CD19-specific chimeric antigen receptors and antibodies

专利摘要:

公开号:ES2833010T9
申请号:ES15760045T
申请日:2015-08-28
公开日:2021-07-20
发明作者:Yan Chen；Steve Shamah；Csaba Pazmany；Jui Dutta-Simmons
申请人:Juno Therapeutics Inc；
IPC主号:

专利说明:

[0001] CD19-specific chimeric antigen receptors and antibodies
[0002] Cross reference to related requests
[0003] [0001] This application claims priority of United States Provisional Application No. 62 / 043,273 filed on August 28, 2014, entitled "Antibodies and Chimeric Antigen Receptors Specific for CD19", and United States Provisional Application No. 62 / 078,942 filed November 12, 2014, entitled "Antibodies and Chimeric Antigen Receptors Specific for CD19".
[0004] Sequence Listing Incorporation by Reference
[0005] [0002] The present application is being filed with a sequence listing in electronic format. The sequence listing is provided as a file titled 735042000740seqlist.txt, created on August 28, 2015, with a size of 215 kilobytes.
[0006] Field
[0007] [0003] The present disclosure relates in some respects to CD19 binding molecules, in particular anti-CD19 antibodies, including antibody fragments. The present disclosure further relates to recombinant receptors that contain such antibodies, including chimeric antigen receptors (CARs), that contain such antibodies. The disclosure further relates to genetically modified cells expressing such receptors and antibodies, and their use in adoptive cell therapy.
[0008] Background
[0009] [0004] CD19 is expressed in normal B cells and in cells and tissues of various diseases and conditions, including most B-cell malignancies. Most patients with B-cell malignancies are not cured by therapies. available, including therapies targeting CD19 and / or other B cell markers. Various CD19-binding molecules are available, including anti-CD19 antibodies and chimeric antigen receptors that contain portions of anti-CD19 antibodies, and cells that express such chimeric receptors. Enhanced CD19-binding molecules and engineered CD19-targeting cells are needed. For example, there is a need for molecules and cells with reduced immunogenicity and / or human antibodies, including antibody fragments that specifically bind to CD19 and chimeric receptors that express such human antibodies for use in adoptive cell therapy. Instances are provided that meet those needs.
[0010] [ 0005] WO2012170807 describes anti-Pseudomonas PSL binding molecules and uses thereof.
[0011] [ 0006] WO2009054863 describes human antibodies that bind to CD19 and their uses.
[0012] [ 0007] WO2009091826 describes compositions and methods related to a human CD19-specific chimeric antigen receptor.
[0013] [ 0008] US2005070693 describes a therapy using anti-CD-19 antibodies.
[0014] [ 0009] Kochenderfer et al. (2012) describe B-cell depletion and remissions of malignancy together with cytokine-associated toxicity in a clinical trial of chimeric-antigen-receptor-induced anti-CD19 T cells (Blood, vol.119 (12): 2709 -2720).
[0015] [ 0010] Turtle et al. (2016) describe CD19 CAR-T cells of defined composition CD4 +: CD8 + in adult patients with B-cell ALL (The Journal of Clinical Investigation, vol.126 (6): 2123-2138).
[0016] Summary
[0017] [0011] The object of the invention is defined by the appended claims.
[0018] [0012] The provided invention antibody or binding fragment antigen therein comprising: a VH region comprising the amino acid sequence of SEQ ID NO: 11 and a VL region comprising the amino acid sequence of SEQ ID NO: 13 ; or a VH region comprising the amino acid sequence of SEQ ID NO: 11, and a VL region comprising the amino acid sequence of SEQ ID NO: 14; or a VH region comprising the amino acid sequence of SEQ ID NO: 11, and a VL region comprising the amino acid sequence of SEQ ID NO: 16; or a VH region comprising the amino acid sequence of SEQ ID NO: 12, and a VL region comprising the amino acid sequence of SEQ ID NO: 15; or a VH region comprising the amino acid sequence of SEQ ID NO: 12, and a VL region comprising the amino acid sequence of SEQ ID NO: 17.
[0019] The embodiments of the invention are described in some of the cases below. The following disclosure provides CD19-binding molecules, including polypeptides, such as anti-CD19 antibodies, including antigen-binding antibody fragments, such as single-chain fragments, including scFv fragments, and polypeptides containing such antibodies, including fusion proteins. , receivers, p. eg, recombinant receptors, including chimeric receptors such as chimeric antigen receptors (CARs) that contain the antibody as an antigen-recognition component. In particular cases, the antibodies are human antibodies, such as human single chain fragments that include scFv.
[0021] [ 0013] Antibodies or antigen-binding fragments thereof are provided, including those that specifically bind to CD19. In some cases, antibodies contain particular complementarity determining regions (CDRs), including heavy chain CDRs (CDR-H) and light chain CDRs (CDR-L). In some cases, CDRs have or include amino acid sequences of the CDRs of a reference antibody or chain or sequence thereof.
[0023] [0014] In some instances, the antibody or fragment thereof includes a variable region heavy chain binding antigen (VH) and variable light (VL) region. In some cases, the antibody, e.g. g., the VH region thereof, includes a region 3 that determines the complementarity of the heavy chain (CDR-H3) that comprises the amino acid sequence established as SEQ ID NO: 20. In some cases, the VH region comprises at at least at or about 90% sequence identity with the amino acid sequence of the VH region set forth in SEQ ID NO: 11, 12, 60, 61, 63 or 62, p. eg, at least at or about 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity therewith. In some cases, the antibody or fragment includes a CDR-H1 of SEQ ID NO: 18 and a CDR-H3 of SEQ ID NO: 20. In some cases, the antibody or fragment further includes a CDR-H2 sequence comprising SEQ ID NO: 81, 82, 19 or 72.
[0025] [0015] In some cases, the antibody is a CDR-H1, a CDR-H2, and / or CDR-H3 respectively include the amino acid sequences of CDR sequences 1, 2 and 3 contained within the heavy chain variable region (Vh) of a reference antibody. In some cases, the VH region of the reference antibody has the amino acid sequence established in SEQ ID NO: 11 or 12. In some cases, it has the amino acid sequence established in SEQ ID NO: 11, 12, 60, 61,63 , or 62.
[0027] [ 0016] In some cases, the antibody has, e.g. g., further includes a CDR-L1, a CDR-L2, and / or a CDR-L3, respectively, comprising the amino acid sequences of CDR sequences 1, 2, and 3 contained within the light chain variable region ( Vl) of a reference antibody. In some cases, the Vl of the reference antibody has the amino acid sequence set forth in SEQ ID NO: 13, 14, 15, 16, or 17. In some cases, the VL of the reference antibody has the amino acid sequence set forth in SEQ ID NO: 13, 14, 15, 16, 17, 71, 65, 64, 66, 70, 69, 67, 90 or 91.
[0029] [0017] In some cases, the CDR within the reference antibody, VH, or VL refers to the CDR as defined by any numbering scheme, p. eg, those defined in this document. In some cases, the CDR in the reference antibody or VH or VL refers to the CDR as defined by the Kabat numbering scheme as described herein, the CDR as defined in the Chothia scheme as described in this document, or the contact scheme as described in this document.
[0031] [ 0018] In some cases, the antibody contains a VH chain that includes a CDR-H1, CDR-H2 and / or CDR-H3 in which the CDR-H1 comprises the amino acid sequence of DYAMH (SEQ ID NO: 18) or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity with SEQ ID NO: 18; the CDR-H2 comprises the amino acid sequence of SEQ ID NO: 81 or 82 or 19 or 72 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity with SEQ ID NO: 81 or with SEQ ID NO: 82 or with SEQ ID NO: 19 or with SEQ ID NO: 72; and / or CDR-H3 comprises the amino acid sequence of SEQ ID NO: 20 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity with SEQ ID NO: 20.
[0033] [0019] In some cases, the antibody comprises a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 18, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 81 or 82 and a CDR- H3 comprising the amino acid sequence set forth as SEQ ID NO: 20.
[0035] [ 0020] In some cases, the antibody has a CDR-1 comprising the amino acid sequence of X1X2X3X4X5X6X7X8X9X10X11X12X13X14 (SEQ ID NO: 110), wherein X1 is T, W, S, or R; X2 is G or A; X3 is I, T, D, or S; X4 is S, R, T, or Q; X5 is null or S; X6 is null, D, N, or G; X7 is null, V or L; X8 is Xo null; X9 is Xo null; X10 is X; X11 is X; X12 is Y, F, D, or W; X13 is V, A, or L and X14 is S, N, or A. For example, in some cases, the antibody has a CDRL1 that comprises the amino acid sequence of X1 X2 X3 X4 X5 X6X7 X8 X9 X10 X11 X12 X13 X14 (SEQ ID NO: 111), where X1 is T, Q, S or R; X2 is G or A; X3 is I, T, D, or S; X4 is S, R, T, or Q; X5 is null or S; X6 is G, D, N or null; X7 is null, V or L; X8 is D, G, I, L, S, or null; X9 is S, G, A, I, R or null; X10 is H, Y, F, S, or N; X11 is R, N, D, H, or Y; X12 is Y, F, D, or W; X13 is V, A, or L; and X14 is S, N, or A; me
[0036] a CDR-L2 comprising the amino acid sequence of X1X2X3X4X5X6X7 (SEQ ID NO: 112), wherein X1 is Two; X2 is F, V, N, K, or A; X3 is S, T, D, or N; X4 is K, V, N, Q, or R; X5 is R, V, or L; X6 is P, K, A, or E; and X7 is S, P, A or T, and / or a CDR-L3 comprising the amino acid sequence of X1X2X3X4X5X6X7X8X9X10X11X12 (SEQ ID NO: 115), where X1 is X; X2 is S, Q, A, or T; X3 is Y, S, W, R; X4 is A, D, R, T, or Y; X5 is X; X6 is X; X7 is S, P, L, Y, G; X8 is Xo null; X9 is Xo null; X10 is L or null; X11 is X; and X12 is V, T or L. For example, in some cases, the antibody has a CDR-L3 that comprises the amino acid sequence X1X2X3X4X5X6X7X8X9X10X11X12 (SEQ ID NO: 114), where X1 is S, G, T, A, Q , With; X2 is S, Q, A, or T; X3 is Y, S, W, R; X4 is A, D, R, T, or Y; X5 is A, S, P, G, N, or D; X6 is I, S, G, T, A, L, H, R, N; X7 is S, P, L, Y, G; X8 is P, T, S, Q, M, R, N or null; X9 is S, L, N, A, M, or null; X10 is L or null; X11 is Y, W, F, V, A, or L; and X12 is V, T, or L.
[0038] [0021] In some such cases, in said CDR-L1, X3 is I, T, or S; X4 is S, T, or Q; X8 is D, G, I, S, or null; X9 is S, G, I or null; X10 is H, Y, S, or N; X11 is R, N, D, or H; X12 is Y or D; and X13 is V or L; and / or in said CDR-L2, X1 is D; X4 is K, V, N, Q, or R; X6 is P, K, or A; and X7 is S, A, or T; and / or in said CDR-L3, X1 is S, G, T, A, Q, C, or N; X5 is A, S, P, G, N, or D; X6 is I, S, G, T, A, L, H, R, or N; X8 is P, T, S, Q, M, R, N or null; X9 is S, L, N, A, M, or null; and X11 is Y, W, F, V, A or L. In some cases, in said CDR-L3, X1 is S, G, Q or N; X2 is S, Q, or T; X4 is A, D, T, or Y; X5 is A, S, or G; and X6 is I, S, N, R, A, H, or T.
[0040] [ 0022] In some cases, the CDR-H2 comprises the amino acid sequence in SEQ ID NO: 19 (g IsW n SGRIGYADSVKG); or CDR-H2 comprises the amino acid sequence set forth in SEQ ID NO: 72 (GISWNSGSIGYADSVKG).
[0042] [0023] In some cases, the CDR-L1 comprising the amino acid sequence in SEQ ID NO: 80, 77, 74, 73, 75, 79, 78, 76, 21, 25, 28, or 31. In some cases , CDR-L1 comprises the amino acid sequence set forth in SEQ ID NO: 80, 77, 74, 73, 78, 21, or 28.
[0044] [0024] In some cases, the CDR-L2 comprises the amino acid sequence in SEQ ID NO: 100, 97, 94, 93, 95, 99, 98, 96, 22, 26, 29 or 32. In some cases, the CDR-L2 comprises the amino acid sequence set forth in SEQ ID NO: 100, 97, 94, 93, 98, 22, or 29.
[0046] [0025] In some cases, the CDR-L3 comprises the amino acid sequence in SEQ ID NO: 109, 106, 103, 101, 104, 108, 107, 105, 102, 23, 24, 27, 30 or 33. In some cases, the CDR-L3 comprises the amino acid sequence established in SEQ ID NO: 109, 106, 103, 101, 107, 24 or 30.
[0048] [ 0026] In some cases, CDR-L1, CDR-L2, and CDR-L3 comprise the sequences of SEQ ID NOs: 21, 22, and 23, respectively, or sequences that have at least or at least about 90%, 91% 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 21, 22 and 24 or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity, respectively; CDR-L1, CDR-L2, and CDRL3 comprise the sequences of SEQ ID NO: 25, 26, and 27, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94% 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 28, 29 and 30, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 31, 32 and 33, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 80, 100 and 109, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 77, 97 and 106, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 74, 94 and 103, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 73, 93 and 101, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 75, 95 and 104, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity, respectively; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 79, 99 and 108, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 78, 98 and 107, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 76, 96 and 105, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity of amino acids, respectively, with the same; CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 73, 93 and 102, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; or CDR-L1, CDR-L2 and CDR-L3 comprise the sequences of SEQ ID NO: 77, 97 and 106, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93% , 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto.
[0050] [0027] In some cases, the CDR-L3 comprises the amino acid sequence as SEQ ID NO: 116, 117, 118, 119, 120, or 121, or a sequence having at the least or at the least about 90%, 91% , 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto.
[0052] [ 0028] In some cases, CDR-H1, CDR-H2, and CDR-H3 comprise the sequences of SEQ ID NOs: 18, 81, and 20, respectively, or sequences that have at least or at least about 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity, respectively, thereto; CDR-H1, CDR-H2 and CDR-H3 comprise the sequences of SEQ ID NO: 18, 19 and 20, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; CDR-H1, CDR-H2, and CDRH3 comprise the sequences of SEQ ID NO: 18, 82, and 20, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94% 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto; or CDR-H1, CDR-H2 and CDR-H3 comprise the sequences of SEQ ID NO: 18, 72 and 20, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93% , 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity, respectively, thereto.
[0054] [0029] In some cases, the antibody has a CDR-L1 comprising the amino acid sequence X1GX3X4X5X6X7X8X9X10X11X12X13S (SEQ ID NO: 36), where X1 is T, S or Q, X3 is T, S or D, X4 is T or S, X5 is null or S, X6 is null, D or N, X7 is null or V, X8 is null, G or I, X9 is null, G or R, X10 is S, Y or N, X11 is D or N, X12 is D or Y, X13 is V or A; CDR-L2 comprises the amino acid sequence X1X2X3X4 RPS (SEQ ID NO: 37), where X1 is D or S, X2 is V, N or K, X3 is S, N or D and X4 is K, Q or N; and / or CDR-L3 comprises the amino acid sequence X1X2X3X4X5X6X7X8X9X10X11X12 (SEQ ID NO: 113), where X1 is C, S, A, G or N; X2 is S, A, or T; X3 is Y, W, or R; X4 is A or D; X5 is G, D, or S; X6 is R, S, or N; X7 is Y, L, or G; X8 is N or S; X9 is S, N or null; X10 is null; X11 is V, A, or W; and X12 is L or V.
[0056] [ 0030] In some cases, the antibody has a CDR-L1 comprising the amino acid sequence X1GX3X4X5X6X7X8X9X10X11X12X13S (SEQ ID NO: 36), where X1 is T, S or Q, X3 is T, S or D, X4 is T or S, X5 is null or S, X6 is null, D or N, X7 is null or V, X8 is null, G or I, X9 is null, G or R, X10 is S, Y or N, X11 is D or N, X12 is D or Y, X13 is V or A; CDR-L2 comprises the amino acid sequence X 1 X 2 X3 X 4 RPS (SEQ ID NO: 37), where X1 is D or S, X2 is V, N or K, X3 is S, N or D and X4 is K, Q or N; and / or CDR-L3 comprises the amino acid sequence X1X2X3X4X5X6X7X8X9X10X11X12 (SEQ ID NO: 38), where X1 is C, S, A, G or N; X2 is S, A, or T; X3 is Y, W, or R; X4 is A or D; X5 is G, D, or S; X6 is R, S, or N; X7 is Y, L, or G; X8 is N or S; X9 is S or null; X10 is V, A, or N; X11 is W or null; and X12 is L or V.
[0058] [0031] In some such cases, the CDR-L1, X1 is T or S, X3 is T or S, X11 is D or N and X13 is V; and / or in the CDR-L2, X2 is V or N and X4 is K or P.
[0060] [ 0032] In some cases, the CDR-H2 comprises the amino acid sequence in SEQ ID NO: 19 (GISWNSGRIGYADSVKG) or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94 %, 95%, 96%, 97%, 98% or 99% amino acid sequence identity with SEQ ID NO: 19.
[0062] [0033] In some cases, the CDR-L1 comprises the sequence set in SEQ ID NO: 21, 25, 28 or 31 or a sequence having at the least or at the least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith; and / or the CDR-L2 comprises the sequence set forth in SEQ ID NO: 22, 26, 29 or 32 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95 %, 96%, 97%, 98% or 99% amino acid sequence identity thereto; and / or CDR-L3 comprises the sequence set forth in SEQ ID NO: 23, 24, 27, 30 or 33 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0064] [ 0034] In some cases, the CDR-L1, CDR-L2, and / or CDR-L3 comprise the sequences of SEQ ID NOs: 21, 22, and / or 23, respectively, or sequences that have at least or at least approximately 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively.
[0066] [ 0035] In some cases, CDR-L1, CDR-L2, and CDR-L3 comprise the sequences of SEQ ID NOs: 21, 22, and 24, respectively, or sequences that have at least or at least about 90%, 91% , 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively.
[0067] [ 0036] In some cases, CDR-L1, CDR-L2, and CDR-L3 comprise the sequences of SEQ ID NOs: 25, 26, and 27, respectively, or sequences that have at least or at least about 90%, 91% , 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively.
