular RNAs. However, the circular RNA did not have a terminating element (stop codon). However, the circular RNA circular translation initiated greater protein production with an IRES and produced more protein product having functional luciferase activity compared to a circular RNA with a Kozak translation initiation termination element. Example 38: Increased protein expressed from circular RNA
[0560] [0560] This Example demonstrates the translation of synthetic circular RNA into cells. In addition, this Example shows that the circular RNA produced more expression product of the correct molecular weight than its linear counterpart.
[0561] [0561] Linear and circular RNAs were designed to include a nanoluciferase gene with a terminating element (stop codon). The cells were transfected with a vehicle: transfection reagent only; linear nLUC (SEQ ID NO: 23): EMCV IRES, stepped element (sequence of 2A), nLuc sequences labeled with 3x FLAG, a stepped element (sequence of 2A) and termination element (stop codon); or circular nLUC (SEQ ID
[0562] [0562] After 24 h, cells were collected by adding 100 µL of RIPA buffer. After centrifugation at 1400xg for 5 min, the supernatant was analyzed on a polyacrylamide / SDS gel with a 10–20% gradient.
[0563] [0563] After being electrotransferred to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG antibody and anti-mouse IgG peroxidase. The transfer was visualized with an ECL kit and the intensity of the Western transfer band was measured by ImageJ.
[0564] [0564] As shown in Figure 35, circular RNA has been translated into protein in cells. In particular, circular RNA produced higher levels of protein having the correct molecular weight compared to its linear RNA counterpart. Example 39: Rolling circle translation of synthetic circular RNA produced discrete protein products in cells
[0565] [0565] This Example demonstrates that discrete protein products have been translated by rolling circle translation from synthetic circular RNA without having a terminating element (stop codon), eg, having a stepped element instead of a terminating element (stop codon), in cells. In addition, this Example shows that RNA circulating with a stepped element expressed more protein product having the correct molecular weight than its linear counterpart.
[0566] [0566] Circular RNAs were designed to include a nanoluciferase gene with a staggered element instead of a termination element (stop codon). The cells were transfected with a vehicle: transfection reagent only; linear nLUC (SEQ ID NO: 24): EMCV IRES, stepped element (2A sequence), 3x FLAG-labeled nLuc sequences and, a stepped element (2A sequence) or circular nLUC (SEQ ID NO: 24): EMCV IRES, stepped element (2A sequence), 3x FLAG-labeled nLuc sequences and one stepped element (2A sequence). As shown in Figure 36, circular RNA produced higher levels of protein having the correct molecular weight compared to linear RNA.
[0567] [0567] After 24 h, cells were collected by adding 100 µL of RIPA buffer. After centrifugation at 1400xg for 5 min, the supernatant was analyzed on a polyacrylamide / SDS gel with a 10–20% gradient.
[0568] [0568] After being electrotransferred to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG and anti-mouse IgG peroxidase antibody. The transfer was visualized with an ECL kit and the intensity of the Western transfer band was measured by ImageJ.
[0569] [0569] As shown in Figure 36, the circular RNA translation product was detected in cells. In particular, circular RNA without a terminating element (stop codon) produced higher levels of discrete protein product having the correct molecular weight than its linear RNA counterpart. Example 40: Preparation of circular RNA with an almost double stranded, helical structure
[0570] [0570] This Example demonstrates that the circular RNA had both a double-stranded and helical strand structure.
[0571] [0571] A non-naturally occurring circular RNA was manipulated to adopt an almost double, helical strand structure. A similar structure was shown to be involved in the condensation of a naturally occurring circular RNA that had a uniquely long in vivo half-life (Griffin et al. 2014, J Virol. Jul 2014; 88 (13): 7402-
[0572] [0572] In this Example, the circular RNA was designed to encode an IRC of EMCV, Nluc labeled 3XFLAG as ORF and stepped sequence (EMCV 2A 3XFLAG Nluc 2A without stop). To evaluate the secondary structure of RNA, the RNA thermodynamic structure prediction tool (RNAfold) (Vienna RNA) was used. Additionally, the tertiary structure of RNA was analyzed using an RNA modeling algorithm.
[0573] [0573] As shown in Figures 37 and 38, the circular RNA is modeled to have adopted an almost double, helical ribbon structure. Example 41: Preparation of circular RNA with an almost helical structure linked with a repetitive sequence
[0574] [0574] This Example demonstrates that circular RNA can be designed to have an almost helical structure linked with a repetitive sequence.
[0575] [0575] A circular RNA not occurring naturally was manipulated to adopt an almost helical structure linked with a repetitive sequence. A similar structure was shown to be involved in the condensation of a naturally occurring circular RNA that had a uniquely long in vivo half-life (Griffin et al. 2014, Guedj et al. 2014).
[0576] [0576] In this Example, the circular RNA was designed to encode an IRES of EMCV, Nluc and spacer including a repetitive sequence (SEQ ID NO: 26). To evaluate the tertiary structure of RNA, an RNA modeling algorithm was used.
[0577] [0577] As shown in Figure 39, the circular RNA is modeled to have adopted an almost helical structure. Example 42: Circularized RNA is circular and non-concatemeric
[0578] [0578] This Example demonstrates that RNAse H degradation of an RNA produced nucleic acid degradation products consistent with a circular, non-concatemeric RNA.
[0579] [0579] RNA, when incubated with a ligase, may not react or form an intra- or intermolecular bond, generating a circular (without free ends) or concatemeric RNA, respectively. Treatment of each type of RNA with a complementary DNA primer and RNAse H, a nonspecific endonuclease that recognizes DNA / RNA duplexes, is expected to produce a unique number of degradation products of specific sizes depending on the starting RNA material.
[0580] [0580] As shown in the following Example it was shown that a bound RNA was circular and not concatemeric based on the number and size of RNAs produced by RNAse H degradation.
[0581] [0581] Circular RNA and linear RNA containing EMCV T2A 3XFLAG-Nluc P2A were generated.
[0582] [0582] To test the RNA circularization status (1299 nts), 0.05 pmole / µL of linear or circulating RNA were incubated with 0.25 U / µL of RNAse H, an endoribonuclease that digests DNA / RNA duplexes and 0.3 pmole / µL oligomer against 1037-1046 nts of RNA (CACCGCTCAGGACAATCCTT, SEQ ID NO: 55) at 37 ° C for 20 min. After incubation, the reaction mixture was analyzed by 6% denaturing PAGE.
[0583] [0583] For the used linear RNA described above it is expected that after binding the DNA primer and subsequent cleavage by RNAse H, two cleavage products of 1041 nt and 258 nt will be obtained. A concatamer is expected to produce three cleavage products of 258, 1041 and 1299 nt. One circle is expected to produce a single 1299 nt cleavage product.
[0584] [0584] The number of bands in the linear RNA range incubated with endonuclease RNAse produced two 1041 nt and 258 nt bands as expected, while a single 1299 nt band was produced in the circular RNA line (see Figure 40), indicating that the circular RNA was in fact circular and not concatemeric. Example 43: Preparation of large circRNAs
[0585] [0585] This Example demonstrates the generation of circular polyribonucleotide in the range of about 20 bases to about 6.2 Kb.
[0586] [0586] A circular RNA not occurring naturally manipulated to include one or more desirable properties has been produced in a range of sizes depending on the desired function. As shown in the following Example, linear RNA of up to 6200 nt was circularized.
[0587] [0587] The plasmid pCDNA3,1 / CAT (6.2 kb) was used here. Primers were designed to pair with pCDNA3,1 / CAT at regular intervals to generate DNA oligonucleotides corresponding to 500 nts, 1000 nts, 2000 nts, 4000 nts, 5000 nts and 6200 nts. In vitro transcription of the indicated DNA oligonucleotides was performed to generate linear RNA of the corresponding sizes. Circular RNAs were generated from these RNA oligonucleotides using DNA splint.
[0588] [0588] To measure the efficiency of RNA circularization, 6 different sizes of linear RNA (500 nts, 1000 nts, 2000 nts, 4000 nts, 5000 nts and 6200 nts) were generated. They were circularized using a DNA splint and T4 DNA ligase 2. As a control, a reaction was performed with T4 RNA ligase. Half of the circularized sample was treated with RNAse R to remove linear RNA.
[0589] [0589] To monitor the circularization efficiency, each sample was analyzed using pPCR. As shown in Figure 41, circular RNA was generated from a wide variety of DNA of different lengths. As shown in Figure 42, RNA circularization was confirmed using RNAse R treatment and qPCR analysis against circular junctions. This Example demonstrates the production of circular RNA for a variety of lengths. Example 44: Circular RNA manipulated with a protein binding site
[0590] [0590] This Example demonstrates the generation of a circular RNA with a protein binding site.
[0591] [0591] In this Example, a circular RNA is designed to include CVB3 IRES (SEQ ID NO: 56) and an ORF encoding Gaussia luciferase (Gluc) (SEQ ID NO: 57) followed by at least one protein binding site . For a specific example, a HuR binding sequence (SEQ ID NO: 52) from the 3'UTR of the Sindbis virus is used to test the effect of protein binding on circular RNA immunogenicity. The HuR binding sequence comprises two elements, URE (U-rich element; SEQ ID NO: 50) and CSE (Conserved sequence element; SEQ ID NO: 51). Circular RNA without binding sequence to HuR or URE is used as a control. Part of Anabaena's autocatalytic intron and exon sequences is located before the CVB3 IRES (SEQ ID NO: 56). Circular RNAs are generated in vitro as described. As shown in Figure 45, circular RNA was generated to contain a HuR binding site.
[0592] [0592] To monitor the effects of DNA-binding protein on linear RNA immunogenicity, cells are plated in each well of a 96-well plate. After 1 day, 500 ng of circular RNA is transfected in each well using a lipid-based transfection reagent (Invitrogen). The efficiency of translation / RNA stability / immunogenicity is monitored daily, until 72 h. The medium is collected to monitor Gluc activity. The cell lysate for measuring the level of RNA is prepared with a kit that allows measurements of the relative expression of genes by RT-PCR in real time (Invitrogen).
[0593] [0593] Translation efficiency is monitored by measuring Gluc activity with a Gaussia luciferase flash assay kit according to the manufacturer's instruction (Pierce).
[0594] [0594] For qRT-PCR analysis, the cDNA is generated with the cell lysate preparation kit according to the manufacturer's instruction (Invitrogen). QRT-PCR analysis is performed in triplicate using a PCR master mix (Brilliant II SYBR Green qRT-PCR Master Mix) and a PCR cycler (LightCycler 480). The stability of the circular RNA is measured by primers against Nluc. The levels of mRNA for known innate immunity regulators such as RIG-I, MDA5, OEA, OASL and PKR are quantified and normalized to actin values. Example 45: Preparation of circular RNA with regulatory nucleic acid sites
[0595] [0595] This Example demonstrates the in vitro production of circular RNA with a regulatory RNA binding site.
[0596] [0596] Different cell types have a unique nucleic acid regulatory mechanism to target specific RNA sequences. The encoding of these specific sequences in a circular RNA could give unique properties in different types of cells. As shown in the following Example, circular RNA was engineered to encode a microRNA binding site.