[0068] [ 0037] In some cases, CDR-L1, CDR-L2, and CDR-L3 comprise the sequences of SEQ ID NOs: 28, 29, and 30, respectively, or sequences that have at least or at least about 90%, 91% , 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively. In some cases, CDR-L1, CDR-L2, and CDR-L3 comprise the sequences of SEQ ID NO: 31, 32, and 33, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity thereto.
[0069] [ 0038] In some cases, the heavy and light chain CDRs are any combination of the CDR-L and aforementioned CDR-H sequences, including sequences that are at least or at least about 90%, 91%, 92% , 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0070] [ 0039] In particular cases, the antibody or fragment comprises a VH region that comprises the amino acid sequence of SEQ ID NO: 11 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0071] [ 0040] In particular cases, the antibody or fragment comprises a VH region that comprises the amino acid sequence of SEQ ID NO: 12 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0072] [ 0041] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 13 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0073] [ 0042] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 14 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0074] [ 0043] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 15 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity therewith.
[0075] [ 0044] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 16 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0076] [ 0045] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 17 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0077] [ 0046] In particular cases, the antibody or fragment comprises a VH region that comprises the amino acid sequence of SEQ ID NO: 63 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0078] [ 0047] In particular cases, the antibody or fragment comprises a VH region that comprises the amino acid sequence of SEQ ID NO: 60 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0079] [ 0048] In particular cases, the antibody or fragment comprises a VH region that comprises the amino acid sequence of SEQ ID NO: 61 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0080] [ 0049] In particular cases, the antibody or fragment comprises a VH region that comprises the amino acid sequence of SEQ ID NO: 63 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0081] [ 0050] In particular cases, the antibody or fragment comprises a VH region that comprises the amino acid sequence of SEQ ID NO: 62 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0082] [ 0051] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 71 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0083] [0052] In particular cases, the antibody or fragment comprises a VL region comprising the amino acid sequence of SEQ ID NO: 90 or a sequence having at the least or at the least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0085] [0053] In particular cases, the antibody or fragment comprises a VL region comprising the amino acid sequence of SEQ ID NO: 91 or a sequence having at the least or at the least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0087] [ 0054] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 68 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0089] [ 0055] In particular cases, the antibody or fragment comprises a VL region comprising the amino acid sequence of SEQ ID NO: 65 or a sequence having at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0091] [ 0056] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 64 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0093] [ 0057] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 66 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0095] [ 0058] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 70 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0097] [0059] In particular cases, the antibody or fragment comprises a VL region comprising the amino acid sequence of SEQ ID NO: 69 or a sequence having at the least or at the least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0099] [ 0060] In particular cases, the antibody or fragment comprises a VL region that comprises the amino acid sequence of SEQ ID NO: 67 or a sequence that has at least or at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0101] [ 0061] In particular cases, the VH region of the antibody or fragment that comprises the amino acid sequence of SEQ ID NO: 11.60, 63, or 62 or a sequence that has at least or at least about 90%, 91% 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity thereto; and / or the VL region of the antibody or fragment comprising the amino acid sequence of SEQ ID NO: 14, 16, 71, 90, 65, 64 or 69 or a sequence that is at least or at least about 90%, 91% , 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0103] [ 0062] In some cases, the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NOs: 12 and 17, respectively, or sequences that have at least or at least about 90%, 91%, 92% 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0104] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NOs: 12 and 15, respectively, or sequences that are at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0105] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 11 and 13, respectively, or sequences having at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0106] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 11 and 14, respectively, or sequences having at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0107] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 11 and 16, respectively, or sequences having at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0108] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 63 and 71, respectively, or sequences having at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0109] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 62 and 68, respectively, or sequences having at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 11 and 65, respectively, or sequences having at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0110] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 60 and 64, respectively, or sequences having at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0111] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NOs: 61 and 66, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0112] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 63 and 70, respectively, or sequences having at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0113] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NOs: 62 and 69, respectively, or sequences having at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0114] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NOs: 12 and 67, respectively, or sequences that are at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively;
[0115] the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NOs: 12 and 91, respectively, or sequences that are at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively; or the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 63 and 90, respectively, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94 %, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto, respectively.
[0117] [0063] In some cases, the VH region comprising SEQ ID NO: 11 and the VL region comprises SEQ ID NO: 13; in some cases, the VH region comprises SEQ ID NO: 11 and the VL region comprises SEQ ID NO: 14; in some cases, the VH region comprises SEQ ID NO: 11 and the VL region comprises SEQ ID NO: 15; in some cases, the VH region comprises SEQ ID NO: 11 and the VL region comprises SEQ ID NO: 16, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94% 95%, 96%, 97%, 98% or 99% amino acid sequence identity thereto; in some cases, the VH region comprises SEQ ID NO: 11 and the VL region comprises SEQ ID NO: 17, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0119] [0064] In some cases, the VH region comprising SEQ ID NO: 12 and the VL region comprises SEQ ID NO: 13; in some cases, the VH region comprises SEQ ID NO: 12 and the VL region comprises SEQ ID NO: 14; in some cases, the VH region comprises SEQ ID NO: 12 and the VL region comprises s Eq ID NO: 15; in some cases, the VH region comprises SEQ ID NO: 12 and the VL region comprises SEQ ID NO: 16, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94% 95%, 96%, 97%, 98% or 99% amino acid sequence identity thereto; in some cases, the VH region comprises SEQ ID NO: 12 and the VL region comprises SEQ ID NO: 16, or sequences that have at least or at least about 90%, 91%, 92%, 93%, 94 %, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity thereto.
[0121] [ 0065] In some cases, the antibody is a single chain fragment, such as one with two or more variable regions linked by one or more flexible immunoglobulin linker. In some cases, the antibody is a scFv. In some cases, the scFv comprises a linker that is rich in serine and / or glycine, such as a linker that comprises repeats of GGGS (SEQ ID NO: 122) or Gg Gg S (SEQ ID NO: 123), such as one that comprises the set of sequences below SEQ ID NO: 34. In some cases the linker comprises a sequence of SEQ ID NO: 43.
[0123] [ 0066] In some cases, the antibody fragment, e.g. eg, scFv, contains a Vh region or portion thereof, followed by a linker, followed by a Vl or parts thereof. In some cases, the antibody fragment, e.g. eg, scFv, contains a Vl region or a portion thereof followed by a linker, followed by a Vh region or portion thereof.
[0125] [ 0067] In some cases, the scFv comprises the amino acid sequence in SEQ ID NO: 2, 4, 6, 8, or 10, or a sequence that is at least or at least about 90%, 91%, 92% , 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity therewith.
[0127] [0068] In some cases, the scFv comprises the amino acid sequence in SEQ ID NO: 2, 4, 6, 8, 10, 45, 47, 49, 51, 53, 55, 57, 59, 87, or 89 , or has a sequence at least or about 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to said sequence.
[0129] [0069] In some instances, the antibody or fragment binds specifically to the same, similar, and / or an overlapping epitope of CD19 as the epitope specifically bound by a reference antibody, and / or competing antibody for binding to CD19 with the reference antibody. In some aspects, the reference antibody is a murine or chimeric or human or humanized anti-CD 19 antibody, FMC63, SJ25C1, an antibody having a variable region sequence of SEQ ID NO: 39 and / or 40, or an antibody having a variable region sequence of SEQ ID NO: 41 and / or 42. In some aspect, the reference antibody is an antibody that includes a sequence as described herein, which includes the sequence or sequences of any of the cases mentioned above. For example, in some cases, the reference antibody can be a scFv containing the amino acid sequence established in SEQ ID NO: 2, 4, 6, 8, 10, 45, 47, 49, 51, 53, 55, 57 ., 59, 87 or 89. In some cases, the provided antibody or fragment contains one or more or all of the CDRs that are different from the reference antibody. For example, in some cases, the provided antibody or fragment contains one or more or all of the CDRs that are different from the corresponding CDRs in the antibody designated FMC63 or SJ25C1.
[0131] [ 0070] For example, human antibodies and antigen-binding fragments that specifically bind thereto or an epitope of the CD19 overlap are provided as the epitope specifically bound by the reference antibody, such as FMC63, SJ25C1, an antibody that has a variable region sequence of SEQ ID NO: 39 and / or 40, or an antibody that has a variable region sequence of SEQ ID NO: 41 and / or 42, and comprises heavy and light chain CDRs that are distinct of the CDRs present in the reference antibody.
[0133] [0071] In some cases, the antibody competes for binding with the antibody reference to the same extent as least the reference antibody compete for binding to CD19 with itself, or a degree of competition not more than 1.5 at 2 times lower, 3 times lower, 4 times lower, 5 times lower or 10 times lower than the competition for the reference antibody, and / or a measured IC50 that is not more than 1.5 times or 2 times or 3 times or 4 times or 5 times or 10 times higher than the IC50 of the reference antibody that competes to bind itself, e.g. eg, measured in the same test.
[0135] [ 0072] In some cases, the antibody has a binding affinity that is at least as high or substantially as high as the binding affinity for c D19 of the reference antibody. In some aspects, the antibody has a binding affinity of an EC50 that is approximately equal to or less than the reference antibody of EC50 or not more than about 1.5 times or not more than about 2 times greater, not more than 3 times. higher, and / or no more than 10 times higher than the EC50 of the reference antibody. In some cases, the binding affinity of the antibody is compared to the corresponding form of the reference antibody. The comparison is generally made by the same or a similar test.
[0137] [ 0073] In some such cases, CD19 is a human CD19. In some such cases, the antibody or fragment specifically binds, shows binding affinity, and / or competes to bind human CD19.
[0139] [ 0074] In some cases, the antibody is human. In some cases, the antibody is recombinant. In some cases, the antibody is monoclonal. In some cases, the antibody is isolated.
[0141] [0075] In some instances, the antibody or fragment further comprises at the least a portion of an immunoglobulin constant region. The constant region can include one or more of CH1, CH2, CH3 and / or CH4, and / or CL, of a human or other antibody, and be of any class, including IgG, IgM, IgA, IgE and IgD, e.g. g., including human IgG, eg. eg, IgG1 or IgG4, constant region domains. In some cases, the constant region comprises or is an Fc region, such as a human IgG Fc region.
[0143] [ 0076] Also provided are molecules such as chimeric and / or fusion molecules, including receptors, such as recombinant receptors, which include the antibody of either case (eg, contained in or part of an extracellular domain) and additional domains, such as intracellular signaling domains, spacers, linkers, and / or transmembrane domains. In some cases, the receptor is a chimeric antigen receptor, comprising an extracellular portion comprising the antibody or fragment of either case and an intracellular signaling domain.
[0145] [ 0077] In some cases, the antibody or fragment comprises an scFv. In some cases, the intracellular signaling domain comprises an ITAM and / or a signaling domain capable of delivering a signal that approximates that of the natural ligation of an ITAM-containing molecule or receptor complex such as a TCR receptor complex. In some aspects, the intracellular signaling domain comprises a signaling domain from a zeta chain of a CD3-zeta chain (CD3Z).
[0147] [ 0078] In some cases, the receptor further includes one or more domains, such as a transmembrane domain, that binds the antibody transmembrane domain that binds the extracellular domain and the intracellular signaling domain. In some aspects, the transmembrane domain comprises a transmembrane portion of a costimulatory molecule, such as a T-cell costimulatory molecule, e.g. eg, CD28 and / or 41BB. In some cases, the T cell costimulatory molecule is selected from the group consisting of CD28 and 41BB, and in some cases, the receptor includes CD28 and 41BB signaling domains.
[0149] [ 0079] Also provided are nucleic acids encoding the antibody (including fragments) of any of the instances or the receptor, e.g. eg, chimeric antigen receptor of either occurrence, vectors that include such nucleic acids, and cells that contain the vectors and / or nucleic acids, e.g. eg, for the expression of antibodies and / or molecules.
[0150] [ 0080] Therefore, cells and vectors are also provided to produce and express molecules, including antibodies and molecules such as receptors, e.g. g., chimeric antigen receptors (CARs). For example, genetically modified cells expressing the chimeric antigen receptor of either occurrence are provided. In some aspects, the cell is a T cell. In some aspects, the cell is a NK cell. In some respects, the cell is a stem cell.
[0152] [ 0081] Compositions comprising the antibodies, receptors, molecules and / or cells are also provided, including pharmaceutical compositions, e.g. g., which further includes pharmaceutically acceptable substances such as carriers.
[0154] [ 0082] Also provided are methods of administration, including methods of treatment, carried out by administering the cell, an antibody, receptor, composition, or other molecule, in any event, to a subject, e.g. eg, in an effective way, eg. eg, therapeutically effective amount. In some cases, the subject has or is suspected of having a CD19-associated disease or disorder, such as a B-cell malignancy, such as B-cell chronic lymphocytic leukemia (CLL), acute lymphocytic leukemia (ALL), pro-lymphocytic leukemias , hairy cell leukemias, common acute lymphocytic leukemias, null acute lymphoblastic leukemias, non-Hodgkin's lymphomas, diffuse large B-cell lymphomas (DLBCL), multiple myelomas, follicular lymphoma, splenic marginal zone lymphoma, mantle cell lymphoma, lymphoma of indolent B cells, or Hodgkin's lymphoma, or an autoimmune or inflammatory disease in which B cells are involved.
[0156] [ 0083] In some cases, the administration of the antibody or receptor is associated with a lower degree of immunogenicity compared to the administration of a reference antibody (or receptor containing the reference antibody) that competes for binding with the antibody or binds to an overlapping epitope. In some aspects, the reference antibody is a humanized, chimeric, or non-human antibody.
[0158] Brief description of the drawings
[0160] [0084]
[0162] Figure 1: Figures 1A and 1B show the results of a binding assay comparing the binding of exemplary human scFvs to CD19 expressing HEK293 cells compared to binding to HEK293 cells that do not express Cd 19. MFI = mean fluorescence intensity .
[0163] Figure 2 shows an SDS gel evaluating the purification of exemplary anti-CD19 antibodies (scFv fragments).
[0164] Figure 3: Figures 3A, 3B and 3C show results of studies evaluating the binding affinities of various exemplary scFv antibodies (scFv fragments), including anti-CD19 antibodies. MFI = mean fluorescence intensity.
[0165] Figure 4 shows the results of studies evaluating the binding affinities of various exemplary scFv antibodies, including anti-CD19 scFv antibody fragments. MFI = mean fluorescence intensity.
[0166] Figure 5: Figures 5A and 5B show the results of competitive binding assays, evaluating the binding of the respective labeled antibody in the presence of varying concentrations of competing antibodies. MFI = mean fluorescence intensity.
[0167] Figure 6 shows the results of competitive binding assays, which assess the binding of a labeled reference scFv antibody in the presence of varying concentrations of competing scFv antibodies. MFI = mean fluorescence intensity.
[0168] Figure 7: Figure 7A shows the results of size exclusion chromatography; A column was calibrated, standard proteins were injected, and fractions were collected to generate references.
[0169] Figure 7B shows the results after the injection of an anti-CD19 scFv (clone 18B) in the same column and the collection of the fraction under the same conditions.
[0170] Figure 8A shows the results of a binding assay evaluating the binding of exemplary human scFv clones to cells expressing CD19 in order from left to right as follows: cells only, mock supernatant (Moc. Supe.) Negative control antibody (Ctrl Neg.), Clone 18, Clones 200 to 287, cells only, Moc. Supe, Ctrl. Neg. and Clone 18. Examples of hits showing specific binding of CD19 (indicated by an asterisk) are (in order from left to right): Clone 213, Clone 227, Clone 241, Clone 255, Clone 272, Clone 278, Clone 283 and Clone 285. IFM = mean fluorescence intensity.
[0171] Figure 8B shows the results of a binding assay evaluating the binding of exemplary human scFv clones to cells expressing CD19 in order from left to right as follows: cells only, mock supernatant (Moc. Supe.) Negative control antibody (Ctrl Neg.), Clone 18B, Clones 300-387, cells only, Moc. Supe., Ctrl. Neg. and Clone 18B. Examples of hits showing specific binding of CD19 (indicated by an asterisk) are (in order from left to right): Clone 302, Clone 305, Clone 313, Clone 314, Clone 318, Clone 324, Clone 327, Clone 328, Clone 336, Clone 339, Clone 377, Clone 379 and Clone 382. IFM = mean fluorescence intensity.
[0172] Figure 8C shows the results of a binding assay evaluating the binding of exemplary human scFv clones to cells expressing CD19 in order from left to right as follows: cells only, mock supernatant (Moc. Supe.) Negative control antibody (Neg. Ctrl), Clone 18B, Clones 400-487, cells only, Moc. Supe., Ctrl. Neg. and Clone 18B. Examples of hits showing specific binding of CD19 (indicated by an asterisk) are (in order from left to right): Clone 440 and Clone 448.
[0173] Figure 8D shows the results of a binding assay comparing the binding of exemplary human scFvs with K562 cells expressing CD19 compared to K562 cells not expressing CD19. MFI = mean fluorescence intensity.
[0174] Figure 9 shows an SDS gel evaluating the purification of exemplary anti-CD19 antibodies (scFv fragments).
[0175] Figure 10: Figures 10A-E show results of separate binding assays evaluating the binding affinities of various exemplary scFv antibodies, including anti-CD19 scFv antibody fragments. MFI = mean fluorescence intensity.
[0176] Figure 11 shows the results of competitive binding assays, which evaluate the binding of a labeled reference scFv antibody in the presence of varying concentrations of competing scFv antibodies. MFI = mean fluorescence intensity.
[0177] Figure 12A shows the cell surface expression of the various CARs, in the VH-VL (HL) HL orientation; dark line) or VL-VH orientation (LH; gray line), in transduced CD8 + T cells measured by EGFRt expression for cells before enrichment (pre) and after enrichment after sorting with an anti-EGFR antibody and expansion by stimulation with CD19 + B-LCL (publication).
[0178] Figure 12B shows an SDS gel evaluating exemplary human anti-CD19 CAR expression in transduced primary human T cells.
[0179] Figures 13A and 13B show the cytolytic activity of primary human CD8 + T cells expressing various anti-CD19 specific CARs against CD19 expressing cells. C is EGFRt alone (negative control); FM is FMC63 scFv CAR, 18 is Clone 18 scFv CAR, 17 is Clone 17 scFv CAR, 76 is Clone 76 scFv CAR, 5 is Clone 5 scFv CAR, and 18B is Clone 18B scFv CAR.