[0597] [0597] In this Example, the circular RNA included a sequence encoding an EMCV WT IRES, a mir692 microRNA binding site (GAGGUGCUCAAAGAGAU) and two spacer elements flanking the IRES-ORF.
[0598] [0598] Circulated RNA was generated in vitro. The unmodified linear RNA was transcribed in vitro from a DNA template including all of the motifs listed above, in addition to the T7 RNA polymerase promoter to direct transcription. The transcribed RNA was purified with an RNA cleaning kit (New England Biolabs, T2050), treated with 5'-phosphohydrolase (RppH) RNA (New England Biolabs, M0356) following the manufacturer's instructions and purified again with a column of RNA purification. RppH-treated RNA was circularized using a DNA splint (GGCTATTCCCAATAGCCGTT) and T4 RNA ligase 2 (New England Biolabs, M0239). The circular RNA was purified by Urea-PAGE (Figure 43), eluted in a buffer (0.5 M Sodium Acetate, 0.1% SDS, 1 mM EDTA), precipitated with ethanol and resuspended in water free of RNase.
[0599] [0599] As shown in Figure 43, circular RNA was generated with a microRNA binding site. Example 46: Circular RNA self-splicing
[0600] [0600] This example demonstrates the ability to produce circular RNA by self-splicing.
[0601] [0601] For this Example, the circular RNAs included a CVB3 IRES, an ORF encoding Gaussia Luciferase (GLuc) and two spacer elements flanking the IRES-ORF.
[0602] [0602] Circulated RNA was generated in vitro. The unmodified linear RNA was transcribed in vitro from a DNA template including all of the motifs listed above. In vitro transcription reactions included 1 µg of the T7 RNA DNA template polymerase promoter, 10X T7 reaction buffer, 7.5 mM ATP, 7.5 mM CTP, 7.5 mM GTP, 7 UTP , 5 mM, 10 mM DTP, DTT, 40 U of RNase inhibitor and T7 enzyme. Transcription was carried out at 37 ° C for 4 h. The transcribed RNA was treated by DNase with 1 U of DNase I at 37 ° C for 15 min.
[0603] [0603] Figure 44 shows the circular RNA generated by self-splicing. Example 47: Circular RNA with a splicing element comprising an encryptogen
[0604] [0604] This Example demonstrates a circular RNA engineered to have reduced immunogenicity.
[0605] [0605] For this Example, a circular RNA included a CVB3 IRES, an ORF encoding Gaussia Luciferase (GLuc) and two spacer elements flanking the IRES-ORF, these two spacer elements comprise a splicing element that is part of the intron sequences and Anabaena's autocatalytic exon (SEQ ID NO: 59).
[0606] [0606] Circulated RNA is generated in vitro.
[0607] [0607] In this Example, the level of innate immune response genes is monitored in the cells by plating cells in each well of a 12-well plate. After 1 day, 1 µg of linear or circular RNA is transfected in each well using a lipid-based transfection reagent (Invitrogen). Twenty-four hours after transfection, the total RNA is isolated from the cells using a phenol-based extraction reagent (Invitrogen). Total RNA (500 ng) is reverse transcribed to generate cDNA. The qRT-PCR analysis is performed using a quantitative dye-based PCR mixture (BioRad).
[0608] [0608] qRT-PCR levels of immunorelated genes from BJ cells transfected with circular RNA comprising a splicing element show a reduction in RIG-I, MDA5, PKR and IFN-beta compared to cells transfected with linear RNA . Thus, it is expected that the induction of immunogenic related genes in recipient cells will be reduced in cells transfected with circular RNA, compared to cells transfected with linear RNA. Example 48: Persistence of circular RNA during cell division
[0609] [0609] This Example demonstrates the persistence of circular polyribonucleotide during cell division. A naturally occurring circular RNA designed to include one or more desirable properties can persist in cells through cell division without being degraded. As shown in the following Example, the circular RNA expressing Gaussia luciferase (GLuc) was monitored over 72 h in HeLa cells.
[0610] [0610] In this Example, a 1307 nt circular RNA included a CVB3 IRES, an ORF encoding Gaussia Luciferase (GLuc) and two spacer elements flanking the IRES-ORF.
[0611] [0611] The persistence of circular RNA throughout cell division was monitored in HeLa cells. 5000 cells / well in a 96-well plate were transfected by suspension with circular RNA. The visualization of shiny cells was performed in an Avos imager (ThermoFisher) and cell counts were performed using luminescent cell viability assay (Promega) at 0 h, 24 h, 48 h, 72 h and 96 h. The activity of the Gaussia Luciferase enzyme was monitored daily as a measure of protein expression and the expression of gLuc was monitored daily in the supernatant removed from the wells every 24 h using the Gaussia Luciferase activity assay (Thermo Scientific Pierce). 50 µL of 1X Gluc substrate was added to 5 µL of plasma to carry out the Gluc luciferase activity assay. The plates were read immediately after mixing in a luminometer instrument (Promega).
[0612] [0612] Protein expression from circular RNA was detected at higher levels than linear RNA in dividing cells (Figure 46). Cells with circular RNA had higher rates of cell division compared to linear RNA at all measured time points. This Example demonstrates increased detection of circular RNA during cell division than its linear RNA counterpart. Example 49: The rolling circle translation produced a plurality of expression strings
[0613] [0613] This Example demonstrates the ability of circular RNA to express multiple proteins from a single construct. In addition, this Example demonstrates the translation of a circular RNA circle encoding several ORFs. This Example further demonstrates the expression of two proteins from a single construct.
[0614] [0614] A circular RNA (mtEMCV T2A 3XFLAG-GFP F2A 3XFLAG- Nluc P2A IS spacer) was designed for the rolling circle translation to include EMCV IRES (SEQ ID NO: 58) and an ORF encoding GFP with a 3XFLAG tag and a ORF encoding Nanoluciferase (Nluc) with 3XFLAG tag. Staggered elements (2A) were flanking the GFP and Nluc ORFs. Another circular RNA was similarly designed, but included a triple stop codon between the Nluc ORF and the spacer. Part of Anabaena's autocatalytic intron and exon sequences was included before the EMCV IRES. Circular RNAs were generated in vitro as described.
[0615] [0615] Protein expression from circular RNA was monitored in vitro or in cells. For in vitro analysis, circular RNAs were incubated for 3 h in rabbit reticulocyte lysate (Promega, Fitchburg, WI, USA) at 30 ° C. The final composition of the reaction mixture included lysate of rabbit reticulocytes at 70%, complete amino acids at 20 μM and RNase inhibitor at 0.8 U / μL (Toyobo, Osaka, Japan).
[0616] [0616] After incubation, the hemoglobin protein was removed by adding acetic acid (0.32 µL) and water (300 µL) to the reaction mixture (16 µL) and centrifugation at 20.817xg for 10 min at 15 ° C. The supernatant was removed and the pellet was dissolved in 2x SDS sample buffer and incubated at 70 ° C for 15 min. After centrifugation at 1400xg for 5 min, the supernatant was analyzed on a polyacrylamide / SDS gel with a 10–20% gradient.
[0617] [0617] For cell analysis, cells were plated in each well of a 12-well plate to monitor the translation efficiency of circular RNA in cells. After 1 day, 500 ng of circular RNA was transfected in each well using a lipid-based transfection reagent (Invitrogen). 48 hours after transfection, cells were collected by adding 200 µL of RIPA buffer to each well. Then, 10 µg of cell lysate proteins were analyzed on polyacrylamide / SDS gel with a 10-20% gradient.
[0618] [0618] After electrotransferring samples from reticulocyte and cell lysate to a nitrocellulose membrane using the dry transfer method, the transfer was incubated with an anti-FLAG antibody and anti-mouse IgG peroxidase. As a load control, anti-tubulin beta antibody was used. The transfer was visualized with an intensified chemiluminescent kit (ECL). The intensity of the Western transfer band was measured by ImageJ.
[0619] [0619] As shown in Figure 47, the circular RNA encoding GFP and nLuc produced 2 protein products. Translation from circular RNA without triple stop generated more of both protein products than circular RNA with triple stop codon. Finally, the circular RNA with and without the triple stop expressed proteins at ratios 1 / 3.24 and 1 / 3.37, respectively. Example 50: Circular RNA shows reduced toxicity compared to linear RNA
[0620] [0620] This example demonstrates that circular RNA is less toxic than linear RNA.
[0621] [0621] For this Example, the circular RNA includes an EMCV IRES, an ORF encoding NanoLuc with a 3XFLAG tag and flanked on both sides by stepped elements (2A) and a terminating element (Stop codon). Circular RNA was generated in vitro and purified as described here. The linear RNA used in this Example was cap-modified poly A-tailed RNA or unmodified capped A-poly RNA encoding nLuc with globin RTU's.
[0622] [0622] To monitor RNA toxicity in cells, human BJ fibroblast cells were plated in each well of a 96-well plate. 50 ng of circular or linear RNA with modified polyA tail in the cap was transfected after zero, forty-eight and seventy-two hours, using a lipid-based transfection reagent (ThermoFisher) following the manufacturer's recommendations. The visualization of bright cells was performed in an Avos imager (ThermoFisher) at 96 h. Total cells by condition were analyzed using ImageJ.
[0623] [0623] As shown in Figure 48, circular RNA transfection demonstrated reduced toxicity compared to linear RNA.
[0624] [0624] This Example demonstrates that circular RNA expressed better under stress conditions than linear RNA.
[0625] [0625] For this Example, circular RNAs include an EMCV IRES, an ORF encoding NanoLuc with a 3XFLAG tag and flanked by staggered elements. Circular RNA was generated in vitro and purified as described. The linear RNA used in this Example was poly A-capped tail RNA encoding nLuc with globin RTU's.
[0626] [0626] To monitor Gaussia Luciferase expression in cells, human BJ fibroblast cells were plated in each well of a 96-well plate. 50 ng of circular or linear RNA with polyA-cap tail were transfected after zero, forty-eight and seventy-two hours, using a lipid-based transfection reagent following the manufacturer's recommendations. The activity of the Gaussia Luciferase enzyme was monitored daily as a measure of protein expression and the expression of gLuc was monitored daily in the supernatant removed from the wells every 24 h using the Gaussia Luciferase activity assay (Thermo Scientific Pierce). 50 µL of 1X Gluc substrate was added to 5 µL of plasma to carry out the Gluc luciferase activity assay. The plates were read immediately after mixing in a luminometer instrument (Promega).
[0627] [0627] As shown in Figure 49, the exemplary circular RNA has been translated to a higher level compared to linear RNA under stress. Example 52: Riboswitches for selective expression
[0628] [0628] This Example demonstrates the ability to control protein expression from circular RNA.
[0629] [0629] For this Example, circular RNAs were designed to include a synthetic riboswitch (SEQ ID NO: 60) regulating the expression of the ORF encoding NanoLuc, see Figure 50. The circulated RNA was generated in vitro. The unmodified linear RNA was transcribed in vitro from a DNA template including all of the motifs listed above, in addition to the T7 RNA polymerase promoter to direct transcription. The transcribed RNA was purified with an RNA cleaning kit (New England Biolabs, T2050), treated with 5'-phosphohydrolase (RppH) RNA (New England Biolabs, M0356) following the manufacturer's instructions and purified again with a column of RNA purification. RppH-treated RNA was circularized using a DNA splint (CCGTTGTGGTCTCCCAGATAAACAGTATTTTGTCC) and T4 RNA ligase 2 (New England Biolabs, M0239). The circular RNA was purified by Urea-PAGE (Figure 50).