[0180] Figures 14A and 14B show cytokine secretion from primary human CD8 + T cells expressing various anti-CD19 specific c Ar after coculture with CD19 expressing cells. C is EGFRt alone (negative control); FM is FMC63 scFv CAR, 18 is Clone 18 scFv CAR, 17 is Clone 17 scFv CAR, 76 is Clone 76 scFv CAR, 5 is Clone 5 scFv CAR, and 18B is Clone 18B scFv CAR.
[0181] Figure 15 shows cytokine secretion from primary human CD4 + T cells expressing various anti-CD19 specific CARs after co-culturing with CD19 expressing cells. C is EGFRt alone (negative control); FM is FMC63 scFv CAR, 18 is Clone 18 scFv CAR, 17 is Clone 17 scFv CAR, 76 is Clone 76 scFv CAR, 5 is Clone 5 scFv CAR, and 18B is Clone 18B scFv CAR.
[0182] Figures 16A and 16B show the proliferation of primary human CD8 + T cells or CD4 + T cells, respectively, expressing various anti-CD19 specific CARs against CD19 expressing cells after coculture with CD19 expressing cells.
[0183] Figure 17: Figure 17A shows the antitumor activity of primary human CD8 + T cells expressing various anti-CD19 specific CARs after administration to NSG mice grafted with Raji cells expressing firefly luciferase. Figure 17B shows the antitumor activity of primary human CD4 + and CD8 + T cells expressing various anti-CD 19 specific CARs and administered in a 1: 1 ratio to Raji cell-grafted NSG mice.
[0184] Figure 18: Figure 18A shows the amino acid sequence of a 74 residue or 75 residue near membrane region for each of the three different chimeric CD19 molecules. Below the three sequences shown in Figure 18A, each aligned position of the represented region in which the human and rhesus sequences contain an identical amino acid is marked with an asterisk ("*"). Positions where the rhesus sequence contains a non-identical but conservative amino acid substitution compared to the human sequence are marked with a ":". Positions where the rhesus sequence contains a non-identical but semi-conservative amino acid substitution compared to human sequences are marked with a ".". Positions where the rhesus sequence contains a non-identical, non-conservative / semi-conservative insertion or substitution compared to the human sequence are not marked with a symbol. Figure 18B shows the cytokine secretion of primary human CD8 + T cells expressing various anti-CD19 specific CARs after coculture with cells expressing human CD19, rhesus CD19 or chimeric rhesus / human CD19 molecules (V1, V2 or V3). C is EGFRt alone (negative control); FM is FMC63 scFv CAR, 18 is Clone 18 scFv CAR, 17 is Clone 17 scFv CAR, 76 is Clone 76 scFv CAR, 5 is Clone 5 scFv CAR, and 18B is Clone 18B scFv CAR.
[0186] Detailed description
[0188] [0085] Provided are CD19-binding molecules, including antibodies (including antigen-binding antibody fragments, such as single-chain fragments, including scFv) and recombinant receptors, including chimeric receptors that contain such antibodies and fragments, acids nucleic agents encoding such antibodies and fragments and cells, such as recombinant cells, expressing and for the production of these antibodies and fragments. Also provided are methods for making and using the antibodies and fragments, as well as cells expressing or containing the antibodies and fragments.
[0190] I. CD19-binding molecules
[0191] [0086] In some aspects, CD19-binding molecules are provided, such as CD19-binding polypeptides. Such binding molecules include antibodies that specifically bind to CD19, such as a human CD19 molecule, including its antigen-binding fragments. Also among the binding molecules are recombinant receptors such as chimeric antigen receptors that contain such antibodies.
[0193] A. CD19 antibodies
[0195] [0087] Anti-CD19 antibodies are provided, including functional antibody fragments, including those comprising a variable heavy chain and a variable light chain, such as scFv. Molecules containing such antibodies are also provided, e.g. eg, fusion proteins and / or recombinant receptors such as chimeric receptors, including antigen receptors. Among the provided anti-CD19 antibodies are human antibodies. In some cases, antibodies, such as human antibodies, specifically bind to a particular epitope or region of CD19, generally an epitope or extracellular region. In some cases, the antibodies bind to the same or similar epitope or region of CD19 bound by another antibody, such as one or more of the mouse antibodies, FMC63 or SJ25C1. In some cases, antibodies bind to an overlapping epitope of CD19 bound by one of these known antibodies and / or compete to bind with said antibody. Antibodies include isolated antibodies. Molecules include isolated molecules.
[0197] [0088] The term "antibody" herein is used in the broadest sense and includes both polyclonal and monoclonal antibodies, including intact antibodies , and antibody fragments (antigen binding) functional, including fragments of antigen binding (Fab) F (ab ') 2 fragments, Fab' fragments, Fv fragments, recombinant IgG fragments (rIgG), single chain antibody fragments, including single chain variable fragments (scFv), and single domain antibody fragments (e.g. ., sdAb, sdFv, nanobody). The term encompasses genetically and / or otherwise modified forms of immunoglobulins, such as intrabodies, peptibodies, chimeric antibodies, fully human antibodies, humanized antibodies, and heteroconjugate, multispecific antibodies, e.g. eg, bispecific, antibodies, diabodies, tribodies and tetrabodies, di-scFv in tandem, triscFv in tandem. Unless otherwise indicated, the term "antibody" is to be understood to include functional antibody fragments thereof. The term also encompasses intact or full-length antibodies, including antibodies of any class or subclass, including IgG and subclasses thereof, IgM, IgE, IgA, and IgD.
[0199] [0089] The terms "complementarity determining region" and "CDR," synonymous "hypervariable region" or "HVR", are known in the art to refer to non - contiguous amino acid sequences within antibody variable regions which they confer antigen specificity and / or binding affinity. In general, there are three CDRs in each heavy chain variable region (CDR-H1, CDR-H2, CDR-H3) and three CDRs in each light chain variable region (CDR-L1, CDR-L2, CDR-L3). The "framework regions" and "FR" are known in the art to refer to the non-CDR portions of the variable regions of the heavy and light chains. In general, there are four FRs in each full-length heavy chain variable region (FR-H1, FR-H2, f R-H3, and FR-H4), and four FRs in each full-length light chain variable region (FR-H -L1, FR-L2, FR-L3 and FR-L4).
[0201] [ 0090] The precise amino acid sequence boundaries of a given CDR or FR can easily be determined using any of a number of well-known schemes, including those described by Kabat et al. (1991), "Sequences of Proteins of Immunological Interest", 5th ed. Public Health Service, National Institutes of Health, Bethesda, MD ("Kabat" numbering scheme), Al-Lazikani et al., (1997) JMB 273,927-948 ("Chothia" numbering scheme), MacCallum et al., J Mol. Biol. 262: 732-745 (1996), "Antibody-antigen interactions: Contact analysis and binding site topography", J. Mol. Biol. 262, 732-745. ("Contact" numbering scheme), Lefranc MP et al., "IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains", Dev Comp Immunol, Jan 2003; 27 (1): 55-77 ("IMGT" numbering scheme), and Honegger A and Plückthun A, "Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool", J Mol Biol, 2001 Jun 8; 309 (3 ): 657-70, ("Aho" numbering scheme).
[0203] [ 0091] The limits of a given CDR or FR may vary depending on the scheme used for identification. For example, the Kabat schema is based on structural alignments, while the Chothia schema is based on structural information. The numbering of the Kabat and Chothia schemes is based on the sequence lengths of the most common antibody region, with insertions arranged by insertion letters, e.g. eg, "30a", and deletions that appear in some antibodies. The two schemes place certain inserts and deletions ("indels") at different positions, resulting in g in differential numbering. The contact scheme is based on the analysis of complex crystal structures and is similar in many respects to the Chothia numbering scheme.
[0205] [ 0092] Table 1, below, lists the exemplary position boundaries of CDR-L1, CDR-L2, CDR-L3 and CDR-H1, CDR-H2, CDRH3 identified by the Kabat, Chothia and Contact schemes, respectively. For CDR-H1, residue numbering is listed using the Kabat and Chothia numbering schemes. The FRs are located between CDR, p. eg, with FR-L1 located between CDR-L1 and CDR-L2, and so on. It is observed that because the Kabat numbering scheme shown places inserts in H35A and H35B, the end of the loop Chothia CDR-H1 when numbered using the Kabat numbering convention shown varies between H32 and H34, depending on the length of the loop.
[0207] Table 1
[0212] [0093] Therefore, unless otherwise a "CDR" or "determining region complementary" specify or CDR specified individual (p. G., "CDR-H1, CDR-H2), of a given antibody or region thereof, such as a variable region thereof, should be understood to encompass a complementary (or specific) determining region as defined in any of the above-mentioned schemes For example, when it is stated that a particular CDR (e.g. g., a CDR-H3) contains the amino acid sequence of a corresponding CDR in a given Vh or Vl amino acid sequence, it is understood that said CDR has a corresponding CDR sequence (eg, CDR-H3) within of the variable region, as defined by any of the aforementioned schemes In some cases, specified CDR sequences are specified.
[0214] [0094] In the same way, unless otherwise specified, a FR or FR (s) specified (s) Individual (s) (p. G., FR-H1, FR-H2), of a given antibody or region thereof, such as a variable region thereof, should be understood to encompass a framework (or specific) region defined by any of the known schemes. In some cases, the scheme for identifying a particular CDR, FR or FR or CDR is specified, such as the CDR defined by the Kabat, Chothia or Contact method. In other cases, the particular amino acid sequence of a CDR or FR is provided.
[0216] [ 0095] The term "variable region" or "variable domain" refers to the domain of an antibody heavy or light chain that is involved in the binding of the antibody to the antigen. The heavy chain and light chain variable domains (Vh and Vl, respectively) of a native antibody generally have similar structures, each domain comprising four framework regions (FRs) and three CDRs. (See, eg, Kindt et al. Kuby Immunology, 6th ed., WH Freeman and Co., page 91 (2007). A single Vh or Vl domain may be sufficient to confer antigen-binding specificity. In addition, Antibodies that bind a particular antigen can be isolated using a Vh or Vl domain of an antibody that binds to the antigen to select for a library of complementary Vl or Vh domains, respectively See, eg, Portolano et al., J. Immunol. 150: 880-887 (1993); Clarkson et al, Nature 352: 624-628 (1991).
[0218] [ 0096] Among the provided antibodies are antibody fragments. An "antibody fragment" refers to a molecule other than an intact antibody that comprises a portion of an intact antibody that binds to the antigen to which the intact antibody binds. Examples of antibody fragments include, but are not limited to, Fv, Fab, Fab ', Fab'-SH, F (ab') 2; diabodies; linear antibodies; single chain antibody molecules (eg, scFv); and multispecific antibodies formed from antibody fragments. In particular cases, the antibodies are single chain antibody fragments comprising a variable heavy chain region and / or a variable light chain region, such as scFv.
[0220] [ 0097] Single domain antibodies are antibody fragments that comprise all or a portion of the heavy chain variable domain or all or part of the light chain variable domain of an antibody. In certain cases, a single domain antibody is a human single domain antibody.
[0222] [ 0098] Antibody fragments can be made by various techniques, including, but not limited to proteolytic digestion of an intact antibody as well as production by recombinant host cells. In some cases, antibodies are recombinantly produced fragments, such as fragments comprising non-naturally occurring arrangements, such as those with two or more antibody regions or chains linked by synthetic linkers, e.g. eg, peptide linkers, and / or which may not be produced by enzymatic digestion of an intact naturally occurring antibody. In some aspects, the antibody fragments are scFv.
[0224] [ 0099] A "humanized" antibody is an antibody in which all or substantially all of the CDR amino acid residues are derived from non-human CDRs and all or substantially all of the FR amino acid residues are derived from human FRs. A humanized antibody can optionally include at least a portion of an antibody constant region derived from a human antibody. A "humanized form" of a non-human antibody refers to a variant of the non-human antibody that has been humanized, typically to reduce immunogenicity in humans, while retaining the specificity and affinity of the non-parent human antibody. In some cases, some FR residues in a humanized antibody are replaced with corresponding residues from a non-human antibody (eg, the antibody from which the CDR residues are derived), e.g. eg, to restore or improve the specificity or affinity of the antibody.
[0226] [ 0100] Among the provided anti-CD19 antibodies are human antibodies. A "human antibody" is an antibody with an amino acid sequence that corresponds to that of an antibody produced by a human or human cell, or a non-human source that uses human antibody repertoires or other sequences that encode human antibodies, including libraries of human antibodies. The term excludes humanized forms of non-human antibodies that comprise non-human antigen-binding regions, such as those in which all or substantially all of the CDRs are non-human.
[0228] [ 0101] Human antibodies can be prepared by administering an immunogen to a transgenic animal that has been modified to produce intact human antibodies or intact antibodies with human variable regions in response to antigen challenge. Such animals typically contain all or a portion of human immunoglobulin loci, which replace endogenous immunoglobulin loci, or which are extrachromosomally present or randomly integrated into the chromosomes of the animal. In such transgenic animals, the endogenous immunoglobulin loci have generally been inactivated. Human antibodies can also be derived from human antibody libraries, including phage display and cell-free libraries, containing antibody-encoding sequences derived from a human repertoire.
[0230] [ 0102] Among the antibodies provided are monoclonal antibodies, including monoclonal antibody fragments. The term "monoclonal antibody" as used herein refers to an antibody obtained from or within a population of substantially homogeneous antibodies, that is, the individual antibodies that comprise the population are identical, except for possible variants that contain natural mutations. or arising during the production of a monoclonal antibody preparation, said variants generally being present in minor amounts. Unlike polyclonal antibody preparations, which typically include different antibodies directed against different epitopes, each monoclonal antibody in a monoclonal antibody preparation is directed against only one epitope on an antigen. The term should not be construed as requiring the production of the antibody by any particular method. A monoclonal antibody can be prepared by a variety of techniques, including, but not limited to, generation from a hybridoma, recombinant DNA methods, phage display, and other antibody display methods.
[0232] [ 0103] The terms "polypeptide" and "protein" are used interchangeably to refer to a polymer of amino acid residues, and are not limited to a minimum length. Polypeptides, including provided antibodies and antibody chains and other peptides, e.g. eg, linkers and CD19-binding peptides, can include amino acid residues that include natural and / or non-natural amino acid residues. The terms also include post-expression modifications of the polypeptide, e.g. eg, glycosylation, sialylation, acetylation, phosphorylation, and the like. In some aspects, polypeptides may contain modifications from a native or natural sequence, as long as the protein maintains the desired activity. These modifications can be deliberate, such as by site-directed mutagenesis, or they can be accidental, such as by host mutations that produce the proteins or errors due to PCR amplification.
[0234] Exemplary anti-CD19 antibodies
[0236] [0104] In some cases, the anti-CD19 antibody, e.g. g., antigen-binding antibody fragment, contains in particular heavy and / or light chain CDR sequences and / or light and / or heavy chain variable region sequences (Vh or Vl). Also among the provided antibodies are those that have sequences at least or about 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to said sequence.
[0238] [ 0105] In some cases, the antibody, e.g. g., antigen-binding fragment thereof, includes a determining region 3 heavy chain complementarity (CDR-H3) comprising an amino acid sequence of a CDR-H3 present in a reference antibody, such as one present in a reference antibody having a VH region with the amino acid sequence established in SEQ ID NO: 11, 12, 60, 61, 63 62, 167 or 185, as established in SEQ ID NO: 11, 12, 60, 61,63 or 62. In some cases, CDR-H3 comprises SEQ ID NO: 20. In some cases, the antibody, e.g. g., its antigen-binding fragment, has a Vh region that has at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity with (or 100% identity with her) the amino acid sequence of the VH region of the reference antibody, as the set of amino acid sequences of the VH region in SEQ ID NO: 11, 12, 60, 61, 6362, 167 or 185, as established in SEQ ID NO: 11, 12, 60, 61, 63 or 62.
[0240] [ 0106] In some cases, CDR-H1 contains the amino acid sequence DYAMH (SEQ ID NO: 18), CDR-H2 contains the amino acid sequence GISWNSGRIG (SEQ ID NO: 81), GISWNSGSIG (SEQ ID NO: 82), the amino acid sequence indicated in SEQ ID NO: 19 (GISWNSGRIGYADSVKG), or the amino acid sequence established in SEQ ID NO: 72 (GISWNSGSIGYADSVKG), and / or the CDR-H3 contains the amino acid sequence of SEQ ID NO: 20.
[0242] [ 0107] In some cases, the provided antibody contains a CDR-H3 having the amino acid sequence of SEQ ID NO: 20.
[0244] [ 0108] In some cases, the antibody contains a Vh that has the amino acid sequence set forth in SEQ ID NO: 11 or 12, or has a sequence at least at or about 90, 91, 92, 93, 94, 95, 96 , 97, 98 or 99% identical to said sequence. In some cases, the antibody, e.g. eg, its antigen-binding fragment contains a VH region having the amino acid sequence set forth in SEQ ID NO: 11, 12, 60, 61, 63 or 62, or a sequence at least at or about 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% identical to such a sequence. In some cases, the antibody, e.g. g., its antigen-binding fragment, contains a VH region having the amino acid sequence set forth in SEQ ID NO: 11, 12, 60, 61, 63, 62, 167 or 185, or a sequence at least at or about 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% identical to said sequence.
[0246] [ 0109] In some cases, the antibody contains the sequence of residues 1-119 of SEQ ID NO: 11,12, 60, 61,63, 62, 167 or 185 or a sequence comprising the part of SEQ ID NO: 11, 12, 60, 61,63, 62, 167 or 185 which include the first three framework regions and the three heavy chain CDRs. In some cases, the antibody contains the sequence of residues 1-119 of SEQ ID NO: 11,12, 60, 61, 63 or 62 or a sequence comprising the part of SEQ ID NO: 11, 12, 60, 61 , 63, or 62 which include the first three framework regions and the three heavy chain CDRs.
[0248] [ 0110] In some cases, the anti-CD19 antibody includes light chain complementarity to determine regions 1, 2, and / or 3 (CDR-L1, CDR-L2, and / or CDR-L3), respectively, which have the amino acid sequences of CDR sequences 1, 2 and / or 3 contained within the amino acid sequence of the light chain variable region (Vl) established in SEQ ID NO: 13, 14, 15, 16, 17, 71 , 65, 64, 66, 70, 69, 67, 90, 91 or 187-205, as set forth in SEQ ID NO: 13, 14, 15, 16 or 17, or in SEQ ID NO: 13, 14, 15, 16, 17, 71, 90, 91,68, 65, 64, 66, 70, 69 or 67.