[0630] [0630] Theophylline or Tetracycline induces activation of its specific riboswitch, resulting in an inactivation of gene expression (as described by Auslander et al. Mol Biosyst. May 2010; 6 (5): 807-14 and Ogawa et al. , RNA. Mar 2011; 17 (3): 478-88. Doi: 10.1261 / rna.2433111. Epub Jan 11
[0631] [0631] The efficiency of the riboswitch is tested in a cell-free translation system and in HeLa cells. Cell-free translation is carried out using a cell-free translation kit (Promega, L4140) following the manufacturer's recommendations and luminescence measurement with a luminometer instrument (Promega) for the NLuc ORF and a multimode reader cell visualization (BioTek) for the GFP ORF.
[0632] [0632] For cell assays, HeLa cells / well are transfected with 1 nM of the circular RNA encoding GFP or NLuc described under the control of theophylline or tetracycline-dependent synthetic riboswitch (first direct PCR primer for theoN5,
[0633] [0633] After 24 h of culture at 37 ° C and 5% CO2, cells are treated with and without theophylline or tetracycline, depending on the riboswitch encoded in the circular RNA, with concentrations ranging from 1 nM-3 mM. After 24 h of continuous culture, fluorescence or luminescence is evaluated. For GFP, live cells are visualized in a fluorescent-neutral DMEM medium with 5% FBS and penicillin / streptomycin and a staining for the nuclei. For NLuc, luminescence is assessed using a luciferase system, following the manufacturer's instructions using a luminometer instrument (Promega). DNA template for NLuc (Blue: Plautia stali intestinal virus IRES, Orange: NLuc ORF) GACACGCGGCCTTCCAAGCAGTTAGGGAAACCGACTTCTTTGAAGAAGAAAGCTGACTA TGTGATCTTATTAAAATTAGGTTAAATTTCGAGGTTAAAAAATAGTTTTAATATTGCTAT AGTCTTAGAGGTCTTGTATATTTATACTTACCACACAAGATGGACCGGAGCAGCCCTCC AATATCTAGTGTACCCTCGTGCTCGCTCAAACATTAAGTGGTGTTGTGCGAAAAGAATC TCACTTCAAGAAAAAGAAACTAGTATGGTCTTCACACTCGAAGATTTCGTTGGGGACTG GCGACAGACAGCCGGCTACAACCTGGACCAAGTCCTTGAACAGGGAGGTGTGTCCAGTT TGTTTCAGAATCTCGGGGTGTCCGTAACTCCGATCCAAAGGATTGTCCTGAGCGGTGAA AATGGGCTGAAGATCGACATCCATGTCATCATCCCGTATGAAGGTCTGAGCGGCGACCA AATGGGCCAGATCGAAAAAATTTTTAAGGTGGTGTACCCTGTGGATGATCATCACTTTA AGGTGATCCTGCACTATGGCACACTGGTAATCGACGGGGTTACGCCGAACATGATCGAC TATTTCGGACGGCCGTATGAAGGCATCGCCGTGTTCGACGGCAAAAAGATCACTGTAAC AGGGACCCTGTGGAACGGCAACAAAATTATCGACGAGCGCCTGATCAACCCCGACGGCT CCCTGCTGTTCCGAGTAACCATCAACGGAGTGACCGGCTGGCGGCTGTGCGAACGCATT CTGGCGTAACTCGAGCTCGGTACCTGTCCGCGGTCGCGACGTACGCGGGCGGCCGCCAT AAATTGGATCCATATATAGGGCCCGGGTTATAATTACCTCAGGTCGACGTCCCATGGTT TTGTATAGAATTTACGGCTAGCGCCGGATGCGACGCCGGTCGCGTCTTATCCGGCCTTC CTATATCAGGCGGTGTTTAAGACGCCGCCGCTTCGCCCAAATCCTTATGCCGGTTCGAC
[0634] [0634] This Example demonstrates the generation of modified circular polyribonucleotide that produced protein product. In addition, this Example demonstrates that circular RNA engineered with nucleotide modifications had reduced immunogenicity compared to a linear RNA.
[0635] [0635] A circular RNA not occurring naturally manipulated to include one or more desirable properties and with complete or partial incorporation of modified nucleotides was produced. As shown in the following Example, the modified full-length linear RNA or a hybrid of modified and unmodified linear RNA was circularized and nLuc expression was evaluated. Additionally, it was shown that the modified circular RNA had reduced activation of immunorelated genes (q-PCR of MDA5, OAS and IFN-beta expression) in BJ cells, compared to an unmodified circular RNA.
[0636] [0636] Circular RNA with WT EMCV Nluc stop spacer was generated. To replace complete modification, the modified nucleotides, pseudouridine and methylcytosine or m6A, were added instead of the standard unmodified nucleotides, uridine and cytosine or adenosine, respectively, during the in vitro transcription reaction. For the hybrid construct, the EMCV WT IRES was synthesized separately from the nLuc ORF. The WT EMCV IRES was synthesized using modified or unmodified nucleotides. In contrast, the nLuc ORF sequence was synthesized using the modified nucleotides, pseudouridine and methylcytosine or m6A, instead of the standard unmodified nucleotides, uridine and cytosine or adenosine, respectively, during the in vitro transcription reaction. After synthesis of the modified or unmodified IRES and the modified ORF, these two oligonucleotides were ligated together using T4 DNA ligase. As shown in Figure 51A, modified circular RNA was generated.
[0637] [0637] To measure the efficiency of nLuc expression from fully modified or hybrid modified constructs, 0.1 pmol of linear and circular RNA was transfected into BJ fibroblasts for 6 h. NLuc expression was measured at 6 h, 24 h, 48 h and 72 h post-transfection.
[0638] [0638] The level of innate immune response genes was monitored in cells for total RNA isolated from the cells using a phenol-based extraction reagent (Invitrogen). The total RNA (500 ng) was reverse transcribed to generate cDNA. The qRT-PCR analysis was performed using a quantitative dye-based PCR mixture (BioRad).
[0639] [0639] As shown in Figures 51B and 51C, the modified circular RNA translated. As shown in Figures 52A-C, levels by qRT-PCR of immunorelated genes from BJ cells transfected with circular RNA showed reduced expression of MDA5, OAS and IFN-beta compared to cells transfected with unmodified linear RNA. Thus, the induction of immunogenic related genes in recipient cells was reduced in cells transfected with modified circular RNA, compared to cells transfected with unmodified circular RNA. Example 54: Circular RNA administered in vivo exhibited a longer half-life / increased stability
[0640] [0640] This Example demonstrates the ability to deliver circular RNA and the increased stability of circular RNA compared to linear RNA in vivo.
[0641] [0641] For this Example, circular RNAs were designed to include an EMCV IRES with an ORF encoding Nanoluciferase (Nluc) and stepped sequence (EMCV 2A 3XFLAG Nluc 2A non-stop and EMCV 2A 3XFLAG Nluc 2A stop). Circulated RNA was generated in vitro.
[0642] [0642] Balb / c mice were injected with circular RNA with Nluc ORF, or linear RNA as a control, through intravenous (IV) administration of tail veins. The animals received a single dose of 5 µg of RNA formulated in a lipid-based transfection reagent (Mirus) according to the manufacturer's instructions.
[0643] [0643] The rats were sacrificed, and the livers were collected at 3, 4 and 7 days post-dosing (n = 2 mice / time). The livers were collected and stored in an RNA stabilizing reagent (Invitrogen). The tissue was homogenized in RIPA buffer with a microtube homogenizer (Fisher scientific) and the RNA was extracted using a phenol-based RNA extraction reagent for cDNA synthesis. The qPCR was used to measure the presence of linear and circular RNA in the liver.
[0644] [0644] The detection of RNA in tissues was performed by qPCR. To detect linear and circular RNA, primers were used that amplify the Nluc ORF. (F: AGATTTCGTTGGGGACTGGC, R: CACCGCTCAGGACAATCCTT). To detect only circular RNA, the primers that amplified the 5´-3´ junction allowed the detection of circular, but non-linear RNA constructs (F: CTGGAGACGTGGAGGAGAAC, R: CCAAAAGACGGCAATATGGT).
[0645] [0645] Circular RNA was detected at higher levels than linear RNA in the livers of mice at 3, 4 and 7 days post-injection (Figure 53). Therefore, circular RNA was administered and detectable in vivo for at least 7 days post-administration. Example 55: Expression in vivo, half-life and non-immunogenicity of circular RNA
[0646] [0646] This Example demonstrates the ability to direct expression from circular RNA in vivo. Demonstrates increased half-life of circular RNA compared to linear RNA. Finally demonstrates that circular RNA was engineered to be non-immunogenic in vivo
[0647] [0647] For this Example, the circular RNAs included a CVB3 IRES, an ORF encoding Gaussia Luciferase (GLuc) and two spacer elements flanking the IRES-ORF.
[0648] [0648] Circulated RNA was generated in vitro. The unmodified linear RNA was transcribed in vitro from a DNA template including all of the motifs listed above, as well as a T7 RNA polymerase promoter to direct transcription. The transcribed RNA was purified with an RNA cleaning kit (New England Biolabs, T2050), treated with 5'-phosphorhydrolase (RppH) RNA (New England Biolabs, M0356) following the manufacturer's instructions and purified again with a column of RNA purification. RppH-treated RNA was circularized using a DNA splint (GTCAACGGATTTTCCCAAGTCCGTAGCGTCTC) and T4 RNA ligase 2 (New England Biolabs, M0239). The circular RNA was purified by Urea-PAGE, eluted in a buffer (0.5 M Sodium Acetate, 0.1% SDS, 1 mM EDTA), precipitated with ethanol and resuspended in RNase-free water.
[0649] [0649] The mice received a single injection dose into the tail vein of 2.5 µg of circular RNA with Gaussia Luciferase ORF, or linear RNA as a control, both formulated in a lipid-based transfection reagent (Mirus ) as a carrier.
[0650] [0650] Blood samples (50 µL) were collected from the tail vein of each mouse in EDTA tubes, at 1, 2, 7, 11, 16 and 23 days post-dosing. The plasma was isolated by centrifugation for 25 min at 1300 g at 4 ° C and the activity of Gaussia Luciferase, a secreted enzyme, was tested using a Gaussia Luciferase activity assay (Thermo Scientific Pierce). 50 µL of 1X Gluc substrate was added to 5 µL of plasma to carry out the Gluc luciferase activity assay. The plates were read immediately after mixing in a luminometer instrument (Promega).
[0651] [0651] Gaussia Luciferase activity was detected in plasma at 1, 2.7, 11, 16 and 23 days after circular RNA dosing (Figures 54A-B).
[0652] [0652] In contrast, Gaussia Luciferase activity was only detected in plasma at 1 and 2 days after dosing the modified linear RNA. Enzyme activity from protein derived from linear RNA was not detected above background levels at day 6 or later (Figures 54A-B).
[0653] [0653] On day 16, the livers were dissected from three animals and the total RNA was isolated from the cells using a phenol-based extraction reagent (Invitrogen). The total RNA (500 ng) was reverse transcribed to generate cDNA. The qRT-PCR analysis was performed using a quantitative dye-based PCR mixture (BioRad).
[0654] [0654] As shown in Figure 55, qRT-PCR levels of circular RNA but not linear RNA were detected in both the liver and spleen at day 16. As shown in Figure 56, the immunorelated genes from livers transfected with linear RNA showed increased expression of RIG-I, MDA5, IFN-B and OEA, while livers transfected with circular RNA did not show increased expression of RIG-I, MDA5, PKR and IFN-beta of these markers compared to animals transfected with transporter at day 16 Thus, the induction of immunogenic related genes in recipient cells was not present in circular RNA from transfected livers.
[0655] [0655] This Example demonstrated that circular RNA expressed protein in vivo for extended periods of time, with levels of protein activity in plasma at multiple days post-injection.
[1] [1] A method of in vivo expression of one or more expression sequences in a subject, comprising: administering a circular polyribonucleotide to a subject cell in which the circular polyribonucleotide comprises one or more expression sequences; and expression of one or more expression sequences from the circular polyribonucleotide in the cell, wherein the circular polyribonucleotide is configured so that the expression of one or more expression sequences in the cell at a later time is equal to or higher than an earlier moment.
[2] [2] A method of in vivo expression of one or more expression sequences in a subject, comprising: administering a circular polyribonucleotide to a subject cell in which the circular polyribonucleotide comprises one or more expression sequences; and expressing one or more expression sequences from the circular polyribonucleotide in the cell, wherein the circular polyribonucleotide is configured so that the expression of one or more expression sequences in the cell over a period of time of at least 7, 8, 9, 10, 12, 14 or 16 days do not decrease by more than about 40%.