[0250] [ 0111] In some cases, the anti-CD19 antibody includes a CDR-L1, CDR-L2 and / or CDR-L3 in which:
[0252] [0112] In some cases, CDR-L1 contains the amino acid sequence: X1X2X3X4X5X6X7X8X9X10X11X12X13X14 (SEQ ID NO: 110), where X1 is T, W, S, or R; X2 is G or A; X3 is I, T, D, or S; X4 is S, R, T, or Q; X5 is null or S; X6 is null, D, N, or G; X7 is null, V or L; Xa is X or null; Xg is X or null; X10 is X; X11 is X; X12 is Y, F, D, or W; X13 is V, A, or L and X14 is S, N, or A. For example, in some cases, CDR-L1 contains the amino acid sequence of X1X2X3X4X5X6X7X8X9X10X11X12X13X14 (SEQ ID NO: 226), where X1 is T, Q , S or R; X2 is G, A, or E; X3 is I, T, A, D, or S; X4 is S, R, TQ, G or I; X5 is null, S, R or T; X6 is G, D, N or null; X7 is null, V, L or I; X8 is D, G, I, L, S, or null; X9 is S, G, A, I, D, R or null; X10 is H, Y, F, S, or N; X11 is R, N, D, H, Y, or T; X12 is Y, F, D, W, H, T, or S; X13 is V, A, or L; and X14 is S, N, or A. In some cases, CDR-L1 contains the amino acid sequence X1X2X3X4X5X6X7X8X9X10X11X12X13X14 (SEQ ID NO: 111), where X1 is T, Q, S, or R; X2 is G or A; X3 is I, T, D, or S; X4 is S, R, T, or Q; X5 is null or S; X6 is G, D, N or null; X7 is null, V or L; X8 is D, G, I, L, S, or null; X9 is S, G, A, I, R or null; X10 is H, Y, F, S, or N; X11 is R, N, D, H, or Y; X12 is Y, F, D, or W; X13 is V, A, or L; and X14 is S, N, or A.
[0254] [ 0113] In some cases, CDR-L2 contains the amino acid sequence of X1X2X3X4X5X6X7 (SEQ ID NO: 227), where X1 is D, S, or G; X2 is F, V, N, K, or A; X3 is S, T, D, or N; X4 is K, V, N, Q, or R; X5 is R, V, or L; X6 is P, K, A, or E; and X7 is S, P, A or T. In some cases, CDR-L2 contains the amino acid sequence of X1X2X3X4X5X6X7 (SEQ ID NO: 112), where X1 is D or S; X2 is F, V, N, K, or A; X3 is S, T, D, or N; X4 is K, V, N, Q, or R; X5 is R, V, or L; X6 is P, K, A, or E; and X7 is S, P, A, or T.
[0256] [ 0114] In some cases, CDR-L3 contains the amino acid sequence of X1X2X3X4X5X6X7XaXgX1oX11X12 (SEQ ID NO: 228), where X1 is S, G, T, A, Q, C, or N; X2 is S, Q, A, or T; X3 is Y, S, W, R; X4 is A, D, R, T, or Y; X5 is A, S, P, G, N, or D; X6 is I, S, G, T, A, L, H, R, or N; X7 is S, P, L, Y, G; X8 is P, T, S, Q, M, R, N or null; X9 is S, L, N, A, M, R or null; X10 is L, D, or null; X11 is Y, W, F, V, A, or L; and X12 is V, T, P, or L. In some cases, CDR-L3 contains the amino acid sequence of X1X2X3X4X5X6X7XaXgX1oX11X12 (SEQ ID NO: 115), where X1 is X; X2 is S, Q, A, or T; X3 is Y, S, W, R; X4 is A, D, R, T, or Y; X5 is X; X6 is X; X7 is S, P, L, Y, G; X8 is X or null; X9 is X or null; X10 is L or null; X11 is X; and X12 is V, T or L. For example, in some cases, the antibody has a CDR-L3 comprising the amino acid sequence X1X2X3X4X5X6X7XaXgX1oX11X12 (SEQ ID NO: 114), where X1 is S, G, T, A, Q , With; X2 is S, Q, A, or T; X3 is Y, S, W, R; X4 is A, D, R, T, or Y; X5 is A, S, P, G, N, or D; X6 is I, S, G, T, A, L, H, R, N; X7 is S, P, L, Y, G; X8 is P, T, S, Q, M, R, N or null; X9 is S, L, N, A, M, or null; X10 is L or null; X11 is Y, W, F, V, A, or L; and X12 is V, T, or L.
[0258] [0115] In some cases, in CDR-L1, as set forth in SEQ ID NO: 110, 226, or 111, X3 is I, T, or S; X4 is S, T, or Q; X8 is D, G, I, S, or null; X9 is S, G, I or null; X10 is H, Y, S, or N; X11 is R, N, D, or H; X12 is Y or D; and X13 is V or L; and / or in CDR-L2, as set forth in SEQ ID NO: 227 or 112, X1 is D; X4 is K, V, N, Q, or R; X6 is P, K, or A; and X7 is S, A, or T; and / or in CDR-L3, as set forth in SEQ ID NO: 228, 114 or 115, X1 is S, G, T, A, Q, C or N; X5 is A, S, P, G, N, or D; Xa is I, S, G, T, A, L, H, R, or N; X8 is P, T, S, Q, M, R, N or null; X9 is S, L, N, A, M, or null; and X11 is Y, W, F, V, A, or L. In some cases, in the CDR-L3, X1 is S, G, Q, or N; X2 is S, Q, or T; X4 is A, D, T, or Y; X5 is A, S, or G; and Xe is I, S, N, R, A, H, or T.
[0260] [ 0116] In some cases, the antibody includes an amino acid sequence that contains a CDR-L1 set forth in SEQ ID NO: 83, a CDR-L2 set forth in SEQ ID NO: 84 and / or a CDR-L3 set forth in SEQ ID NO: 85.
[0262] [ 0117] In some cases, the antibody, e.g. For example, the antibody fragment contains a CDR-L1 that contains the amino acid sequence set forth in SEQ ID NO: 21, 25, 28, or 31. In some cases, the antibody or fragment contains a CDR-L1 that contains the sequence of amino acids established in SEQ ID NO: 80, 77, 74, 73, 75, 79, 78, 76, 21,25, 28, 31 or 146 to 152, as it contains the amino acid sequence established in SEQ ID NO: 80 , 77, 74, 73, 75, 79, 78, 76, 21, 25, 28 or 31. In some cases, the antibody or fragment contains a CDR-L1 that contains the amino acid sequence established in SEQ ID NO: 80, 77, 74, 73, 78, 21 or 28.
[0264] [ 0118] In some cases, the antibody or fragment contains a CDR-L2 that contains the amino acid sequence established in SEQ ID NO: 22, 26, 29 or 32. In some cases, the antibody or fragment contains a CDR-L2 that contains the amino acid sequence SEQ ID NO: 100, 97, 94, 93, 95, 99, 98, 96, 22, 26, 29, 32 or 153 to 157, as it contains the amino acid sequence established in SEQ ID NO: 100, 97, 94, 93, 95, 99, 98, 96, 22, 26, 29 or 32. In some cases, the antibody or fragment contains a CDR-L2 that contains the amino acid sequence established in SEQ ID NO: 100, 97, 94, 93, 98, 22, or 29.
[0266] [ 0119] In some cases, the antibody or fragment contains a CDR-L3 that includes the sequence established in SEQ ID NO: 23, 24, 27, 30 or 33. In some cases, the antibody or fragment contains a CDR-L3 that includes the sequence established in SEQ ID NO: 109, 106, 103, 101, 104, 108, 107, 105, 102, 23, 24, 27, 30, 33, 158 or 159, as it contains the amino acid sequence established in SEQ ID NO: 109, 106, 103, 101, 104, 108, 107, 105, 102, 23, 24, 27, 30 or 33. In some cases, the antibody or fragment contains a CDR-L3 that includes the established sequence in SEQ ID NO: 109, 106, 103, 101, 107, 24 or 30.
[0268] [ 0120] In some cases, CDR-L1, CDR-L2 and CDR-L3 contain the sequences of SEQ ID NO: 21, 22 and 23, respectively; CDR-L1, CDR-L2 and CDR-L3 include the sequences of SEQ ID NO: 21, 22 and 24, respectively; CDR-L1, CDR-L2 and CDR-L3 include the sequences of SEQ ID NO: 25, 26 and 27, respectively; CDR-L1, CDR-L2 and CDR-L3 contain the sequences of SEQ ID NO: 28, 29 and 30, respectively; or CDR-L1, CDR-L2 and CDR-L3 contain the sequences of SEQ ID NO: 31, 32 and 33, respectively.
[0270]
[0272] respectively.
[0273] [ 0122] Also provided are antibodies that have sequences at least or about 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to such sequences.
[0275] [ 0123] In some cases, CDR-H1, CDR-H2, and CDR-H3 comprise the sequences of SEQ ID NOs: 18, 81, and 20, respectively; CDR-H1, CDR-H2 and CDR-H3 comprise the sequences of SEQ ID NO: 18, 19 and 20, respectively; CDR-H1, CDR-H2 and CDR-H3 comprise the sequences of SEQ ID NO: 18, 82 and 20, respectively; or CDR-H1, CDR-H2 and CDR-H3 comprise the sequences of SEQ ID NO: 18, 72 and 20, respectively.
[0277] [ 0124] Also provided are antibodies that have sequences at least or about 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to such sequences.
[0279] [ 0125] In some cases, the VH region of the antibody or fragment comprising the amino acid sequence of SEQ ID NO: 11, 12, 60, 61, 6362, 167 or 185, such as SEQ ID NO: 11, 12, 60, 61, 63 or 62; and / or the VL region of the antibody or fragment comprising the amino acid sequence of SEQ ID NO: 13, 14, 15, 16, 17, 71, 90, 91, 68, 65, 64, 66, 70, 6967 or 187 to 205, such as SEQ ID NO: 13, 14, 15, 16, 17, 71, 90, 91,68, 65, 64, 66, 70, 69 or 67. In some cases, the VH region of the antibody or fragment comprising the amino acid sequence of SEQ ID NO: 11.60, 63 or 62; and / or the VL region of the antibody or fragment comprising the amino acid sequence of SEQ ID NO: 14, 16, 71, 90, 65, 64, or 69.
[0281] [ 0126] Also provided are antibodies that have sequences at least at or about 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to such sequences.
[0283] [ 0127] In some cases, the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 12 and 17, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 12 and 15, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 11 and 13, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 11 and 14, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 11 and 16, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 63 and 71, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 62 and 68, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of s Eq ID NO: 11 and 65, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 60 and 64, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 61 and 66, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 63 and 70, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 62 and 69, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of s Eq ID NO: 12 and 67, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 12 and 91, respectively; or the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 63 and 90, respectively. In some cases, the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 11 and 14, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of s Eq ID NO: 11 and 16, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 63 and 71, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 11 and 65, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 60 and 64, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 62 and 69, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of s Eq ID NO: 63 and 90, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 167 and 207, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 168 or 63 and 208, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 169 or 11 and 209, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 170 or 61 and 210, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 171 or 61 and 211, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 172 and 212, respectively; the VH and VL regions of the antibody or fragment comprise amino acid sequences of SEQ ID NO: 173 or 11 and 213, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 174 or 11 and 214, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 175 or 11 and 215, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 176 or 61 and 216, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 177 or 61 and 217, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 178 or 61 and 218, respectively; the VH and VL regions of the antibody or fragment comprise the sequences of amino acids of SEQ ID NO: 179 or 61 and 219, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 180 or 12 and 220, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 181 or 12 and 221, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 182 or 11 and 222, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 183 or 60 and 223, respectively; the VH and VL regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NO: 184 or 11 and 224, respectively; or the VH and Vl regions of the antibody or fragment comprise the amino acid sequences of SEQ ID NOs: 185 and 225, respectively.
[0285] [ 0128] Also provided are antibodies that have sequences at least at or about 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to such sequences.
[0287] [ 0129] In some cases, the antibody or fragment contains a Vh region that includes the amino acid sequence of s Eq ID NO: 11 or 12 or residues 1-119 of said sequence or a sequence that is at least at or about 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% identical to said sequence.
[0289] [ 0130] In some cases, the antibodies include or may further include a V1 region that includes the amino acid sequence of SEQ ID NO: 13, 14, 15, 16, 17, or a sequence that is at least or about 90, 91 , 92, 93, 94, 95, 96, 97, 98 or 99% identical to said sequence.
[0291] [ 0131] In some cases, the antibody is a single chain antibody fragment, such as a scFv or diabody. In some cases, the single chain antibody includes one or more linkers that join two antibody domains or regions, such as a variable heavy chain (Vh) region and a variable light chain (Vl). The linker is typically a peptide linker, e.g. eg, a flexible and / or soluble peptide linker. Among the linkers are those rich in glycine and serine and / or in some cases threonine. In some cases, the linkers further include charged residues such as lysine and / or glutamate, which can improve solubility. In some cases, the linkers further include one or more of proline.
[0293] [0132] Accordingly, single chain antibody fragments are also provided, such as scFv and diabodies, in particular human single chain fragments, which normally comprise linker (s) of binding of two antibody domains or regions, such as Vh and Vl domains. . The linker is typically a peptide linker, e.g. g., a flexible and / or soluble peptide linker, such as one rich in glycine and serine.
[0295] [ 0133] In some aspects, glycine and serine (and / or threonine) rich linkers include at least 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% of such amino acids (s). In some cases, they include at least or about 50%, 55%, 60%, 70%, or 75% glycine, serine, and / or threonine. In some cases, the linker is composed substantially entirely of glycine, serine, and / or threonine. Linkers are generally between about 5 and about 50 amino acids in length, typically between about 10 and about 30, e.g. e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30, and in some examples between 10 and 25 amino acids in length. Exemplary linkers include linkers that have multiple repeat numbers of the sequence GGGGS (4GS; SEQ ID NO: 123) or GGGS (3GS; SEQ ID NO: 122), such as between 2, 3, 4, and 5 repeats of said sequence. . Exemplary linkers include those that have or consist of a sequence set forth in SEQ ID NO: 34 (GGGGSGGGGSGGGGS). Exemplary linkers further include those that have or consist of the sequence set forth in SEQ ID NO: 43 (GSTSGSGKPGSGEGSTKG).
[0297] [ 0134] Accordingly, in some cases, single-stranded fragments are also provided, eg. eg, scFv, comprising one or more of the above-mentioned linkers, such as glycine / serine rich linkers, including linkers having GGGS (SEQ ID NO: 122) or GGGGS (SEQ ID NO: 123) repeats, such as the linker indicated as SEQ ID NO: 34. In some cases, the linker has an amino acid sequence that contains the indicated sequence SEQ ID NO: 34.
[0299] [ 0135] The fragment, p. eg, scFv, may include a Vh region or a part thereof, followed by the linker, followed by a Vl or parts thereof. The fragment, p. eg, the scFv, may include the Vl, followed by the linker, followed by the Vh.
[0301] [ 0136] In some aspects, the scFv has the amino acid sequence in SEQ ID NO: 2, 4, 6, 8, or 10, or has a sequence of at least or about 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% identical to such a sequence.
[0303] [ 0137] In some aspects, the scFv has the amino acid sequence set forth in SEQ ID NO: 2, 4, 6, 8, 10, 45, 47, 49, 51, 53, 55, 57, 59, 87, or 89 , or has a sequence of at least or about 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% identical to said sequence.
[0305] [ 0138] In some aspects, the scFv has the amino acid sequence set forth in SEQ ID NO: 2, 4, 6, 8, 10, 45, 47, 49, 51, 53, 55, 57, 59, 87, 89, or 207 to 225 or has a sequence at least at or about 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% identical to said sequence.
[0307] [ 0139] In some aspects, the scFv contains the VH, the linker, and the VL as set forth in SEQ ID NO: 2, 4, 6, 8, 10, 45, 47, 49, 51, 53, 55, 57, 59, 8789, or 207 to 225, or a sequence at least at or about 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to that sequence, but in which VH and VL are configured in the opposite orientation, ie VL-VH, compared to that sequence.
[0309] [ 0140] The antibody, e.g. eg, antibody fragment, may contain at least a portion of an immunoglobulin constant region, such as one or more constant region domains. In some cases, the constant regions include a light chain constant region and / or a heavy chain constant region 1 (CH1). In some cases, the antibody includes a CH2 and / or CH3 domain, such as an Fc region. In some cases, the Fc region is an Fc region from a human IgG, such as IgG1 or IgG4.
[0311] [ 0141] In some cases, any of the above antibodies, eg. eg, antibody fragments, is human. For example, provided herein are human anti-CD19 antibodies that specifically bind to CD19, just as they specifically bind to human CD19.
[0313] [ 0142] In some cases of a provided human anti-CD 19 antibody, the human antibody contains a Vh region that contains a portion that has at least 95%, 96%, 97%, 98%, 99%, or 100% identity. sequence with an amino acid sequence encoded by a germline nucleotide human heavy chain V segment, a portion with at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of amino acids encoded by a germline nucleotide human heavy chain D segment, and / or a portion that has at least 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence encoded by a germline nucleotide human heavy chain J segment; and / or contains a Vl region that contains a portion with at least 95%, 96%, 97%, 98%, 99% or 100% identity to an amino acid sequence encoded by a nucleotide V segment of the kappa germline human or lambda chain, and / or a portion with at least 95%, 96%, 97%, 98%, 99% or 100% identity to an amino acid sequence encoded by a J segment of the human lambda or kappa chain of germ line nucleotides. In some cases, the part of the Vh region corresponds to CDR-H1, CDR-H2 and / or CDR-H3. In some cases, the part of the Vh region corresponds to the framework region 1 (FR1), FR2, FR2 and / or FR4. In some cases, the part of the V1 region corresponds to CDR-L1, CDR-L2 and / or CDR-L3. In some cases, the part of the Vl region corresponds to FR1, FR2, FR2 and / or Fr 4.
[0315] [ 0143] In some cases, the human antibody contains a CDR-H1 that has at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with an amino acid sequence of the CDR- region. Corresponding H1 within a sequence encoded by a germline nucleotide human heavy chain V segment. For example, the human antibody in some cases contains a CDR-H1 that has a sequence that is 100% identical or with no more than one, two, or three amino acid differences compared to the corresponding CDR-H1 region within an encoded sequence. by a V segment of the human germline nucleotide heavy chain.
[0317] [ 0144] In some cases, the human antibody contains a CDR-H2 that has at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with an amino acid sequence of the CDR- region. Corresponding H2 within a sequence encoded by a germline nucleotide human heavy chain V segment. For example, the human antibody in some cases contains a CDR-H2 that has a sequence that is 100% identical or no more than one, two, or three amino acids apart compared to the corresponding CDR-H2 region within an encoded sequence. by a V segment of the human germline nucleotide heavy chain.
[0319] [ 0145] In some cases, the human antibody contains a CDR-H3 that has at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with an amino acid sequence of the CDR region. Corresponding -H3 within a sequence encoded by a V segment, D segment, and J segment of the human germline nucleotide heavy chain. For example, the human antibody in some cases contains a CDR-H3 that has a sequence that is 100% identical or with no more than one, two, or three amino acid differences compared to the corresponding CDR-H3 region within an encoded sequence. by a V segment, D segment and J segment of the human germline nucleotide heavy chain.
[0321] [ 0146] In some cases, the human antibody contains a CDR-L1 that has at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with an amino acid sequence of the CDR region. Corresponding -L1 within a sequence encoded by a germline nucleotide human light chain V segment. For example, the human antibody in some cases contains a CDR-L1 that has a sequence that is 100% identical or with no more than one, two, or three amino acid differences compared to the corresponding CDR-L1 region within an encoded sequence. by a V segment of the human germline nucleotide light chain.
[0323] [ 0147] In some cases, the human antibody contains a CDR-L2 that has at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with an amino acid sequence of the CDR region. Corresponding -L2 within a sequence encoded by a germline nucleotide human light chain V segment. By For example, the human antibody in some cases contains a CDR-L2 that has a sequence that is 100% identical or no more than one, two, or three amino acids apart compared to the corresponding CDR-L2 region within a sequence encoded by a V segment of the human germline nucleotide light chain.
[0325] [ 0148] In some cases, the human antibody contains a CDR-L3 that has at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with an amino acid sequence of the CDR- region. Corresponding L3 within a sequence encoded by a V segment and a J segment of the human germline nucleotide light chain. For example, the human antibody in some cases contains a CDR-L3 that has a sequence that is 100% identical or with no more than one, two, or three amino acid differences compared to the corresponding CDR-L3 region within an encoded sequence. by a V segment and J segment of the human germline nucleotide light chain.
[0327] [ 0149] In some cases, the human antibody contains a framework region containing human germline gene segment sequences. For example, in some cases, the human antibody contains a Vh region in which the framework region, e.g. e.g., FR1, FR2, f R3, and FR4, have at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with a framework region encoded by a germline antibody segment human, such as a V and / or J segment. In some cases, the human antibody contains a V1 region in which the framework region, e.g. e.g., FR1, FR2, FR3, and FR4, have at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a framework region encoded by a human germline antibody segment , such as a V and / or segment. For example, in some such cases, the framework sequence of the Vh V and / or L sequence differs by no more than 10 amino acids, such as no more than 9, 8, 7, 6, 5, 4, 3, 2 or 1 amino acids, compared to the framework region encoded by a human germline antibody segment.
[0329] [ 0150] The antibody, e.g. eg, antibody fragment, may contain at least a portion of an immunoglobulin constant region, such as one or more constant region domains. In some cases, the constant regions include a light chain constant region and / or a heavy chain constant region 1 (CH1). In some cases, the antibody includes a CH2 and / or CH3 domain, such as an Fc region. In some cases, the Fc region is an Fc region from a human IgG, such as IgG1 or IgG4.
[0331] [ 0151] Also provided are nucleic acids encoding the antibodies and / or moieties, e.g. eg, strings, of the same. Among the nucleic acids provided are those encoding the anti-CD19 antibodies described herein. Nucleic acids can include those that encompass natural and / or non-natural nucleotides and bases, e.g. eg, including those with modifications to the main structure. The terms "nucleic acid molecule", "nucleic acid" and "polynucleotide" can be used interchangeably and refer to a polymer of nucleotides. Such nucleotide polymers can contain natural and / or non-natural nucleotides and include, but are not limited to, DNA, RNA, and PNA. "Nucleic acid sequence" refers to the linear sequence of nucleotides that the nucleic acid or polynucleotide molecule comprises. Examples of nucleic acids and vectors are those that have the sequences established as SEQ ID NO: 1, 3, 5, 7, 9, 44, 46, 48, 50, 52, 54, 56, 58, 86 and 88, and portions encoding CDRs thereof, as well as sequences containing at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% identity therewith. The nucleic acid may encode an amino acid sequence comprising the Vl and / or an amino acid sequence comprising the Vh of the antibody (eg, the light and / or heavy chains of the antibody).
[0333] [ 0152] Vectors containing the nucleic acids are also provided, host cells containing the vectors, e.g. eg, for the production of antibodies. Methods for producing the antibodies are also provided. In a further case, one or more vectors (eg, expression vectors) comprising said nucleic acid are provided. In a further case, a host cell comprising said nucleic acid is provided. In one of these cases, a host cell comprises (eg, has been transformed with): (1) a vector comprising a nucleic acid encoding an amino acid sequence comprising the Vl of the antibody and an amino acid sequence comprising comprises the Vh of the antibody, or (2) a first vector comprising a nucleic acid encoding an amino acid sequence comprising the Vl of the antibody and a second vector comprising a nucleic acid encoding an amino acid sequence comprising the Vh of the antibody. In some cases, a method of preparing the anti-CD19 antibody is provided, wherein the method comprises culturing a host cell comprising a nucleic acid encoding the antibody, as provided above, under conditions suitable for expression of the antibody and , optionally, recovering the antibody from the host cell (or host cell culture medium).
[0335] [ 0153] Methods for the preparation of anti-CD 19 antibodies (including antigen-binding fragments) are also provided. For the recombinant production of the anti-CD 19 antibody, the nucleic acid encoding an antibody, e.g. For example, as described above, it can be isolated and inserted into one or more vectors for cloning and / or further expression in a host cell. Such nucleic acid can be easily isolated and sequenced using standard procedures (eg, using oligonucleotide probes that are capable of specifically binding to genes encoding the heavy and light chains of the antibody).
[0337] [ 0154] In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeasts are suitable cloning or host expression hosts for vectors encoding the antibody, including fungi and yeast strains whose glycosylation pathways have been modified to mimic or approximate those of human cells, resulting in the production of an antibody with a partially or fully human glycosylation pattern. See Gerngross, Nat. Biotech. 22: 1409-1414 (2004) and Li et al., Nat. Biotech. 24: 210-215 (2006).
[0339] [ 0155] Examples of eukaryotic cells that can be used to express polypeptides include, but are not limited to, COS cells, including Os 7 cells; 293 cells, including 293-6E cells; CHO cells, including CHO-S, DG44. Lec13 CHO cells and FUT8 CHO cells; PER.C6® cells; and NSO cells. In some cases, the heavy and / or light chains of the antibody can be expressed in yeast. See, p. eg, US Publication No. US 2006/0270045 A1. In some cases, a particular eukaryotic host cell is selected based on its ability to make desired post-translational modifications to heavy chains and / or light chains. For example, in some cases, CHO cells produce polypeptides that have a higher level of sialylation than the same polypeptide produced in 293 cells.
[0341] [ 0156] In some cases, the antibody is produced in a cell-free system. Examples of cell-free systems are described, e.g. eg, in Sitaraman et al., Methods Mol. Biol. 498: 229-44 (2009); Spirin, Trends Biotechnol. 22: 538-45 (2004); Endo et al., Biotechnol. Adv. 21: 695-713 (2003).
[0343] [ 0157] The provided examples further include vectors and host cells and other expression systems for expressing and producing the antibodies and other binding proteins, including eukaryotic and prokaryotic host cells, including bacteria, filamentous fungi and yeast, as well as mammalian cells such as human cells, as well as cell-free expression systems.
[0345] Example Features
[0347] [0158] In some aspects, the provided antibodies, including antigen-binding fragments, have one or more specified functional characteristics, such as binding properties, including binding to particular epitopes, such as epitopes that are similar to or overlap with of other antibodies, the ability to compete for binding with other antibodies and / or particular binding affinities.
[0349] [ 0159] In some cases, the antibodies specifically bind to the CD19 protein. In some aspects of any of the cases herein, CD19 refers to human CD19. Generally, the observation that an antibody or other binding molecule binds to CD19 or binds specifically to CD19 does not necessarily mean that it binds to CD19 of all species. For example, in some cases, the characteristics of CD19 binding, such as the ability to specifically bind to it and / or compete to bind it with a reference antibody, and / or to bind with a particular affinity or compete in a Particular degree, in some cases, refers to the capacity with respect to the human CD19 protein and many of the antibodies do not have this characteristic with respect to a CD19 of another species, such as the monkey or the mouse.
[0351] [ 0160] In some cases, the provided antibodies, including antigen-binding fragments, bind to human CD19, such as an epitope or region of human CD19, such as human CD19 exposed at 92 (Accession No. P15391), or an allelic variant or a splice variant thereof. In certain cases, the anti-CD19 antibody binds to a CD19 epitope that is conserved among CD19s of different species. In some cases, the anti-CD19 antibody binds to an epitope of CD19 that is not conserved or completely conserved between c D19 of different species, such as between humans and Macaca mulatta (rhesus (rhesus) macaque) CD19.
[0353] [ 0161] In some cases, the antibody binds to an epitope that contains one or more amino acids within (or is entirely within) an extracellular domain of a CD19 and / or within (or is entirely within) a proximal region. to the membrane of the extracellular portion of CD19. In some cases, the antibody binds to an epitope that contains one or more amino acids within, or is entirely within, the Ig-like domain 2 of CD19, a portion encoded by the fourth exon of CD19, a portion corresponding to positions 176 -277 of the human CD19 sequence established in SEQ ID NO: 92, and / or the membrane closest to 100, 90, 80, 75, 70, 65, 60, 55, 50, 45, 44, 43, 43, 41 or 40 amino acids of the extracellular portion of CD19. In some cases, such a portion or domain is required for the binding of the antibody to CD19. In some cases, the epitope contains (or additionally contains) one or more amino acids that are within, or are completely within, the Ig-like domain 1 of CD19, a portion encoded by the second exon of CD19, and / or a portion corresponding to positions 20-117 of the human CD19 sequence established in SEQ ID NO: 92. In some cases, said portion or domain is necessary for the binding of the antibody against CD19. In some cases, the antibody specifically binds to a peptide that comprises or consists of or consists essentially of the sequence of such a portion and does not contain the complete full-length CD19 sequence.
[0355] [ 0162] In some cases, the epitope contains one or more amino acids within, is within, or includes a portion of CD19 corresponding to residues 218 to 249 of the human CD19 sequence set in SEQ ID NO: 92, such as a part having the sequence set forth in SEQ ID NO: 143.
[0357] [ 0163] In some cases, the epitope includes an amino acid at a position corresponding to one or more of the CD19 positions that correspond to the following amino acids at the following positions in the sequence of Human CD19 set forth in SEQ ID NO: 92: histidine (H) at position 218, alanine (A) at position 236, methionine (M) at position 242, glutamate (E) at position 243, proline (P) at position 249, and / or lysine (K) and / or serine (s) at positions 223 and 224. In some cases, an amino acid at one or more of these positions is important or necessary for the binding of the antibody against CD19. In some cases, the amino acid in the epitope at one or more positions corresponds to the amino acid at the respective position in the human sequence of CD19 set forth in SEQ ID NO: 92.
[0359] [ 0164] In some cases, the epitope includes an amino acid (such as a histidine) at a CD19 position corresponding to histidine at position 218 of the human CD19 sequence set forth in SEQ ID NO: 92; in some cases, said amino acid is important for the binding of the antibody to CD19.
[0361] [ 0165] In some cases, the epitope includes an amino acid (eg, an alanine) at a position on CD19 corresponding to alanine at position 236 of the human CD19 sequence set forth in SEQ ID NO: 92; in some cases, said amino acid is important for the binding of the antibody to CD19.
[0363] [ 0166] In some cases, the epitope includes an amino acid (eg, a methionine) at a CD19 position corresponding to the methionine at position 242 of the human CD19 sequence set forth in SEQ ID NO: 92; in some cases, said amino acid is important for the binding of the antibody to CD19.
[0365] [ 0167] In some cases, the epitope includes an amino acid (such as a glutamate) at a CD19 position corresponding to glutamate at position 243 of the human CD19 sequence set forth in SEQ ID NO: 92; in some cases, said amino acid is important for the binding of the antibody to CD19.
[0367] [ 0168] In some cases, the epitope includes an amino acid (such as proline) at a CD19 position corresponding to proline at position 249 of the human CD19 sequence set forth in SEQ ID NO: 92; in some cases, said amino acid is important for the binding of the antibody to CD19.
[0369] [ 0169] In some cases, the epitope contains amino acid (s) (such as lysine and / or serine) at one or two positions corresponding to lysine and / or serine at positions 223 and 224 of the human CD19 sequence. set forth in SEQ ID NO: 92; in some cases, such amino acids are important for the binding of the antibody to CD19.
[0371] [ 0170] In some cases, the epitope is the same as, similar to, overlapping with, or contains one or more of the same amino acids as an epitope that is specifically bound by a reference antibody, such as FMC63 or SJ25C1. In some cases, the same one or more amino acids is important for the binding of the provided antibody and the reference antibody.
[0373] [ 0171] In some cases, the degree of binding of an anti-CD19 antibody to an unrelated non-CD19 protein, such as non-human CD19 or other non-CD19 protein, is less than about 40% of the binding of the anti-CD19 antibody. measured human, e.g. g., by radioimmunoassay (RIA). In some instances, antibodies provided include antibodies in which the binding to a non-human CD19 protein or other non-CD19 protein is less than or about 30%, less than or about 20%, or less than or about 10% of the binding of the antibody against human CD19.
[0375] [ 0172] In some cases, such properties of provided antibodies, including antigen-binding fragments, are described in relation to properties observed for another antibody, e.g. eg, a reference antibody. In some cases, the reference antibody is a non-human anti-CD 19 antibody, such as a murine or chimeric or humanized anti-CD 19 antibody. In some aspects, the reference antibody is the antibody designated FMC63 or the antibody designated SJ25C1 (see, eg, Zola H et al., Immunol Cell Biol. 1991 Dec; 69 (Pt 6): 411-22; Patent US 7,446,190), and / or a fragment derived therefrom such as a scFv fragment thereof, and / or an antibody containing the Vh and Vl sequences of such an antibody and / or the heavy and light chain CDRs of such an antibody.
[0377] [ 0173] For example, in some cases, the reference antibody has a Vh region that contains the set of sequences set forth in SEQ ID NO: 39 or 41, or comprises CDR1, CDR2 and / or CDR3 within such a sequence, and / or has a Vl that contains the sequence established in SEQ ID NO: 40 or 42, or comprises CDR1, CDR2 and / or CDR3 within said sequence. Thus, in some cases, the antibody competes to bind and / or binds to itself or an overlapping CD19 epitope such as FMC63 or SJ25C1 or an antigen-binding fragment thereof.
[0379] [ 0174] In some cases, the reference antibody has a sequence present in an antibody or portion thereof as described herein. For example, in some cases, the reference antibody has an amino acid sequence of the light chain variable region (Vl) set out in SEQ ID NO: 13, 14, 15, 16 or 17 and / or set out in SEQ ID NO: 13, 14, 15, 16, 17, 71, 90, 91, 68, 65, 64, 66, 70, 69 or 67, and / or has a heavy chain (VH) variable region set out in SEQ ID NO: 11 , 12, 60, 61, 63 or 62. In some cases, the antibody has CDR 1, 2 and / or 3 heavy and / or light chain present in said antibody. In some cases, the reference antibody can be a scFv containing the amino acid sequence established in SEQ ID NO: 2, 4, 6, 8, 10, 45, 47, 49, 51, 53,55, 57, 59, 87 or 89.
[0380] [ 0175] However, in some cases, the antibody contains heavy and light chain CDRs that are distinct from the CDRs present in the reference antibody or antibodies, such as FMC63 and SJ25C1. For example, among the provided antibodies are those that compete to bind and / or bind to the same or overlapping CD19 epitopes as those bound by a reference antibody or antibody, but which nonetheless contain different CDRs, e.g. g., different heavy and / or light chains of CDR1, CDR2 and c DR3. In some cases, the provided antibody contains heavy and light chain CDRs that are distinct from the CDRs present in the antibody designated FMC63, such as those present in the VH region set out in SEQ ID NO: 39 and / or the VL region set out in SEQ ID NO: 40. In some cases, the provided antibody contains heavy and light chain CDRs that are different from the CDRs present in the antibody designated SJ25C1, such as those present in the VH region set forth in SEQ ID NO: 41 and / or the VL region established in SEQ ID NO: 42.
[0382] [ 0176] For example, in some cases, the antibody specifically binds to an epitope that overlaps the CD19 epitope bound by a reference antibody, such as antibodies that bind to the same or a similar epitope as the reference antibody. . In some cases, the antibody competes to bind CD19 with the reference antibody.
[0384] [ 0177] In some cases, antibodies show a binding preference for CD19 expressing cells compared to CD19 negative cells, such as particular cells known in the art and / or described herein. In some cases, binding preference is observed when a significantly higher degree of binding is measured to cells that express CD19, compared to those that do not express. In some cases, the change in the degree of binding detected, e.g. For example, measured by mean fluorescence intensity in an assay based on flow cytometry and / or dissociation constant or EC50, to cells that express CD19 compared to cells that are not c D 19 that express cells, is al less than or about 1.5, 2, 3, 4, 5, 6 or more, and / or is about as large, about the same, at least as large, or at least about as large, or greater than the times change observed for the reference antibody, as the corresponding form of the reference antibody. In some cases, the total degree of binding observed to CD19 or CD19-expressing cells is approximately the same, at least as great or greater than that observed for the reference antibody. In any of the cases provided, comparison of binding properties, such as affinities or competition, can be done by measurement by the same or a similar test.
[0386] [ 0178] An antibody "competes for binding" to CD19 with a reference antibody if it competitively inhibits the binding of the reference antibody to CD19, and / or if the reference antibody competitively inhibits the antibody's binding to CD19. An antibody competitively inhibits the binding of a reference antibody to an antigen if the presence of the excess antibody detectably inhibits (blocks) the binding of the other antibody to its antigen. A particular degree of inhibition can be specified.