[3] [3] A method of in vivo expression of one or more expression sequences in a subject, comprising:
[4] [4] The method of any of paragraphs [1] to [3], wherein the expression product of one or more expression sequences comprises a therapeutic protein.
[5] [5] The method of paragraph [4], in which the therapeutic protein has antioxidant activity, binding, charge receptor activity, catalytic activity, molecular transporter activity, molecular function regulator, molecular transducer activity, nutrient reservoir activity, protein tag, structural molecule activity, toxin activity, transcription regulatory activity, translation regulatory activity, or carrier activity.
[6] [6] The method of any of paragraphs [1] to [5], The expression product of one or more expression sequences comprises a secretory protein.
[7] [7] The method of paragraph [6], wherein the secretory protein comprises a secretory enzyme.
[8] [8] The method of paragraph [6], wherein the secretory protein comprises a secretory antibody.
[9] [9] The method of any of paragraphs [1] to [8], wherein the circular polyribonucleotide has at least about 20 nucleotides, at least about 30 nucleotides, at least about 40 nucleotides, at least about 50 nucleotides, at least about 75 nucleotides, at least about 100 nucleotides, at least about 200 nucleotides, at least about 300 nucleotides, at least about 400 nucleotides, at least about 500 nucleotides, at least about 1,000 nucleotides , at least about 2,000 nucleotides, at least about 5,000 nucleotides, about 6,000 nucleotides, at least about 7,000 nucleotides, at least about 8,000 nucleotides, at least about 9,000 nucleotides, at least about 10,000 nucleotides, at least about of 12,000 nucleotides, at least about 14,000 nucleotides, at least about 15,000 nucleotides, at least about 16,000 nucleotides, at least about 17,000 nucleotides, at least about about 18,000 nucleotides, at least about 19,000 nucleotides or at least about 20,000 nucleotides.
[10] [10] The method of any of paragraphs [1] to [9], in which the circular polyribonucleotide has a persistence in the cell for at least about 1 h, 2 h, 6 h, 12 h, 18 h, 24 h , 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days,
[11] [11] The method of any of paragraphs [1] to [10], in which the circular polyribonucleotide has a persistence in the cell when the cell is dividing for at least about 1 h, 2 h, 6 h, 12 h , 18 h, 24 h, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 22 days, 23 days, 24 days, 25 days, 26 days, 27 days, 28 days, 29 days, 30 days, 60 days or more or whatever intermediate moment.
[12] [12] The method of any of paragraphs [1] to [11], in which the circular polyribonucleotide has a persistence in the post-division cell for at least about 1 h, 2 h, 6 h, 12 h, 18 h , 24 h, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 22 days, 23 days, 24 days, 25 days, 26 days, 27 days, 28 days, 29 days, 30 days, 60 days or more or any intermediate time.
[13] [13] The method of any of paragraphs [1] to [12], wherein the circular polyribonucleotide comprises at least one spacer sequence.
[14] [14] The method of paragraph [13], in which the spacer sequence is configured to provide conformational flexibility between elements of the circular polyribonucleotide on both sides of the spacer sequence.
[15] [15] The method of paragraph [13] or [14], in which a ratio between the spacer sequence and a non-spacer sequence of the circular polyribonucleotide, e.g., expression sequences, is about 0.05: 1 , about 0.06: 1, about 0.07: 1, about 0.08: 1, about 0.09: 1, about 0.1: 1, about 0.12: 1, about 0.125: 1, about 0.15: 1, about 0.175: 1, about 0.2: 1, about 0.225: 1, about 0.25: 1, about 0.3: 1, about 0.35: 1, about 0.4: 1, about 0.45: 1, about 0.5: 1, about 0.55: 1, about 0.6: 1, about 0, 65: 1, about 0.7: 1, about 0.75: 1, about 0.8: 1, about 0.85: 1, about 0.9: 1, about 0.95: 1, about 0.98: 1, about 1: 1, about 1.02: 1, about 1.05: 1, about 1.1: 1, about 1.15: 1, about 1.2: 1, about 1.25: 1, about 1.3: 1, about 1.35: 1, about 1.4: 1, about 1.45: 1, about 1, 5: 1, about 1.55: 1, about 1.6: 1, about 1.65: 1, about 1.7: 1, about 1.75: 1, about 1.8: 1, about 1.85: 1, about 1.9: 1, about 1.95: 1, about 1.975: 1, about 1.98: 1 or about 2: 1.
[16] [16] The method of any of paragraphs [13] to [15], wherein the spacer sequence comprises at least 3 ribonucleotides, at least 4 ribonucleotides, at least 5 ribonucleotides, at least about 8 ribonucleotides, at least about 10 ribonucleotides, at least about 12 ribonucleotides, at least about 15 ribonucleotides, at least about 20 ribonucleotides, at least about 25 ribonucleotides, at least about 30 ribonucleotides, at least about 40 ribonucleotides, at least about 50 ribonucleotides, at least about 60 ribonucleotides, at least about 70 ribonucleotides, at least about 80 ribonucleotides, at least about 90 ribonucleotides, at least about 100 ribonucleotides, at least about 120 ribonucleotides, at least about 150 ribonucleotides , at least about 200 ribonucleotides, at least about 250 ribonucleotides, at least about 300 ribonucleotides, at least about 400 r ibonucleotides, at least about 500 ribonucleotides, at least about 600 ribonucleotides, at least about 700 ribonucleotides, at least about 800 ribonucleotides, at least about 900 ribonucleotides or at least about 100 ribonucleotides.
[17] [17] The method of any of paragraphs [13] to [16], wherein the spacer sequence comprises at least 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 55%, 50%, 45%, 40%, 35%, 30%, 20% or any intermediate percentage of adenine ribonucleotides.
[18] [18] The method of any of paragraphs [1] to [17], in which the circular polyribonucleotide is competent for rolling translation.
[19] [19] The method of paragraph [18], in which each of the one or more expression sequences is separated from a subsequent expression sequence by a stepped element in the circular polyribonucleotide, in which the rolling circle translation of one or more sequences of expression generates at least two polypeptide molecules.
[20] [20] The method of paragraph [19], in which the scaled element prevents the generation of a single polypeptide (a) from two translation rounds of a single expression sequence or (b) from one or more rounds translation of two or more expression sequences.
[21] [21] The method of paragraph [19] or [20], where the scaled element is a sequence separate from one or more expression sequences.
[22] [22] The method of paragraph [19] or [20], wherein the scaled element comprises a portion of an expression sequence of one or more expression sequences.
[23] [23] The method of any of paragraphs [18] to [22], wherein the circular polyribonucleotide is configured so that at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% of the total polypeptides (molar / molar) generated during the circle translation of the circular polyribonucleotide are polypeptides discrete and in which each of the discrete polypeptides is generated from a single round of translation or less than a single round of translation of one or more expression sequences.
[24] [24] The method of paragraph [23], in which the circular polyribonucleotide is configured so that at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% at least 96%, at least 97%, at least 98%, at least 99% or 100% of the total polypeptides (molar / molar) generated during the translation of circular polyribonucleotide are the discrete polypeptides, and in which the ratio of the quantities between discrete products and total polypeptides is tested in an in vitro translation system.
[25] [25] The method of paragraph [24], wherein the in vitro translation system comprises rabbit reticulocyte lysate.
[26] [26] The method of any of paragraphs [19] to [25], in which the scaled element is at a 3 'end of at least one of the one or more expression strings, and in which the scaled element is configured to interrupt a ribosome during translation of the circular polyribonucleotide rolling circle.
[27] [27] The method of any of paragraphs [19] to [26], in which the scaled element encodes a peptide sequence selected from the group consisting of a 2A sequence and a type 2A sequence.
[28] [28] The method of any of paragraphs [19] to [27], in which the scaled element encodes a sequence with a sequence of the C terminal which is GP.
[29] [29] The method of any of paragraphs [19] to [28], in which the scaled element encodes a sequence with a C-terminal consensus sequence that is D (V / I) ExNPGP, where x = any amino acid.
[30] [30] The method of any of paragraphs [19] to [29], in which the scaled element encodes a selected sequence from the group consisting of GDVESNPGP, GDIEENPGP, VEPNPGP, IETNPGP, GDIESNPGP, GDVELNPGP, GDIETNPGP, GDVEENPGP, GDVEENPGP, GDVEENPGP, GDVEENPGP, GDVEENPGP, GDVEENPGP, GDVEENPGP , IESNPGP, GDIELNPGP, HDIETNPGP, HDVETNPGP, HDVEMNPGP, GDMESNPGP, GDVETNPGP, GDIEQNPGP and DSEFNPGP.
[31] [31] The method of any of paragraphs [19] to [30], in which the scaled element is at the 3 'end of each of the one or more expression sequences.
[32] [32] The method of any of paragraphs [19] to [31], in which the staggered element of a first expression sequence in the circular polyribonucleotide is upstream of (5 'with respect to) a first translation initiation sequence an expression sequence that succeeds the first expression sequence in the circular polyribonucleotide, and in which a distance between the stepped element and the first translation initiation sequence allows continuous translation of the first expression sequence and the subsequent expression sequence.
[33] [33] The method of any of paragraphs [19] to [32], in which the staggered element of a first expression sequence in the circular polyribonucleotide is upstream of (5 'with respect to) a first translation initiation sequence of an expression sequence succeeding the first expression in the circular polyribonucleotide, in which the circular polyribonucleotide is continuously translated, in which a corresponding circular polyribonucleotide comprising a second stepped element upstream of a second translation initiation sequence of a second expression sequence in the corresponding circular polyribonucleotide is not continuously translated, and the second stepped element in the corresponding circular polyribonucleotide is at a greater distance from the second translation initiation sequence, eg at least 2x, 3x, 4x, 5x, 6x, 7x , 8x, 9x, 10x, than a distance between the stepped element and the first initiation of translation in the polyribonucleus circular video.
[34] [34] The method of any of paragraphs [19] to [33], in which the distance between the staggered element and the first initiation of the translation is at least 2 nt, 3 nt, 4 nt, 5 nt, 6 nt, 7 nt, 8 nt, 9 nt, 10 nt, 11 nt, 12 nt, 13 nt, 14 nt, 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, 25 nt, 30 nt, 35 nt , 40 nt, 45 nt, 50 nt, 55 nt, 60 nt, 65 nt, 70 nt, 75 nt or more.
[35] [35] The method of any of paragraphs [19] to [34], in which the distance between the second stepped element and the second translation initiation is at least 2 nt, 3 nt, 4 nt, 5 nt, 6 nt , 7 nt, 8 nt, 9 nt, 10 nt, 11 nt, 12 nt, 13 nt, 14 nt, 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, 25 nt, 30 nt, 35 nt, 40 nt, 45 nt, 50 nt, 55 nt, 60 nt, 65 nt, 70 nt, 75 nt or more than the distance between the stepped element and the first translation initiation.
[36] [36] The method of any of paragraphs [19] to [35], wherein the expression sequence following the first expression sequence in the circular polyribonucleotide is an expression sequence other than the first expression sequence.
[37] [37] The method of any of paragraphs [19] to [35], wherein the subsequent expression sequence of the first expression sequence in the circular polyribonucleotide is the first expression sequence.
[38] [38] The method of any of paragraphs [1] to [37], wherein the circular polyribonucleotide comprises at least one structural element selected from:
[39] [39] The method of any of paragraphs [1] to [38], in which the circular polyribonucleotide comprises at least one functional characteristic selected from: a) greater translation efficiency than a linear counterpart; b) a stoichiometric translation efficiency of multiple translation products; c) less immunogenicity than a counterpart without an encryptogen; d) increased half-life in relation to a linear counterpart; and e) persistence during cell division.
[40] [40] The method of any of paragraphs [1] to [39], wherein the circular polyribonucleotide has a translation efficiency of at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 2 times, at least 3 times, at least 4 times, at least 5 times, at least 6 times, at least 7 times, at least 8 times, at least 9 times, at least 10 times, at least 20 times, at least 50 times or at least 100 times larger than a linear counterpart.
[41] [41] The method of any of paragraphs [1] to [40], in which the circular polyribonucleotide has a translation efficiency at least 5 times greater than a linear counterpart.
[42] [42] The method of any of paragraphs [1] to [41], in which the circular polyribonucleotide does not have at least one of: a) a 5'-RTU; b) a 3'-RTU; c) a poly-A sequence; d) a 5'-cap; e) a terminating element; f) an internal ribosomal entry site; g) susceptibility to exonuclease degradation; and h) binding to a cap binding protein.
[43] [43] The method of anyone from [1] to [42], in which the circular polyribonucleotide comprises an internal ribosomal entry site.
[44] [44] The method of anyone from [1] to [42], in which the circular polyribonucleotide does not have an internal ribosomal entry site.
[45] [45] The method of any one from [1] to [43], wherein the one or more expression sequences comprise a Kozak initiation sequence.
[46] [46] The method of any one from [38] to [45], wherein the quasi-helical structure comprises at least one double-stranded RNA segment with at least one non-double-stranded segment.
[47] [47] The method of paragraph [38] or [46], in which the quasi-helical structure comprises a first sequence and a second sequence connected to a repetitive sequence, eg an A-rich sequence.
[48] [48] The method of any of paragraphs [38] to [47], in which the encryptogen comprises an element of splicing.
[49] [49] The method of any of paragraphs [38] to [48], wherein the circular polyribonucleotide comprises at least one modified ribonucleotide.
[50] [50] The method of any of paragraphs [38] to [49], wherein the circular polyribonucleotide comprises modified ribonucleotides over a portion of its entire length.
[51] [51] The method of any of paragraphs [38] to [50], wherein the encryptogen comprises at least one modified ribonucleotide, eg, pseudouridine, N (6) methyladenosine (m6A).
[52] [52] The method of any of paragraphs [38] to [51], wherein the encryptogen comprises a protein binding site, eg, ribonucleotide binding protein.
[53] [53] The method of any of paragraphs [38] to [52], wherein the encryptogen comprises an immunoprotein binding site, eg, to escape immune responses, eg, CTL responses.
[54] [54] The method of any of paragraphs [38] to [53], wherein the circular polyribonucleotide has at least 2x less immunogenicity than a counterpart without the encryptogen, eg, as assessed by expression or signaling or activation of at least one of RIG-I, TLR-3, TLR-7, TLR-8, MDA-5, LGP-2, OAS, OASL, PKR, IFN-beta.
[55] [55] The method of any of paragraphs [38] to [54], wherein the circular polyribonucleotide additionally comprises a riboswitch.
[56] [56] The method of any of paragraphs [38] to [55], wherein the circular polyribonucleotide additionally comprises an aptazime.
[57] [57] The method of any of paragraphs [38] to [56], wherein the circular polyribonucleotide comprises a translation initiation sequence, eg, GUG, CUG start codon, eg, expression under stress conditions.
[58] [58] The method of any of paragraphs [38] to [57], wherein the circular polyribonucleotide comprises a stepped element, eg, 2A.
[59] [59] The method of any of paragraphs [38] to [58], wherein the circular polyribonucleotide comprises a regulatory nucleic acid, e.g., a non-coding RNA.
[60] [60] The method of any of paragraphs [38] to [59], wherein the circular polyribonucleotide has a size in the range of about 20 bases to about 20 kb.
[61] [61] The method of any of paragraphs [38] to [60], in which the circular polyribonucleotide is synthesized by circularizing a linear polynucleotide.
[62] [62] The method of any of paragraphs [38] to [61], wherein the circular polyribonucleotide comprises a plurality of expression sequences, the same or different.
[63] [63] The method of any of paragraphs [38] to [62], wherein the circular polyribonucleotide is substantially resistant to degradation, eg, exonuclease.
[64] [64] The method of any of paragraphs [38] to [63], wherein the circular polyribonucleotide does not have at least one of: a) a 5'-RTU; b) a 3'-RTU; c) a poly-A sequence; d) a 5'-cap; e) a terminating element; f) an internal ribosomal entry site; g) susceptibility to exonuclease degradation; and h) binding to a cap binding protein.
[65] [65] A pharmaceutical composition comprising a circular polyribonucleotide that comprises at least one structural element selected from: a) an encryptogen; b) a staggered element; c) a regulatory element;
[66] [66] The composition of paragraph [65], in which the circular polyribonucleotide is competent for translation.
[67] [67] The composition of paragraph [65] or [66], wherein the quasi-helical structure comprises at least one double-stranded RNA segment with at least one non-double-stranded segment.
[68] [68] The composition of any of paragraphs [65] to [67], in which the quasi-helical structure comprises a first sequence and a second sequence connected to a repetitive sequence, eg an A-rich sequence.
[69] [69] The composition of any of paragraphs [65] to [68], in which the encryptogen comprises an element of splicing.
[70] [70] The composition of any of paragraphs [65] to [69], wherein the circular polyribonucleotide comprises at least one modified ribonucleotide.
[71] [71] The composition of any of paragraphs [65] to [70], wherein the encryptogen comprises at least one modified ribonucleotide, eg, pseudouridine, N (6) methyladenosine (m6A).
[72] [72] The composition of any of paragraphs [65] to [71], wherein the encryptogen comprises a protein binding site, eg, ribonucleotide binding protein.
[73] [73] The composition of any of paragraphs [65] to [72], wherein the encryptogen comprises an immunoprotein binding site, eg, to escape immune responses, eg, CTL responses.
[74] [74] The composition of any of paragraphs [65] to [73], wherein the circular polyribonucleotide has at least 2x less immunogenicity than a counterpart without the encryptogen, eg, as assessed by expression or signaling or activation of at least one of RIG-I, TLR-3, TLR-7, TLR-8, MDA-5, LGP-2, OAS, OASL, PKR, IFN-beta.
[75] [75] The composition of any of paragraphs [65] to [74], wherein the circular polyribonucleotide additionally comprises a riboswitch.
[76] [76] The composition of any of paragraphs [65] to [75], wherein the circular polyribonucleotide additionally comprises an aptazime.
[77] [77] The composition of any of paragraphs [65] to [76], wherein the circular polyribonucleotide comprises a translation initiation sequence, eg, GUG, CUG start codon, eg, expression under stress conditions.
[78] [78] The composition of any of paragraphs [65] to [77], wherein the circular polyribonucleotide comprises at least one expression sequence, e.g., encoding a polypeptide.
[79] [79] The composition of paragraph [78], wherein the expression sequence encodes a peptide or polynucleotide.
[80] [80] The composition of any of paragraphs [65] to [79], wherein the circular polyribonucleotide comprises a stepped element, e.g., 2A.
[81] [81] The composition of any of paragraphs [65] to [80], wherein the circular polyribonucleotide comprises a regulatory nucleic acid, e.g., a non-coding RNA.
[82] [82] The composition of any of paragraphs [65] to [81], wherein the circular polyribonucleotide has a size in the range of about 20 bases to about 20 kb.
[83] [83] The composition of any of paragraphs [65] to [82], in which the circular polyribonucleotide is synthesized by circularizing a linear polynucleotide.
[84] [84] The composition of any of paragraphs [65] to [83], wherein the circular polyribonucleotide comprises a plurality of expression sequences, the same or different.
[85] [85] The composition of any of paragraphs [65] to [84], wherein the circular polyribonucleotide is substantially resistant to degradation, eg, exonuclease.
[86] [86] The composition of any of paragraphs [65] to [85], wherein the circular polyribonucleotide does not have at least one of: a) a 5'-RTU; b) a 3'-RTU; c) a poly-A sequence; d) a 5'-cap; e) a terminating element; f) an internal ribosomal entry site; g) susceptibility to exonuclease degradation; and h) binding to a cap binding protein.
[87] [87] A method of producing the composition of any of paragraphs [65] to [86] comprising combining the circular polyribonucleotide with a pharmaceutically acceptable carrier or excipient.
[88] [88] A method of treatment comprising administering the composition of any of paragraphs [65] to [86].
[89] [89] A method for expressing proteins, comprising translating at least one region of the circular polyribonucleotide from any of paragraphs [65] to [86].
[90] [90] A method of paragraph [89], in which the translation of at least one region of the circular polyribonucleotide takes place in vitro.
[91] [91] A method of paragraph [89], in which the translation of at least one region of the circular polyribonucleotide takes place in vivo.
[92] [92] A polynucleotide encoding the circular polyribonucleotide of any of paragraphs [65] to [86].
[93] [93] A pharmaceutical composition comprising a pharmaceutically acceptable carrier or excipient and a circular polyribonucleotide comprising one or more expression sequences, in which the circular polyribonucleotide is competent for translation of a rolling circle.
[94] [94] The composition of paragraph [93], in which each of the one or more expression sequences is separated from a subsequent expression sequence by a stepped element in the circular polyribonucleotide, in which the rolling circle translation of one or more sequences of expression generates at least two polypeptide molecules.
[95] [95] The composition of paragraph [94], in which the scaled element prevents the generation of a single polypeptide (a) from two rounds of translation of a single expression sequence or (b) from one or more rounds translation of two or more expression sequences.
[96] [96] The composition of paragraph [94] or [95], where the scaled element is a sequence separate from one or more expression sequences.
[97] [97] The composition of paragraph [94] or [95], wherein the scaled element comprises a portion of an expression sequence of one or more expression sequences.
[98] [98] A pharmaceutical composition comprising a pharmaceutically acceptable carrier or excipient and a circular polyribonucleotide that comprises one or more expression sequences and is competent for circle translation, wherein the circular polyribonucleotide is configured so that at least 50%, at least at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% of the total polypeptides ( molar / molar) generated during the rolling circle translation of the circular polyribonucleotide are discrete polypeptides and where each of the discrete polypeptides is generated from a single translation round or less than a single translation round of one or more sequences of expression.
[99] [99] The composition of paragraph [98], in which the circular polyribonucleotide is configured so that at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% at least 96%, at least 97%, at least 98%, at least 99% or 100% of the total polypeptides (molar / molar) generated during the translation of circular polyribonucleotide are the discrete polypeptides, and in which the ratio of the quantities between discrete products and total polypeptides is tested in an in vitro translation system.
[100] [100] The composition of paragraph [99], wherein the in vitro translation system comprises rabbit reticulocyte lysate.
[101] [101] The composition of any of the paragraphs [93] to
[100] [100], in which the stepped element is at a 3 'end of at least one of the one or more expression sequences, and where the stepped element is configured to interrupt a ribosome during the rolling circle translation of the circular polyribonucleotide.
[102] [102] A pharmaceutical composition comprising a pharmaceutically acceptable carrier or excipient and a circular polyribonucleotide comprising one or more expression sequences and a stepped element at the 3 'end of at least one of the one or more expression sequences, wherein the stepped element is configured to interrupt a ribosome during translation of the circular polyribonucleotide rolling circle.
[103] [103] The composition of paragraph [101] or [102], wherein the scaled element encodes a peptide sequence selected from the group consisting of a 2A sequence and a type 2A sequence.
[104] [104] The composition of any of paragraphs [101] to [103], in which the scaled element encodes a sequence with a sequence of the C terminal which is GP.
[105] [105] The composition of any of paragraphs [101] to [104], in which the scaled element encodes a sequence with a C-terminal consensus sequence which is D (V / I) ExNPGP, where x = any amino acid.
[106] [106] The composition of any of paragraphs [101] to [105], in which the scaled element encodes a selected sequence from the group consisting of GDVESNPGP, GDIEENPGP, VEPNPGP, IETNPGP, GDIESNPGP, GDVELNPGP, GDIETNPGP, GDVENPGP, GDVEENPGP, GDVEENPGP, GDVEENPGP, GDVEENPGP, GDVEENPGP, GDVEENPGP , IESNPGP, GDIELNPGP, HDIETNPGP, HDVETNPGP, HDVEMNPGP, GDMESNPGP, GDVETNPGP, GDIEQNPGP and DSEFNPGP.
[107] [107] The composition of any of paragraphs [101] to [106], in which the scaled element is at the 3 'end of each of the one or more expression sequences.
[108] [108] The composition of any of the paragraphs [93] to
[107] [107], in which the stepped element of a first expression sequence in the circular polyribonucleotide is upstream of (5 'with respect to) a first translation initiation sequence of an expression sequence that succeeds the first expression sequence in the polyribonucleotide circular, and in which a distance between the stepped element and the first translation initiation sequence allows continuous translation of the first expression sequence and the subsequent expression sequence.
[109] [109] The composition of any of the paragraphs [93] to
[107] [107], in which the stepped element of a first expression sequence in the circular polyribonucleotide is upstream (5 'with respect to) a first translation initiation sequence of an expression sequence succeeding the first expression in the circular polyribonucleotide, in that the circular polyribonucleotide is continuously translated, wherein a corresponding circular polyribonucleotide comprising a second stepped element upstream of a second translation initiation sequence of a second expression sequence in the corresponding circular polyribonucleotide is not continuously translated, and in which the second element staggered in the corresponding circular polyribonucleotide is at a greater distance from the second translation initiation sequence, eg at least 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x, than a distance between the element staggered and the first initiation of translation in the circular polyribonucleotide.
[110] [110] The composition of paragraph [108] or [109], where the distance between the stepped element and the first translation initiation is at least 2 nt, 3 nt, 4 nt, 5 nt, 6 nt, 7 nt, 8 nt, 9 nt, 10 nt, 11 nt, 12 nt, 13 nt, 14 nt, 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, 25 nt,
[111] [111] The composition of paragraph [108] or [109], where the distance between the second stepped element and the second translation initiation is at least 2 nt, 3 nt, 4 nt, 5 nt, 6 nt, 7 nt , 8 nt, 9 nt, 10 nt, 11 nt, 12 nt, 13 nt, 14 nt, 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, 25 nt, 30 nt, 35 nt, 40 nt, 45 nt, 50 nt, 55 nt, 60 nt, 65 nt, 70 nt, 75 nt or more than the distance between the stepped element and the first translation initiation.
[112] [112] The composition of any of paragraphs [108] to [110], wherein the expression sequence following the first expression sequence in the circular polyribonucleotide is an expression sequence other than the first expression sequence.
[113] [113] The composition of any of paragraphs [108] to [110], wherein the subsequent expression sequence of the first expression sequence in the circular polyribonucleotide is the first expression sequence.
[114] [114] The composition of any of the paragraphs [93] to
[113] [113], wherein the circular polyribonucleotide comprises at least one structural element selected from: a) an encryptogen; b) a staggered element; c) a regulatory element; d) an element of replication; and f) secondary structure of almost double tape.
[115] [115] The composition of any of the paragraphs [93] to
[114] [114], in which the circular polyribonucleotide comprises at least one functional characteristic selected from: a) greater translation efficiency than a linear counterpart; b) a stoichiometric translation efficiency of multiple translation products; c) less immunogenicity than a counterpart without an encryptogen; d) increased half-life in relation to a linear counterpart; and e) persistence during cell division.
[116] [116] The composition of any of the paragraphs [93] to
[115] [115], where the circular polyribonucleotide has a translation efficiency of at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 2 times, at least 3 times, at least 4 times, at least 5 times, at least at least 6 times, at least 7 times, at least 8 times, at least 9 times, at least 10 times, at least 20 times, at least 50 times or at least 100 times greater than a linear counterpart.
[117] [117] The composition of any of the paragraphs [93] to
[115] [115], in which the circular polyribonucleotide has a translation efficiency at least 5 times greater than a linear counterpart.
[118] [118] The composition of any of the paragraphs [93] to
[117] [117], in which the circular polyribonucleotide does not have at least one of: a) a 5'-RTU; b) a 3'-RTU; c) a poly-A sequence; d) a 5'-cap; e) a terminating element; f) an internal ribosomal entry site; g) susceptibility to exonuclease degradation; and h) binding to a cap binding protein.
[119] [119] The composition of any of the paragraphs [93] to
[118] [118], in which the circular polyribonucleotide does not have an internal ribosomal entry site.
[120] [120] The composition of any of the paragraphs [93] to
[119] [119], wherein the one or more expression sequences comprise a Kozak initiation sequence.
[121] [121] The composition of any of paragraphs [114] to [120], wherein the quasi-helical structure comprises at least one segment of double-stranded RNA with at least one non-double-stranded segment.
[122] [122] The composition of paragraph [121], in which the quasi-helical structure comprises a first sequence and a second sequence connected to a repetitive sequence, eg an A-rich sequence.
[123] [123] The composition of any of paragraphs [114] to [122], in which the encryptogen comprises an element of splicing.
[124] [124] The composition of any of the paragraphs [93] to
[123] [123], wherein the circular polyribonucleotide comprises at least one modified ribonucleotide.
[125] [125] The composition of any of the paragraphs [93] to
[124] [124], where the encryptogen comprises at least one modified ribonucleotide, e.g., pseudouridine, N (6) methyladenosine (m6A).
[126] [126] The composition of any of the paragraphs [93] to
[125] [125], where the encryptogen comprises a protein-binding site, e.g., ribonucleotide-binding protein.
[127] [127] The composition of any of the paragraphs [93] to
[126] [126], in which the encryptogen comprises an immunoprotein-binding site, e.g., to escape immune responses, e.g., CTL responses.
[128] [128] The composition of any of the paragraphs [93] to
[127] [127], in which the circular polyribonucleotide has at least 2x less immunogenicity than a counterpart without the encryptogen, eg, as assessed by expression or signaling or activation of at least one of RIG-I, TLR-3, TLR-7, TLR-8, MDA-5, LGP-2, OAS, OASL, PKR, IFN-beta.
[129] [129] The composition of any of the paragraphs [93] to
[128] [128], wherein the circular polyribonucleotide additionally comprises a riboswitch.
[130] [130] The composition of any of the paragraphs [93] to
[129] [129], wherein the circular polyribonucleotide additionally comprises an aptazime.
[131] [131] The composition of any of the paragraphs [93] to
[130] [130], in which the circular polyribonucleotide comprises a non-canonical translation initiation sequence, e.g., GUG, CUG start codon, e.g., a translation initiation sequence that initiates expression under stress conditions .
[132] [132] The composition of any of the paragraphs [93] to
[131] [131], in which one or more expression sequences encode a peptide.
[133] [133] The composition of any of the paragraphs [93] to
[132] [132], wherein the circular polyribonucleotide comprises a regulatory nucleic acid, e.g., a non-coding RNA.
[134] [134] The composition of any of the paragraphs [93] to
[133] [133], wherein the circular polyribonucleotide has a size in the range of about 20 bases to about 20 kb.
[135] [135] The composition of any of the paragraphs [93] to
[134] [134], in which the circular polyribonucleotide is synthesized by circularizing a linear polyribonucleotide.
[136] [136] The composition of any of the paragraphs [93] to
[135] [135], wherein the circular polyribonucleotide comprises a plurality of expression sequences having the same nucleotide sequence or different nucleotide sequences.
[137] [137] The composition of any of the paragraphs [93] to
[136] [136], in which the circular polyribonucleotide is substantially resistant to degradation, e.g., exonuclease.
[138] [138] The circular polyribonucleotide of any of paragraphs [94] to [137].
[139] [139] A method of producing the composition of any of paragraphs [93] to [137], comprising combining the circular polyribonucleotide of any of paragraphs [93] to [137] and the pharmaceutically acceptable carrier or excipient of any of the paragraphs
[93] [93] to [137].
[140] [140] A treatment method comprising administering the composition of any of the paragraphs
[93] [93] to [137].
[141] [141] A method for expressing proteins, comprising translating at least one region of the circular polyribonucleotide from any of paragraphs [93] to [137].
[142] [142] A method of paragraph [141], in which the translation of at least one region of the circular polyribonucleotide takes place in vitro.
[143] [143] A method of paragraph [141], in which the translation of at least one region of the circular polyribonucleotide takes place in vivo.
[144] [144] A polynucleotide encoding the circular polyribonucleotide of any of paragraphs [65] to [137].
[145] [145] A method of producing the circular polyribonucleotide of any of paragraphs [65] to [137].
[146] [146] The method of paragraph [145], comprising circularization mediated by splint bonding of a linear polyribonucleotide.
[147] [147] The method of paragraph [146], where circularization mediated by splint bonding has an efficiency of at least 2%, at least 5%, at least 10%, at least 15%, at least 20%, at least at least 25%, at least 30%, at least 32%, at least 34%, at least 36%, at least 38%, at least 40%, at least 42%, at least 44%, at least 46%, at least least 48% or at least 50%.
[148] [148] The method of paragraph [146], wherein circularization mediated by splint bonding has an efficiency of about 40% to about 50% or more than 50%.