[0388] [ 0179] In some cases, adding excess antibody, e.g. eg, a 1.2, 5, 10, 50, or 100-fold excess, compared to the amount or concentration of the reference antibody, inhibits antigen binding by the reference antibody (or vice versa). In some cases, the inhibition of binding is at least 50% and, in some cases, at least 75%, 90%, or 99%. In some aspects, competitive inhibition is measured in a competitive binding assay (see, eg, Junghans et al., Cancer Res. 1990: 50: 1495-1502).
[0390] [ 0180] In some cases, when the reference antibody is present at a concentration of 10 nM, the provided antibody inhibits the binding of the reference antibody with an IC50 of less than or about 100, 50, 40, 30, 25, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, or 10 nM, or less than at or about 9, 8, 7, 6, or 5 nM. In some cases, when the provided antibody is present at a concentration of 10 nM, the reference antibody inhibits the binding of the provided antibody with an IC50 of less than or about 100, 50, 40, 30, 25, 20, 19, 18 , 17, 16, 15, 14, 13, 12, 11, or 10 nM, or less than at or about 9, 8, 7, 6, or 5 nM.
[0392] [ 0181] In some cases, the competitive inhibition of reference antibody binding by the provided antibody (or vice versa) is to or about or at least to or about the same degree as the degree of competitive inhibition of reference antibody binding to reference by the reference antibody itself, e.g. eg, unlabeled reference antibody. In some cases, the provided antibody inhibits the binding of the reference antibody, such as the binding of FMC63 or SJ25C1, to human CD19 by at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%. Competitive inhibition assays are known and include ELISA-based, flow cytometry-based, and RIA-based assays. In some aspects, competitive inhibition assays are carried out by incorporating an excess of an unlabeled form of one of the antibodies and evaluating its ability to block the binding of the other antibody, which is labeled with a detectable marker, such that the degree Binding and reduction thereof can be assessed by detecting the tag or marker.
[0394] [ 0182] In some cases, two antibodies specifically bind to the same epitope if all or essentially all amino acid mutations in the antigen that reduce or eliminate the binding of one antibody reduce or eliminate the binding of the other antibody. In some cases, two antibodies specifically bind to an overlapping epitope if at least some of the amino acid mutations in the antigen that reduce or eliminate binding to the antigen by one antibody also reduce or eliminate the binding to the antigen by the other antibody. .
[0395] [ 0183] In some cases, the antibodies provided are capable of binding to CD19, such as human CD19, with at least some affinity, as measured by any of a number of known methods. In some cases, the affinity is represented by a dissociation constant (Kd); in some cases, the affinity is represented by EC50. In certain cases, the binding affinity (EC50) and / or the dissociation constant of the antibody against CD19 is equal to or less than 100 nM, 50 nM, 40 nM, 30 nM, 25 nM, 20 nM, 19, 18, 17 , 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 nM, such as between a or about 1 nM and at or about 15 nM, e.g. eg, between at or about 5 and at or about 10 nM. In one case, the degree of binding of an anti-CD19 antibody to an unrelated non-CD19 protein is less than or about 10% of the measured antibody's binding to CD19, e.g. g., by radioimmunoassay (RIA).
[0397] [ 0184] In some aspects, the affinity is to or about the same degree or substantially the same degree of affinity compared to the reference antibody, such as a murine CD19 antibody, for example FMC63 or SJ25C1. In some aspects, the affinity is at least 80, 85, 90, 95, or 99% the same as that of the reference antibody. In some cases, the binding affinity is compared to the corresponding form of the reference antibody.
[0399] [ 0185] In some cases, the antibody has an affinity, e.g. eg, EC50 or Kd, approximately equal to or less than that of the reference antibody, as the corresponding form of the reference antibody, e.g. eg, not more than about 1.5 times or not more than about 2 times greater, not more than 3 times greater and / or not more than 10 times greater than the EC50 of the reference antibody, e.g. eg, measured in the same test or in a similar test.
[0401] [ 0186] The anti-CD19 antibodies provided herein can be identified, selected, or characterized for their physical / chemical properties and / or biological activities by various known assays. In one aspect, the antibody is tested for its antigen-binding activity, e.g. eg, by known methods such as ELISA, Western blotting and / or flow cytometric assays, including cell-based binding assays, e.g. g., evaluating the binding of the antibody (eg, conjugated to a fluorescent marker or labeled) to a cell expressing the target antigen, eg. g., CD19, in some cases compared to results using cells that do not express the target antigen, eg. eg, CD19. The binding affinity can be measured as Kd or EC50.
[0403] [ 0187] Competition assays can be used to identify an antibody that competes with any of the antibodies described herein. Assays for mapping epitopes bound by the reference antibodies and antibodies can also be used and are known.
[0405] Immunoconjugates
[0407] [0188] In some cases, the antibody is or is part of an immunoconjugate, where the antibody is conjugated to one or more heterologous molecules, such as, but not limited to, a cytotoxic agent, an imaging agent, a detectable moiety a multimerization domain or other heterologous molecule. Cytotoxic agents include, but are not limited to, radioactive isotopes (eg, At211, 131I, 125I, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212, and radioactive Lu isotopes); chemotherapeutic agents (eg, methotrexate, adriamycin, vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin, melphalan, mitomycin C, chlorambucil, daunorubicin, or other intercalating agents); growth inhibiting agents; enzymes and fragments thereof such as nucleolytic enzymes; antibiotic toxins such as small molecule toxins or enzymatically active toxins. In some cases, the antibody is conjugated to one or more cytotoxic agents, such as chemotherapeutic agents or drugs, growth inhibitory agents, toxins (eg, protein toxins, enzymatically active toxins of bacterial, fungal, plant or animal origin, or fragments thereof), or radioactive isotopes.
[0409] [ 0189] Immunoconjugates include antibody-drug conjugates (ADCs), in which an antibody is conjugated to one or more drugs, including but not limited to a maytansinoid (see US Patent Nos. 5,208,020 , 5,416,064 and European Patent EP 0425235 B1); an auristatin such as DE and DF monomethylauristatin drug moieties (MMa E and MMAF) (see US Patent Nos. 5,635,483 and 5,780,588 and 7,498,298); a dolastatin; a calicheamicin or derivative thereof (see US Patent Nos. 5,712,374, 5,714,586, 5,739,116, 5,767,285, 5,770,701, 5,770,710, 5,773,001, and 5,877,296; Hinman et al., Cancer Res.
[0410] 53: 3336-3342 (1993); and Lode et al., Cancer Res. 58: 2925-2928 (1998)); an anthracycline such as daunomycin or doxorubicin (see Kratz et al., Current Med. Chem. 13: 477-523 (2006); Jeffrey et al., Bioorganic & Med. Chem. Letters 16: 358-362 (2006); Torgov and col., Bioconj. Chem. 16: 717-721 (2005); Nagy et al., Proc. Natl. Acad. Sci. USA 97: 829-834 (2000); Dubowchik et al., Bioorg. & Med. Chem. Letters 12: 1529-1532 (2002); King et al., J. Med. Chem. 45: 4336-4343 (2002); and US Patent No. 6,630,579); methotrexate; vindesine; a taxane such as docetaxel, paclitaxel, larotaxel, tesetaxel, and ortataxel; a trichothecene; and CC1065.
[0412] [ 0190] Also among the immunoconjugates are those in which the antibody is conjugated to an enzymatically active toxin or fragment thereof, including, but not limited to diphtheria A chain, non-binding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modecin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII and PAP-S), inhibitor from momordica charantia, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogelin, restrictocin, phenomycin, enomycin and trichothecenes.
[0413] [ 0191] Also among immunoconjugates are those in which the antibody is conjugated to a radioactive atom to form a radioconjugate. Exemplary radioactive isotopes include At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212, and radioactive isotopes of Lu.
[0415] [ 0192] Conjugates of an antibody and the cytotoxic agent can be made using any of a number of known protein coupling agents, e.g. eg, linkers, (see Vitetta et al, Science 238: 1098 (1987)), WO94 / 11026. The linker can be a "cleavable linker" that facilitates the release of a cytotoxic drug into the cell, such as acid-labile linkers, peptidase-sensitive linkers, photolabile linkers, dimethyl linkers, and disulfide-containing linkers (Chari et al., Cancer Res. 52: 127-131 (1992); US Patent No. 5,208,020).
[0417] [ 0193] Conjugates can also include fusion proteins such as Fc fusions and chimeric molecules.
[0418] Multispecific antibodies
[0420] [0194] In certain cases, CD19 binding molecules, e.g. eg, the antibodies are multispecific. Multispecific binding molecules include multispecific antibodies, including, e.g. eg, bispecific. Multispecific binding partners, e.g. Eg, antibodies have binding specificities for at least two different sites, which may be on the same or different antigens. In certain cases, one of the binding specificities is for CD19 and the other is for another antigen. In certain cases, bispecific antibodies can bind to two different epitopes on CD19. Bispecific antibodies can also be used to localize cytotoxic agents in cells expressing CD19. Bispecific antibodies can be prepared as full-length antibodies or antibody fragments. Bispecific antibodies include multispecific single chain antibodies, e.g. eg, diabodies, tri-bodies, and tetrabodies, di-scFv in tandem and tri-scFv in tandem. Also provided are chimeric multispecific receptors, such as multispecific CARs, which contain the antibodies.
[0422] [0195] Exemplary additional antigens include other B cell specific antigens and T cell expressed antigens. Exemplary antigens include CD4, CD5, CD8, CD14, CD15, CD20, CD21, CD22, CD23, CD25, CD33, CD37, CD38 , CD40, CD40L, CD46, CD52, CD54, CD74, CD80, CD126, CD138, B7, MUC-1, LA, HM1.24, HLA-DR, tenascin, angiogenesis factor, VEGF, PIGF, ED-B fibronectin , an oncogene, an oncogene product, CD66a-d, necrosis antigens, li, IL-2, T101, TAC, IL-6, TRAIL-R1 (DR4) and TRAIL-R2 (DR5).
[0424] Variants
[0426] [0196] In certain cases, the antibodies include one or more amino acid variations, e.g. g., substitutions, deletions, insertions, and / or mutations, compared to the sequence of an antibody described herein. Exemplary variants include those designed to enhance the binding affinity and / or other biological properties of the antibody. Variants of the amino acid sequence of an antibody can be prepared by making appropriate modifications to the nucleotide sequence encoding the antibody, or by peptide synthesis. Such modifications include, e.g. eg, deletions and / or insertions and / or substitutions of residues within the amino acid sequences of the antibody. Any combination of deletion, insertion and substitution can be performed to arrive at the final construct, as long as the final construct possesses the desired characteristics, e.g. eg, antigen binding.
[0428] [ 0197] In certain cases, the antibodies include one or more amino acid substitutions, e.g. g., compared to an antibody sequence described herein and / or compared to a sequence from a natural repertoire, eg. eg, the human repertoire. Sites of interest for substitutional mutagenesis include CDRs and FRs. Amino acid substitutions can be introduced into an antibody of interest and the products can be screened for a desired activity, e.g. eg, retained / enhanced antigen binding, decreased immunogenicity, enhanced half-life, and / or enhanced effector function, such as the ability to promote antibody dependence. Cellular cytotoxicity (ADCC) or complement-dependent cytotoxicity (CDC). In some cases, the antibody variant exhibits retained or enhanced binding to CD19.
[0430] [ 0198] In some cases, one or more residues within a CDR of a parental antibody (eg a humanized or human antibody) is / are substituted. In some cases, the substitution is made to revert a sequence or position in the sequence to a germline sequence, such as an antibody sequence found in the germline (eg, human germline), e.g. eg, to reduce the likelihood of immunogenicity, eg. eg, after administration to a human subject.
[0432] [ 0199] In some cases, alterations are made in CDR "hot spots", codon-encoded residues that undergo high-frequency mutation during the somatic maturation process (see, eg, Chowdhury, Methods Mol Biol 207 : 179-196 (2008)), and / or antigen-contacting residues, with the resulting Vh or Vl variant tested for binding affinity. Affinity maturation by secondary library construction and reselection has been described, e.g. eg, in Hoogenboom et al. in Methods in Molecular Biology 178: 1-37 (O'Brien et al., ed., Human Press, Totowa, NJ, (2001)). In some cases of affinity maturation, introduces diversity into the variable genes chosen for maturation by any of a variety of methods (eg, error-prone PCR, strand shuffling, or oligonucleotide-directed mutagenesis). Then a secondary library is created. The library is then screened to identify any antibody variant with the desired affinity. Another method of introducing diversity involves CDR-targeted approaches, in which several CDR residues are randomized (eg, 4-6 residues at a time). CDR residues involved in antigen binding can be specifically identified, e.g. eg, using alanine screening or modeling mutagenesis. CDRH3 and CDR-L3 in particular are often targeted.
[0434] [ 0200] In certain cases, substitutions, insertions or deletions may occur within one or more CDRs provided that such alterations do not substantially reduce the ability of the antibody to bind antigen. For example, conservative alterations (eg, conservative substitutions as provided herein) that do not substantially reduce binding affinity can be made on CDRs. Such alterations can, e.g. g., be out of the residues in contact with the antigen in the CDRs. In certain cases of the variant sequences Vh and Vl provided above, each CDR is unaltered or does not contain more than one, two, or three amino acid substitutions.
[0436] [ 0201] Amino acid sequence insertions include amino and / or carboxyl terminal fusions that vary in length from one residue to polypeptides containing one hundred or more residues, as well as single or multiple amino acid residue intrasequence insertions. Examples of terminal insertions include an antibody with an N-terminal methionyl residue. Other insertion variants of the antibody molecule include fusion to the N- or C-terminus of the antibody to an enzyme or polypeptide that increases the serum half-life of the antibody.
[0437] Modifications
[0439] [0202] In certain cases, the antibody is altered to increase or decrease the degree to which the antibody is glycosylated, e.g. eg, by removing or inserting one or more glycosylation sites by altering the amino acid sequence and / or by modifying the oligosaccharide (s) attached to the glycosylation sites, e.g. . eg, using certain cell lines. Glycosylation sites include heavy chain 297 asparagine (according to Kabat numbering).
[0441] [ 0203] Examples of modifications, variants, and cell lines are described, e.g. eg, in Patent Publication Nos. US 2003/0157108, US 2004/0093621, US 2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614; US 2002/0164328; US 2004/0093621; US 2004/0132140; US 2004/0110704; US 2004/0110282; US 2004/0109865; WO 2003/085119; WO 2003/084570; WO 2005/035586; WO 2005/035778; WO2005 / 053742; WO2002 / 031140; Okazaki et al. J. Mol. Biol. 336: 1239-1249 (2004); Yamane-Ohnuki et al. Biotech. Bioeng. 87: 614 (2004). Ripka et al. Arch. Biochem. Biophys. 249: 533-545 (1986); US Patent Application No. US 2003/0157108 A1, Presta, L; and WO 2004/056312 A1, YamaneOhnuki et al. Biotech. Bioeng. 87: 614 (2004); Kanda, Y. et al., Biotechnol. Bioeng., 94 (4): 680-688 (2006); and WO2003 / 085107); WO 2003/011878 (Jean-Mairet et al.); US Patent No. 6,602,684 (Umana et al.); and US 2005/0123546 (Umana et al.); WO 1997/30087 (Patel et al.); WO 1998/58964 (Raju, S.); and WO 1999/22764 (Raju, S.).
[0443] [ 0204] Modified antibodies include those that have one or more amino acid modifications in the Fc region, such as those that have a human Fc region sequence or another portion of a constant region (eg, an Fc region human IgG1, IgG2, IgG3 or IgG4) comprising an amino acid modification (eg, a substitution) at one or more amino acid positions.
[0445] [ 0205] Such modifications can be made, e.g. eg, to improve half-life, alter binding to one or more types of Fc receptors, and / or alter effector functions.
[0447] [ 0206] Also among the variants are cysteine-engineered antibodies such as "thioMAbs" and other cysteine-modified variants, in which one or more residues of an antibody are substituted with cysteine residues, in order to generate reactive thiol groups on the accessible sites, p. eg, for use in the conjugation of agents and linkers, to produce immunoconjugates. Cysteine modified antibodies are described, e.g. eg, in US Patent Nos. 7,855,275 and 7,521,541.
[0449] [ 0207] In some cases, antibodies are modified to contain additional non-protein moieties, including water soluble polymers. Exemplary polymers include, but are not limited to, polyethylene glycol (PEG), ethylene glycol / propylene glycol copolymers, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinylpyrrolidone, poly-1,3-dioxolane, poly-1,3,6-trioxane, copolymer ethylene / maleic anhydride, polyamino acids (homopolymers or random copolymers), and dextran or poly (n-vinylpyrrolidone) polyethylene glycol, propropylene glycol homopolymers, polypropylene oxide / ethylene oxide copolymers, polyoxyethylene polyols (e.g., blends of polyvinyl alcohol, and polyvinyl alcohol blends (e.g., blends of polyvinyl alcohol) Polyethylene glycol propionaldehyde may have manufacturing advantages due to its stability in water. The polymer may have any molecular weight and may be branched or unbranched. The number of polymers attached to the antibody may vary, and whether more binds of a polymer, they can be the same or different molecules.In general, the number and / or type of polymers used for derivatization can be determined based on In consideration of considerations that include, but are not limited to, the particular properties or functions of the antibody to be enhanced, whether the antibody derivative will be used in a therapy under defined conditions, etc.
[0451] B. Recombinant receptors
[0453] [0208] Among the provided CD19-binding molecules are recombinant receptors, such as antigen receptors and other chimeric receptors, that specifically bind to CD19, such as receptors containing the provided anti-CD19 antibodies, e.g. eg, antibody fragments. Among the antigen receptors are functional antigen receptors other than TCRs, such as chimeric antigen receptors (CARs). Also provided are cells expressing the recombinant receptors and uses thereof in adoptive cell therapy, such as the treatment of diseases and disorders associated with the expression of CD19.