权利要求:
Claims (33)
[1]
1. Rolling circle translation method of one or more expression sequences characterized by the fact that it comprises expression of one or more expression sequences from a circular polyribonucleotide through rolling circle translation, in which the circular polyribonucleotide comprises a or more expression strings, a stepped element at the 3 'end of at least one of the expression strings and does not have a terminating element.
[2]
2. Method, according to claim 1, characterized by the fact that the stepped element is configured to interrupt a ribosome during the translation of the circular polyribonucleotide circle.
[3]
3. Method, according to claim 1, characterized by the fact that the scaled element encodes a sequence with a C-terminal consensus sequence which is D (V / I) ExNPGP, where x = any amino acid.
[4]
4. Method according to claim 1, characterized by the fact that the expression of one or more expression sequences generates at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80 %, 90% or 95% of discrete polypeptides of total polypeptides (molar / molar) generated during the circular circle translation of the circular polyribonucleotide, and in which each of the discrete polypeptides is generated from a single expression sequence.
[5]
5. Method according to claim 1, characterized by the fact that at least one of the expression sequences encodes a secreted protein.
[6]
6. Method according to claim 1, characterized by the fact that the circular polyribonucleotide does not have an internal ribosomal entry site.
[7]
7. Method according to claim 1, characterized by the fact that the one or more expression sequences comprise a Kozak initiation sequence.
[8]
8. Method according to claim 1, characterized by the fact that the circular polyribonucleotide additionally comprises at least one structural element selected from: (a) an encryptogen; (b) a regulatory element; (c) an element of replication; and (d) secondary structure of almost double tape.
[9]
9. Method, according to claim 1, characterized by the fact that the circular polyribonucleotide comprises at least one functional characteristic selected from: (i) greater translation efficiency than a linear counterpart; (ii) a stoichiometric translation efficiency of multiple translation products;
(iii) less immunogenicity than a counterpart without an encryptogen; (iv) increased half-life in relation to a linear counterpart; and (v) persistence during cell division.
[10]
10. Method according to claim 1, characterized by the fact that the expression of one or more expression sequences generates at least 5 times more expression product than a linear counterpart.
[11]
11. Method according to claim 1, characterized in that the expression of one or more expression sequences comprises expression of the one or more expression sequences in a cell comprising the circular polyribonucleotide.
[12]
12. Method according to claim 11, characterized by the fact that the circular polyribonucleotide persists during cell division.
[13]
13. Method according to claim 11, characterized in that at least about 60% of an amount of the circular polyribonucleotide persists for at least about 7 days in the cell.
[14]
14. Method according to claim 11, characterized by the fact that: (a) the expression of one or more expression sequences in the cell at a later time is equal to or higher than an earlier time; or
(b) the expression of one or more expression sequences in the cell over a period of time of at least about 7 days does not decrease by 40%; or (c) the expression of one or more expression sequences in the cell is maintained at a level that does not vary by more than 40% for at least about 7 days.
[15]
15. Method according to claim 1, characterized in that the expression of one or more expression sequences comprises expression of the expression sequences in a mammalian subject.
[16]
16. Method according to claim 1, characterized by the fact that the terminating element comprises a stop codon.
[17]
17. Method according to claim 11, characterized in that the circular polyribonucleotide additionally comprises a replication domain configured to mediate the self-replication of the circular polyribonucleotide.
[18]
18. Pharmaceutical composition characterized by the fact that it comprises a circular polyribonucleotide comprising (a) a circular polyribonucleotide comprising one or more expression sequences and a stepped element at a 3 'end of at least one of the one or more expression sequences, wherein the circular polyribonucleotide is competent for translation of a rolling circle and does not have a terminating element; and (b) a pharmaceutically acceptable excipient.
[19]
19. Cell characterized by the fact that it comprises a circular polyribonucleotide that comprises one or more expression sequences and a stepped element at a 3 'end of at least one of the one or more expression sequences, in which the circular polyribonucleotide is competent for translation rolling circle and does not have a terminating element.
[20]
20. Method of in vivo expression of one or more expression sequences in a subject, characterized by the fact that it comprises: administration of a circular polyribonucleotide to a cell of the subject in which the circular polyribonucleotide comprises one or more expression sequences; and expression of one or more expression sequences from the circular polyribonucleotide in the cell, wherein the circular polyribonucleotide is configured so that the expression of one or more expression sequences in the cell at a later time is equal to or higher than an earlier moment.
[21]
21. Method of in vivo expression of one or more expression sequences in a subject, characterized by the fact that it comprises: administration of a circular polyribonucleotide to a cell of the subject in which the circular polyribonucleotide comprises one or more expression sequences; and expressing one or more expression sequences from the circular polyribonucleotide in the cell, wherein the circular polyribonucleotide is configured so that the expression of one or more expression sequences in the cell over a period of time of at least 7, 8, 9, 10, 12, 14 or 16 days do not decrease by more than about 40%.
[22]
22. Method of in vivo expression of one or more expression sequences in a subject, characterized by the fact that it comprises: administration of a circular polyribonucleotide to a cell of the subject in which the circular polyribonucleotide comprises one or more expression sequences; and expressing one or more expression sequences from the circular polyribonucleotide in the cell, wherein the circular polyribonucleotide is configured so that the expression of one or more expression sequences of the one or more expression sequences in the cell is maintained at a level which does not vary by more than about 40% for at least 7, 8, 9, 10, 12, 14 or 16 days.
[23]
23. Pharmaceutical composition characterized by the fact that it comprises a circular polyribonucleotide that comprises at least one structural element selected from: a) an encryptogen; b) a staggered element; c) a regulatory element; d) an element of replication; f) secondary structure of almost double tape; and g) expression sequence; and at least one functional feature selected from: a) greater translation efficiency than a linear counterpart; b) a stoichiometric translation efficiency of multiple translation products; c) less immunogenicity than a counterpart without an encryptogen; d) increased half-life in relation to a linear counterpart; and e) persistence during cell division.
[24]
24. Pharmaceutical composition characterized by the fact that it comprises a pharmaceutically acceptable carrier or excipient and a circular polyribonucleotide that comprises one or more expression sequences, in which the circular polyribonucleotide is competent for translation of a rolling circle.
[25]
25. Pharmaceutical composition characterized by the fact that it comprises a pharmaceutically acceptable carrier or excipient and a circular polyribonucleotide that comprises one or more expression sequences and is competent for translation of a rolling circle, in which the circular polyribonucleotide is configured so that at least 50 %, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% of total polypeptides (molar / molar) generated during the rolling circle translation of the circular polyribonucleotide are discrete polypeptides and where each of the discrete polypeptides is generated from a single translation round or less than a single translation round of the one or more expression strings.
[26]
26. Pharmaceutical composition characterized by the fact that it comprises a pharmaceutically acceptable carrier or excipient and a circular polyribonucleotide comprising one or more expression sequences and a stepped element at the 3 'end of at least one of the one or more expression sequences, wherein the stepped element is configured to interrupt a ribosome during the rolling circle translation of the circular polyribonucleotide.
[27]
27. Method of production of the composition, as defined in any of claims 18 or 23, 24, 25 and 26, characterized in that it comprises a combination of the circular polyribonucleotide, as defined in any of claims 18 or 23, 24, 25 and 26, and the pharmaceutically acceptable carrier or excipient, as defined in any of claims 18 or 23, 24, 25 and 26.
[28]
28. Treatment method characterized by the fact that it comprises administration of the composition, as defined in any one of claims 18 or 23, 24, 25 and 26.
[29]
29. Method for the expression of proteins, characterized in that it comprises translation of at least one region of the circular polyribonucleotide, as defined in any one of claims 18 or 23, 24, 25 and 26.
[30]
30. Method according to claim 29, characterized in that the translation of at least one region of the circular polyribonucleotide takes place in vitro.
[31]
31. Method according to claim 29, characterized in that the translation of at least one region of the circular polyribonucleotide takes place in vivo.
[32]
32. Polynucleotide characterized by the fact that it encodes the circular polyribonucleotide, as defined in any one of claims 18 or 23, 24, 25 and 26.
[33]
33. Method characterized by the fact that it produces circular polyribonucleotide, as defined in any one of claims 18 or 23, 24, 25 and 26.