[0455] Exemplary antigen receptors, including CARs, and methods for manipulating and introducing such receptors into cells include those described, e.g. e.g. in international patent application publication numbers WO200014257, WO2013126726, WO2012 / 129514, WO2014031687, WO2013 / 166321, WO2013 / 071154, WO2013 / 123061 US patent application publication Nos US2002131960, US2013287748, US20130149337, US Patent Nos: 6,451,995, 7,446,190, 8,252,592, 8,339,645, 8,398,282, 7,446,179, 6,410,319, 7,070,995, 7,265,209, 7,354,762, 7,446,191, 8,324,353, and 8,479,118, and European patent application number EP2537416 and / or those described by Sadelain et al., Cancer Discov. April 2013; 3 (4): 388-398; Davila et al. (2013) PLoS ONE 8 (4): e61338; Turtle et al., Curr. Opin. Immunol. 2012 Oct; 24 (5): 633-39; Wu et al., Cancer, 2012 Mar 18 (2): 160-75. In some aspects, antigen receptors include a CAR as described in US Patent No. 7,446,190, and those described in International Patent Application Publication No. WO / 2014055668 A1. Examples of the c Ar include the CARs which are described in any of the publications mentioned above, such as WO2014031687, US 8,339,645, US 7,446,179, US 2013/0149337, US Patent No.: 7,446,190, US Patent No. 8,389,282, p. g., and wherein the antigen-binding portion, eg. eg, scFv, is replaced by an antibody, eg. eg, as provided herein.
[0457] [ 0210] Among the chimeric receptors are chimeric antigen receptors (CARs). Chimeric receptors, such as CARs, generally include an extracellular antigen-binding domain that includes, is, or is comprised within one of the provided anti-CD19 antibodies. Thus, chimeric receptors, e.g. g., CAR, typically include in their extracellular portions one or more CD19-binding molecules, such as one or more antigen-binding fragments, domains or portions, or one or more variable domains of antibody and / or antibody molecules, such as those described in this document. In some cases, the CAR includes a CD19-binding portion or portions of the antibody molecule, such as a variable heavy chain (Vh) region and / or variable light chain (Vl) region of the antibody, e.g. eg, a scFv antibody fragment.
[0459] [ 0211] CARs targeting CD19 are described, e.g. eg, by Kochenderfer et al., 2013, Nature Reviews Clinical Oncology, 10, 267-276 (2013); Wang et al. (2012) J. Immunother. 35 (9): 689-701; and Brentjens et al., Sci Transl Med.
[0460] 2013 5 (177). See also WO2014031687, US 8,339,645, US 7,446,179, US 2013/0149337, US Patent No.: 7,446,190 and US Patent No.: 8,389,282.
[0462] [ 0212] In some cases, the recombinant receptor, such as a CAR, such as the antibody portion thereof, which further includes a spacer, which may be or include at least a portion of an immunoglobulin constant region or a variant or modified version thereof, such as a hinge region, e.g. eg, an IgG4 hinge region and / or a CH1 / CL and / or Fc region. In some aspects, the constant region portion serves as a spacer region between the antigen-recognition component, e.g. eg, scFv, and the transmembrane domain. The spacer may be of a length that provides greater responsiveness of the cell after antigen binding, compared to the absence of the spacer. In some examples, the spacer is about 12 amino acids long or no more than 12 amino acids long. Exemplary spacers include those that have at least about 10 to 229 amino acids, about 10 to 200 amino acids, about 10 to 175 amino acids, about 10 to 150 amino acids, about 10 to 125 amino acids, about 10 to 100 amino acids, about 10 to 75 amino acids. , about 10 to 50 amino acids, about 10 to 40 amino acids, about 10 to 30 amino acids, about 10 to 20 amino acids, or about 10 to 15 amino acids, and including any integer between the end points of any of the listed ranges. In some cases, a spacer region is about 12 amino acids or less, about 119 amino acids or less, or about 229 amino acids or less. Exemplary spacers include IgG4 hinge alone, IgG4 hinge linked to CH2 and CH3 domains, or IgG4 hinge linked to CH3 domain. Exemplary spacers include, but are not limited to, those described in Hudecek et al. (2013) Clin. Cancer Res., 19: 3153, International Patent Application Publication No. WO2014031687, US Patent No. 8,822,647 or Published Application No. US2014 / 0271635.
[0464] [ 0213] In some cases, the constant region or portion is from a human IgG, such as IgG4 or IgG1. In some cases, the spacer has the sequence ESKYGPPCPPCP (established in SEQ ID NO: 124), and is encoded by the sequence established in SEQ ID NO: 125. In some cases, the spacer has the sequence established in SEQ ID NO: 126 In some cases, the spacer has the sequence established in SEQ ID NO: 127. In some cases, the constant region or portion is IgD. In some cases, the spacer has the sequence established in SEQ ID NO: 128. In some cases, the spacer has an amino acid sequence that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95 %, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 124, 126, 127 or 128.
[0466] [ 0214] The antigen recognition domain is generally bound to one or more intracellular signaling components, such as signaling components that mimic activation through an antigen receptor complex, such as a TCR complex, in the case of a CAR, and / or signal through another cell surface receptor. Thus, in some cases, the CD19-specific binding component (eg, antibody) binds to one or more transmembrane and intracellular signaling domains. In some cases, the transmembrane domain is fused with the extracellular domain. In one case, a transmembrane domain is used that is naturally associated with one of the domains in the receptor, e.g. eg, CAR. In some cases, the transmembrane domain is selected or modified by amino acid substitution to avoid binding of these domains to the transmembrane domains of the same membrane surface proteins or of different proteins to minimize interactions with other members of the receptor complex. .
[0468] [ 0215] The transmembrane domain in some cases is derived from a natural or synthetic source. When the source is natural, the domain in some respects is derived from any membrane-bound or transmembrane protein. Transmembrane regions include those derived from (i.e., comprise at least the transmembrane region or regions of) the alpha, beta or zeta chain of the T cell receptor, c D28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD 16, CD22, CD33, CD37, CD64, CD80, CD86, CD 134, CD137, CD 154 and / or transmembrane regions that contain functional variants thereof such as those that retain a substantial part of the structural properties, e.g. eg, transmembrane thereof. In some cases, the transmembrane domain is a transmembrane domain derived from CD4, CD28, or CD8, e.g. eg, CD8alpha, or a functional variant thereof. In some cases, the transmembrane domain in some cases is synthetic. In some aspects, the synthetic transmembrane domain predominantly comprises hydrophobic residues such as leucine and valine. In some aspects, a phenylalanine, tryptophan, and valine triplet will be found at each end of a synthetic transmembrane domain. In some cases, the binding is via linkers, spacers, and / or transmembrane domain (s).
[0470] [ 0216] Among the intracellular signaling domains are those that mimic or approximate a signal through a natural environment of the antigen receptor, a signal through such a receptor in combination with a costimulatory receptor, and / or a signal through a costimulatory receptor alone. In some cases, a short oligo or polypeptide linker, e.g. eg, a linker between 2 and 10 amino acids in length, such as one containing glycines and the serines, e.g. The glycine-serine doublet, eg, is present and forms a bond between the transmembrane domain and the cytoplasmic signaling domain of CAR.
[0472] [ 0217] The receiver, p. For example, CAR, generally includes at least one intracellular signaling component or components. In some cases, the receptor includes an intracellular component of a TCR complex, such as a CD3 chain of TCR that mediates T-cell activation and cytotoxicity, e.g. eg, the CD3 zeta chain. Thus, in some aspects, the CD19-binding antibody is bound to one or more cell signaling modules. In some cases, cell signaling modules include the CD3 transmembrane domain, CD3 intracellular signaling domains, and / or other CD transmembrane domains. In some cases, the receiver, e.g. eg, CAR, further includes a portion of one or more additional molecules such as the receptor and of Fc, CD8, CD4, CD25 or CD16. For example, in some aspects, CAR includes a chimeric molecule between CD3-zeta (CDS-Z) or Fc receptor and and CD8, CD4, CD25, or CD16.
[0474] [ 0218] In some cases, after CAR ligation, the cytoplasmic domain or intracellular signaling domain of CAR activates at least one of the functions or responses of the immune cell, e.g. eg, normal effectors, T cells designed to express CAR. For example, in some contexts, CAR induces a T cell function, such as cytolytic activity or Thelper activity, such as cytokine secretion or other factors. In some cases, a truncated portion of an intracellular signaling domain of an antigen receptor component or costimulatory molecule is used in place of an intact immunostimulatory chain, e.g. eg, if it transduces the signal of the effector function. In some cases, the intracellular signaling domain or domains include the cytoplasmic sequences of the T cell receptor (TCR) and, in some aspects, also those of the coreceptors that in the natural context act in concert with said receptor to initiate transduction of signals after antigen. receptor coupling and / or any derivative or variant of such molecules, and / or any synthetic sequence having the same functional capacity.
[0476] [ 0219] In the context of a natural TCR, complete activation generally requires not only signaling through the TCR, but also a costimulatory signal. Thus, in some cases, to promote complete activation, a component to generate a secondary or costimulatory signal is also included in the CAR. In other cases, the CAR does not include a component to generate a costimulatory signal. In some aspects, an additional CAR is expressed in the same cell and provides the component to generate the secondary or costimulatory signal.
[0478] [ 0220] T cell activation is, in some respects, described as mediated by two classes of cytoplasmic signaling sequences: those that initiate antigen-dependent primary activation via TCRs (primary cytoplasmic signaling sequences), and acting in an antigen-independent manner to provide a secondary or costimulatory signal (secondary cytoplasmic signaling sequences). In some aspects, the CAR includes one or both of the signaling components.
[0480] [ 0221] In some aspects, CAR includes a primary cytoplasmic signaling sequence that regulates primary activation of the TCR complex. Primary cytoplasmic signaling sequences that act in a stimulatory manner may contain signaling motifs that are known as tyrosine-based immunoreceptor activation motifs or ITAMs. Examples of ITAMs containing primary cytoplasmic signaling sequences include those derived from TCR zeta, FcR gamma, FcR beta, CD3 gamma, CD3 delta, CD3 epsilon, CD8, CD22, CD79a, CD79b, and CD66d. In some cases, the cytoplasmic signaling molecule (s) in CAR contain a cytoplasmic signaling domain, a part of it, or a sequence derived from CD3 zeta.
[0482] [ 0222] In some cases, the car includes a signaling domain and / or the transmembrane portion of a costimulatory receptor, such as CD28, 41BB, OX40, DAP10 or ICOS, or CD27. In some aspects, the CAR itself includes both the activating component and the costimulator component.
[0484] [ 0223] In some cases, the activation domain (eg, CD3 zeta) is included within a CAR, while the costimulatory component (eg, CD28 or 4-1BB) is provided by another CAR that recognizes another antigen. In some cases, CARs include activating or stimulating CARs, costimulatory CARs, both expressed in the same cell ( see WO2014 / 055668). In some respects, the CAR that targets CD19 is the stimulating or activating CAR; in other respects, it is the costimulatory CAR. In some cases, the cells also include inhibitory CARs (iCAR, see Fedorov et al., Sci. Transl. Medicine, 5 (215) (December 2013), such as a CAR that recognizes an antigen other than CD19, so a Activation signal delivered via CD19-oriented CAR is decreased or inhibited by binding of the inhibitory CAR to its ligand, eg, to reduce off-target effects.
[0486] [ 0224] In some cases, the intracellular signaling component of the recombinant receptor, such as CAR, comprises an intracellular CD3 zeta domain and a costimulatory signaling region. In certain cases, the intracellular signaling domain comprises a CD28 transmembrane and a signaling domain linked to a CD3 intracellular domain (eg, CD3-zeta). In some cases, the intracellular signaling domain comprises CD28 and / or CD137 chimeric costimulatory domains (41BB, TNFRSF9), linked to the intracellular domain of a CD3 zeta.
[0488] [ 0225] In some cases, the CAR encompasses one or more, eg. g., two or more costimulatory domains and an activating domain, eg. eg, primary activation domain, in the cytoplasmic portion. Exemplary CARs include intracellular components of CD3-zeta, c D28, and 4-1BB.
[0490] [ 0226] In some cases, the CAR or other antigen receptor further includes a marker, such as a cell surface marker, that can be used to confirm transduction or modify the cell to express the receptor, such as a truncated version. of a cell surface receptor, such as truncated EGFR (tEGFR). In some aspects, the marker includes all or part (eg, truncated form) of CD34, an NGFR or epidermal growth factor receptor (eg, t EGFR), or a functional variant thereof. In some cases, the nucleic acid encoding the marker is operably linked to a polynucleotide encoding a linker sequence, such as a cleavable linker sequence, e.g. eg, T2A. For example, a marker, and optionally a linker sequence, can be any of those described in published patent application No. WO2014031687. For example, the marker can be a truncated EGFR (tEGFR) that is optionally linked to a linker sequence, such as a T2A cleavable linker sequence. An exemplary polypeptide for a truncated EGFR (eg, tEGFR) comprises the amino acid sequence set forth in Se Q iD NO: 138 or an amino acid sequence exhibiting at least 85%, 86%, 87%, 88%, 89 %, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity with SEQ ID NO: 138. An exemplary T2A linker sequence comprises the amino acid sequence established in SEQ ID NO: 137 or an amino acid sequence exhibiting at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% , 95%, 96%, 97%, 98%, 99% or more sequence identity with SEQ ID NO: 137.
[0492] [ 0227] In some cases, the marker is a molecule, eg. eg, cell surface protein, which is not naturally found on T cells or is not found naturally on the surface of T cells, or a portion thereof.
[0494] [ 0228] In some cases, the molecule is a non-self molecule, eg. eg, non-autonomous protein, that is, one that is not recognized as "self" by the host's immune system into which the cells will be adoptively transferred.
[0496] [ 0229] In some cases, the marker has no therapeutic function and / or has no effect other than being used as a marker for genetic engineering, e.g. eg, to select successfully engineered cells. In other cases, the marker may be a therapeutic molecule or molecule that otherwise exerts some desired effect, such as a ligand for a cell found in vivo, such as a costimulatory molecule or immune checkpoint to enhance and / or monitor cell responses after adoptive transfer and ligand encounter.
[0498] [ 0230] In some cases, CARs are called first, second and / or third generation CARs. In some aspects, a first generation CAR is one that provides only a signal induced by the CD3 chain. by binding to the antigen; In some aspects, a second generation CAR is one that provides such a signal and costimulatory signal, such as one that includes an intracellular signaling domain of a costimulatory receptor such as CD28 or CD137; in some respects, a third generation CAR is in some respects one that includes multiple costimulatory domains of different costimulatory receptors.
[0500] [ 0231] In some cases, the chimeric antigen receptor includes an extracellular portion that contains the antibody or fragment described herein. In some aspects, the chimeric antigen receptor includes an extracellular portion that contains the antibody or fragment described herein and an intracellular signaling domain. In some cases, the antibody or fragment includes an scFv and the intracellular domain contains an ITAM. In some aspects, the intracellular signaling domain includes a signaling domain from a zeta chain of a CD3-zeta chain (CD3Z). In some cases, the chimeric antigen receptor includes a transmembrane domain that links the extracellular domain and the intracellular signaling domain. In some aspects, the transmembrane domain contains a transmembrane portion of CD28. The extracellular domain and the transmembrane domain can be linked directly or indirectly. In some cases, the extracellular domain and the transmembrane are linked by a spacer, like any of those described herein. In some cases, the receptor contains an extracellular portion of the molecule from which the transmembrane domain is derived, such as an extracellular portion of CD28. In some cases, the chimeric antigen receptor contains an intracellular domain derived from a T cell costimulatory molecule or a functional variant thereof, such as between the transmembrane domain and the intracellular signaling domain. In some aspects, the T cell costimulatory molecule is CD28 or 41BB.
[0502] [ 0232] For example, in some cases, CAR contains an antibody, eg. eg, an antibody fragment, as provided herein, a transmembrane domain that is or contains a transmembrane portion of CD28 or a functional variant thereof, and an intracellular signaling domain that contains a signaling portion of CD28 or a functional variant thereof and a CD3 zeta signaling portion or a functional variant thereof. In some cases, CAR contains an antibody, e.g. eg, an antibody fragment, as provided herein, a transmembrane domain that is or contains a transmembrane portion of CD28 or a functional variant thereof, and an intracellular signaling domain that contains a signaling portion of a 4 -1BB or functional variant thereof and a CD3 zeta signaling portion or functional variant thereof. In some of these cases, the receptor further includes a spacer that contains a portion of an Ig molecule, such as a human Ig molecule, such as an Ig hinge, e.g. eg, an IgG4 hinge, such as a hinge-only spacer.
[0504] [ 0233] In some cases, the transmembrane domain of the recombinant receptor, e.g. g., the car, is or includes a human CD28 transmembrane domain (eg, Accession No. P01747.1) or variant thereof, such as a transmembrane domain comprising the amino acid sequence set forth in SEQ ID NO: 129 or an amino acid sequence exhibiting at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97% , 98%, 99% or more sequence identity with SEQ ID NO: 129; In some cases, the portion that contains the transmembrane domain of the recombinant receptor comprises the amino acid sequence established in SEQ ID NO: 130 or an amino acid sequence that is at least or about 85%, 86%, 87%, 88%, 89 %, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity therewith.
[0506] [ 0234] In some cases, the intracellular signaling component (s) of the recombinant receptor, e.g. For example, CAR contains an intracellular domain of human CD28 or a functional variant or costimulatory signaling portion thereof, such as a domain with an LL to the GG substitution at positions 186-187 of a native CD28 protein. For example, the intracellular signaling domain may comprise the amino acid sequence set forth in s Eq ID NO: 131 or 132 or an amino acid sequence exhibiting at least 85%, 86%, 87%, 88%, 89%, 90 %, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity for SEQ ID NO: 131 or 132. In some cases, the intracellular domain comprises an intracellular costimulatory signaling domain of 4-1BB (e.g. (accession no. Q07011.1) or functional variant or part thereof, such as the amino acid sequence set out in SEQ ID NO: 133 or a sequence of amino acids exhibiting at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or plus sequence identity with SEQ ID NO: 133.
[0508] [ 0235] In some cases, the intracellular signaling domain of the recombinant receptor, e.g. For example, CAR, comprises a human CD3 zeta stimulatory signaling domain or functional variant thereof, such as a 112 AA cytoplasmic domain of human CD3Z isoform 3 (Accession No .: P20963.2) or a zeta signaling domain of Cd 3 as described in US Patent No. 7,446,190 or US Patent No. 8,911,993. For example, in some cases, the intracellular signaling domain comprises amino acid sequence 134, 135, or 136 or an amino acid sequence exhibiting at least 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity with SEQ ID NO: 134, 135 or 136.