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同族专利:

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公开号 | 公开日

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EP3724208A4|2021-09-01|

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US20210275565A1|2021-09-09|

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WO2019118919A1|2019-06-20|

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US20190307785A1|2019-10-10|

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MA51155A|2020-10-21|

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CN111819185A|2020-10-23|

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US11058706B2|2021-07-13|

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CA3084824A1|2019-06-20|

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US20210161938A1|2021-06-03|

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KR20200127152A|2020-11-10|

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JP2021508490A|2021-03-11|

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US20220023331A1|2022-01-27|

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IL275205D0|2020-07-30|

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US10953033B2|2021-03-23|

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US20200306286A1|2020-10-01|

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EP3724208A1|2020-10-21|

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US11160822B2|2021-11-02|

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AU2018385757A1|2020-06-25|

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SG11202005060YA|2020-06-29|

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法律状态:
2021-12-07| B350| Update of information on the portal [chapter 15.35 patent gazette]|

优先权:

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申请号 | 申请日 | 专利标题

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US201762599547P| true| 2017-12-15|2017-12-15|

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US62/599,547|2017-12-15|

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US201862676688P| true| 2018-05-25|2018-05-25|

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PCT/US2018/065836|WO2019118919A1|2017-12-15|2018-12-14|Compositions comprising circular polyribonucleotides and uses thereof|

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