[0510] [ 0236] In some aspects, the spacer contains only a hinge region of an IgG, such as only one hinge of IgG4 or IgG1, such as the single-hinge spacer set out in SEQ ID NO: 124. In other cases, the spacer is or contains an Ig hinge, e.g. eg, a hinge derived from IgG4, optionally linked to CH2 and / or CH3 domains. In some cases, the spacer is an Ig hinge, e.g. eg, an IgG4 hinge, bound to the CH2 and CH3 domains, as set forth in SEQ ID NO: 127. In some cases, the spacer is an Ig hinge, e.g. eg, an IgG4 hinge, bound to a CH3 domain only, as set forth in SEQ ID NO: 126. In some cases, the spacer is or comprises a glycine-serine rich sequence or other flexible linker such as flexible linkers known.
[0512] [ 0237] For example, in some cases, CAR includes an anti-CD19 antibody such as an anti-CD19 antibody fragment, such as any of the provided human anti-CD19 antibodies, e.g. eg, single chain antibodies including scFv, described herein, a spacer, such as a spacer containing a portion of an immunoglobulin molecule, such as a hinge region and / or one or more constant regions of a heavy chain molecule, as an Ig hinge-containing spacer, a transmembrane domain containing all or a portion of a CD28-derived transmembrane domain, a CD28-derived intracellular signaling domain, and a CD3 zeta-signaling domain. In some cases, CAR includes an anti-CD19 antibody or fragment, such as any of the human anti-CD 19 antibodies, including the scFvs described herein, a spacer such as any of the Ig hinge-containing spacers, a transmembrane CD28-derived domain, an intracellular signaling domain derived from 4-1BB, and a CD3-derived signaling domain zeta.
[0514] [ 0238] In some cases, such CAR constructs further include a ribosomal T2A element and / or a tEGFR sequence, e.g. g., downstream of the car, as set forth in SEQ ID NO: 137 and / or 138, respectively, or an amino acid sequence exhibiting at least 85%, 86%, 87%, 88%, 89%, 90 %, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more of sequence identity with SEQ ID NO: 137 or 138.
[0516] C. Modified cells
[0518] [ 0239] Also provided are cells, cell populations and compositions containing the cells, e.g. g., engineered cells, eg. ex. containing a genetically modified antigen receptor, eg, containing an extracellular domain that includes the anti-CD19 antibody or fragment, described herein. Among the compositions are pharmaceutical compositions and formulations for administration, such as for adoptive cell therapy. Therapeutic methods for administering the cells and compositions to subjects are also provided, e.g. eg, patients.
[0520] [ 0240] Therefore, cells expressing the recombinant receptors containing the antibodies are also provided, e.g. g., cells containing CARs. The cells are generally eukaryotic cells, such as mammalian cells, and are typically human cells. In some cases, the cells are derived from blood, bone marrow, lymph or lymphoid organs, they are cells of the immune system, such as cells of innate or adaptive immunity, e.g. eg, myeloid or lymphoid cells, including lymphocytes, typically T cells and / or NK cells. Other examples of cells include stem cells, such as multipotent and pluripotent stem cells, including induced pluripotent stem cells (iPSCs). The cells are typically primary cells, such as those isolated directly from a subject and / or isolated from a subject and frozen. In some cases, cells include one or more subsets of T cells or other cell types, such as whole T cell populations, CD4 + cells, CD8 + cells, and subpopulations thereof, as defined by function, activation state, maturity, potential for differentiability, expansion, recirculation, localization and / or persistence, antigen specificity, antigen receptor type, presence in a particular organ or compartment, marker or cytokine secretion profile, and / or degree of differentiation. With reference to the subject to be treated, the cells can be allogeneic and / or autologous. Methods include ready-to-use methods. In some aspects, as in commercially available technologies, cells are pluripotent and / or multipotent, like stem cells, like induced pluripotent stem cells (iPSCs). In some cases, the methods include isolating cells from the subject, preparing, processing, culturing and / or manipulating them, as described herein, and reintroducing them into the same patient, before or after cryopreservation.
[0522] [ 0241] Among the subtypes and subpopulations of T cells and / or CD4 + and / or CD8 + T cells are naive T cells (Tn), effector T cells (Teff), memory T cells and subtypes thereof. , such as T-stem cell memory (Tscm), central memory T (Tcm), effector memory T (Tem), or terminally differentiated effector memory T cells, tumor infiltrating lymphocytes (TIL), immature T lymphocytes, mature T lymphocytes, helper T lymphocytes, cytotoxic T lymphocytes, mucosa associated invariant T lymphocytes (MAIT), natural and adaptive regulatory T lymphocytes (Treg), helper T lymphocytes cells, such as TH1 cells, TH2 cells, TH3 cells, TH17 cells , TH9 cells, TH22 cells, follicular helper T cells, alpha / beta T cells, and delta / gamma T cells.
[0524] [ 0242] In some cases, the cells are natural killer (NK) cells. In some cases, the cells are monocytes or granulocytes, e.g. eg, myeloid cells, macrophages, neutrophils, dendritic cells, mast cells, eosinophils, and / or basophils.
[0526] [ 0243] In some cases, cells include one or more nucleic acids introduced through genetic engineering, and therefore express recombinant or genetically modified products of such nucleic acids. In some cases, nucleic acids are heterologous, that is, they are not normally present in a cell or sample obtained from the cell, such as one obtained from another organism or cell, which for example is not found usually in the cell being manipulated and / or an organism from which said cell is derived. In some cases, nucleic acids are not found in nature, such as a nucleic acid that is not found in nature, including one that comprises chimeric combinations of nucleic acids that encode multiple domains from multiple different cell types.
[0528] Vectors and methods for genetic engineering
[0530] [0244] Also provided are methods, nucleic acids, compositions and kits, for expressing binding molecules, including receptors comprising antibodies, and for the production of genetically modified cells expressing such binding molecules. Genetic engineering generally involves the introduction of a nucleic acid encoding the recombinant or modified component into the cell, such as by retroviral transduction, transfection, or transformation.
[0532] [ 0245] In some cases, gene transfer is achieved by first stimulating the cell, for example combining it with a stimulus that induces a response such as proliferation, survival and / or activation, e.g. g., measured by expression of a cytokine or activation marker, followed by transduction of activated cells and expansion in culture to amounts sufficient for clinical applications.
[0534] [ 0246] In some contexts, overexpression of a stimulating factor (eg, a lymphokine or a cytokine) can be toxic to a subject. Thus, in some contexts, genetically modified cells include gene segments that render cells susceptible to negative selection in vivo, such as after administration in adoptive immunotherapy. For example, in some aspects, cells are designed so that they can be killed as a result of a change in the in vivo condition of the patient to whom they are administered. The negative selectable phenotype can result from the insertion of a gene that confers sensitivity to an administered agent, e.g. eg, a compound. Negative selectable genes include the Herpes simplex virus type I thymidine kinase (HSV-I TK) gene (Wigler et al., Cell II: 223, I977) which confers sensitivity to ganciclovir; the cellular hypoxanthine phosphribosyltransferase (HPRT) gene, the cellular adenine phosphoribosyltransferase (APRT) gene, the bacterial cytosine deaminase, (Mullen et al., Proc. Natl. Acad. Sci. USA 89:33 (1992 )).
[0536] [ 0247] In some aspects, cells are further engineered to promote the expression of cytokines or other factors. Various methods for the introduction of engineered components are well known, e.g. g., antigen receptors, eg. g., CAR, and can be used with the provided methods and compositions. Exemplary methods include those for the transfer of nucleic acids encoding receptors, including viral ones, e.g. eg, retroviral or lentiviral, transduction, transposons, and electroporation.
[0538] [ 0248] In some cases, recombinant nucleic acids are transferred into cells using recombinant infectious virus particles, such as, e.g. g., vectors derived from simian virus 40 (SV40), adenovirus, adeno-associated virus (AAV). In some cases, recombinant nucleic acids are transferred to T cells using recombinant lentiviral vectors or retroviral vectors, such as gamma-retroviral vectors (see, e.g., Koste et al. (2014) Gene Therapy, April 3, 2014, doi: 10.1038 / gt. 2014.25; Carlens et al. (2000) Exp Hematol 28 (10): 1137-46; Alonso-Camino et al. (2013) Mol Ther Nucl Acids 2, e93; Park et al., Trends Biotechnol. 2011 Nov 29 (11): 550-557.
[0540] [ 0249] In some cases, the retroviral vector has a long terminal repeat sequence (LTR), eg. e.g., a retroviral vector derived from Moloney murine leukemia virus (MoMLV), myeloproliferative sarcoma virus (MPSV), murine embryonic stem cell leukemia virus (MESV), murine stem cell virus (MSCV), virus spleen focus former (SFFV) or adeno-associated virus (AAV). Most retroviral vectors are derived from murine retroviruses. In some cases, retroviruses include those derived from any source of avian or mammalian cells. Retroviruses are typically amphotropic, meaning that they are capable of infecting host cells of various species, including humans. In one case, the gene to be expressed replaces the retroviral gag, pol and / or env sequences. Several illustrative retroviral systems have been described (eg, US Patent Nos. 5,219,740; 6,207,453; 5,219,740; Miller and Rosman (1989) BioTechniques 7: 980-990; Miller, AD (1990) Human Gene Therapy 1: 5-14, Scarpa et al (1991) Virology 180: 849-852, Burns et al (1993) Proc Natl Acad Sci USA.
[0541] 90: 8033-8037; and Boris-Lawrie and Temin (1993) Cur. Opin. Genet. Develop. 3: 102-109.
[0543] [ 0250] Lentiviral transduction methods are known. Exemplary methods are described in, p. eg, Wang et al (2012) J .. Immunother 35 (9): 689-701; Cooper et (2003) Blood. 101: 1637-1644; Verhoeyen et al. (2009) Methods Mol Biol.
[0544] 506: 97-114; and Cavalieri et al. (2003) Blood. 102 (2): 497-505.
[0546] [ 0251] In some cases, recombinant nucleic acids are transferred to T cells by electroporation ( see, eg, Chicaybam et al, (2013) PLoS ONE 8 (3): e60298 and Van Tedeloo et al. (2000 ) Gene Therapy 7 (16): 1431-1437). In some cases, recombinant nucleic acids are transferred to T cells by transposition (see, eg, Manuri et al. (2010) Hum Gene Ther 21 (4): 427-437; Sharma et al. (2013) Molec Ther Nucl Acids 2, e74; and Huang et al. (2009) Methods Mol Biol 506: 115-126). Other methods of introduction and expression of genetic material into immune cells include calcium phosphate transfection (eg, as described in Current Protocols in Molecular Biology, John Wiley & Sons, New York, NY), protoplast fusion, transfection liposome-mediated cationic; microparticle bombardment facilitated by tungsten particles (Johnston, Nature, 346: 776-777 (1990)); and strontium phosphate DNA coprecipitation (Brash et al., Mol. Cell Biol., 7: 2031-2034 (1987)).
[0548] [ 0252] Other approaches and vectors for the transfer of the nucleic acids encoding the recombinant products are as described, e.g. eg, in International Patent Application Publication No. WO2014055668, and in US Patent No. 7,446,190.
[0550] [ 0253] Among the additional nucleic acids, p. eg, genes for introduction are those for enhancing the efficacy of therapy, such as by promoting the viability and / or function of transferred cells; genes to provide a genetic marker for selection and / or evaluation of cells, such as to assess survival or localization in vivo; genes to improve safety, p. g., making the cell susceptible to negative selection in vivo, as described by Lupton SD et al., Mol. and Cell Biol., 11: 6 (1991); and Riddell et al., Human Gene Therapy 3: 319-338 (1992); see also Lupton et al. publications PCT / US91 / 08442 and PCT / US94 / 05601. which describes the use of bifunctional selectable fusion genes derived from the fusion of a dominant positive selectable marker with a negative selectable marker. See, p. eg, Riddell et al., US Patent No. 6,040,177, at columns 14-17.
[0552] Cell Preparation for Engineering
[0554] [0254] In some cases, the preparation of the engineered cells includes one or more cultivation and / or preparation steps. Cells for the introduction of the CD19-binding molecule, e.g. eg, CAR, can be isolated from a sample, such as a biological sample, e.g. eg, one obtained or derived from a subject. In some cases, the subject from whom the cell is isolated is one who has the disease or condition or who is in need of cell therapy or to whom cell therapy will be administered. In some cases, the subject is a human in need of a particular therapeutic intervention, such as adoptive cell therapy for which cells are isolated, processed, and / or manipulated.
[0556] [ 0255] Therefore, the cells in some cases are primary cells, e.g. eg, primary human cells. Samples include tissues, fluids, and other samples taken directly from the subject, as well as samples resulting from one or more processing steps, such as separation, centrifugation, genetic engineering (eg, viral vector transduction), washing, and / or incubation. . The biological sample can be a sample obtained directly from a biological source or a sample that is processed. Biological samples include, but are not limited to, body fluids, such as blood, plasma, serum, cerebrospinal fluid, synovial fluid, urine and sweat, tissue and organ samples, including processed samples derived therefrom.
[0558] [ 0256] In some aspects, the sample from which the cells are derived or isolated is blood or a sample derived from blood, or is or is derived from an apheresis or leukapheresis product. Examples of samples include whole blood, peripheral blood mononuclear cells (PBMC), leukocytes, bone marrow, thymus, tissue biopsy, tumor, leukemia, lymphoma, lymph node, gut-associated lymphoid tissue, mucosa-associated lymphoid tissue, spleen, other lymphoid tissues, liver, lung, stomach, intestine, colon, kidney, pancreas, breast, bone, prostate, cervix, testicles, ovaries, tonsils or other organ and / or cells derived therefrom. Samples include, in the context of cell therapy, e.g. eg, adoptive cell therapy, samples from autologous and allogeneic sources.
[0560] [ 0257] In some cases, cells are derived from cell lines, e.g. eg, T cell lines. In some cases, the cells are obtained from a xenogeneic source, eg. g., mouse, rat, non-human primate, and pig.
[0562] [ 0258] In some cases, cell isolation includes one or more non-affinity-based cell preparation and / or separation steps. In some examples, cells are washed, centrifuged, and / or incubated in the presence of one or more reagents, e.g. eg, to remove unwanted components, enrich for desired components, lyse or kill cells sensitive to particular reagents. In some examples, cells are separated based on one or more properties, such as density, adherent properties, size, sensitivity, and / or resistance to particular components.
[0564] [ 0259] In some examples, cells are obtained from the circulating blood of a subject, e.g. eg, by apheresis or leukapheresis. The samples, in some respects, contain lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and / or platelets, and in some respects they contain cells other than red blood cells and platelets.
[0566] [ 0260] In some cases, blood cells collected from the subject are washed, eg. g., to remove the plasma fraction and place the cells in an appropriate buffer or medium for subsequent processing steps. In some cases, cells are washed with phosphate buffered saline (PBS). In some cases, the wash solution lacks calcium and / or magnesium and / or many or all of the divalent cations. In some aspects, a wash step is performed with a semi-automatic "flow-through" centrifuge (eg, Cobe 2991 cell processor, Baxter) according to the manufacturer's instructions. In some aspects, a wash step is accomplished by Tangential Flow Filtration (TFF) according to the manufacturer's instructions. In some cases, cells are resuspended in a variety of biocompatible buffers after washing, such as e.g. eg, Ca ++ / Mg ++ free PBS. In certain cases, components are removed from a sample of blood cells and the cells are resuspended directly in the culture medium.
[0568] [ 0261] In some cases, the methods include density-based cell sorting methods, such as preparing white blood cells from peripheral blood by lysis of blood cells and red centrifugation through a gradient of Percoll or Ficoll.
[0570] [ 0262] In some cases, isolation methods include separating different cell types based on the expression or presence in the cell of one or more specific molecules, such as surface markers, e.g. eg, surface proteins, intracellular markers, or nucleic acid. In some cases, any known method for separation based on such markers can be used. In some cases, the separation is an affinity or immunoaffinity-based separation. For example, isolation in some aspects includes the separation of cells and cell populations based on the expression of the cells or the level of expression of one or more markers, typically cell surface markers, e.g. eg, by incubation with an antibody or binding partner that specifically binds to such markers, generally followed by steps of washing and separating cells that have bound to the antibody or binding partner from those cells that have not bound to the antibody or binding partner.
[0572] [ 0263] Such separation steps can be based on positive selection, in which cells that have bound the reagents are retained for later use, and / or negative selection, in which cells that have not bound to the antibody or binding partner are retained. In some examples, both fractions are kept for later use. In some aspects, negative selection can be particularly useful when no antibody is available that specifically identifies a cell type in a heterogeneous population, so that separation is best carried out based on markers expressed by cells other than the desired population. .
[0574] [ 0264] The separation need not result in 100% enrichment or removal of a particular cell population or cells expressing a particular marker. For example, positive selection or enrichment for cells of a particular type, such as those expressing a marker, refers to an increase in the number or percentage of those cells, but does not have to result in a complete absence of cells that do not express the marker. Likewise, negative selection, elimination, or depletion of cells of a particular type, such as those expressing a marker, refers to a decrease in the number or percentage of those cells, but does not have to result in the complete elimination of cells. all those cells.
[0576] [ 0265] In some examples, multiple rounds of separation steps are carried out, in which the positively or negatively selected fraction from one step is subjected to another separation step, such as a subsequent positive or negative selection. In some examples, a single separation step can deplete cells that express multiple markers simultaneously, such as by incubating cells with a plurality of antibodies or binding partners, each specific for a marker directed to negative selection. Also, multiple cell types can be positively selected simultaneously by incubating cells with a plurality of antibodies or binding partners expressed on the various cell types.
[0578] [ 0266] For example, in some respects, specific subpopulations of T cells, such as cells positive or expressing high levels of one or more surface markers, e.g. For example, CD28 +, CD62L +, CCR7 +, CD27 +, CD127 +, CD4 +, CD8 +, CD45RA + and / or CD45RO + T cells are isolated by positive or negative selection techniques.
[0580] [ 0267] For example, CD3 +, CD28 + T cells can be positively selected using conjugated CD3 / CD28 magnetic beads (eg, Dynabeads® M-450 CD3 / CD28 T Cell Expander).
[0582] [ 0268] In some cases, isolation is carried out by enriching a particular cell population by positive selection, or depletion of a particular cell population by negative selection. In some cases, positive or negative selection is achieved by incubating cells with one or more antibodies or other binding agent that specifically bind to one or more expressed or expressed surface markers (+ marker) at a relatively higher level (high-labeling) in positively or negatively selected cells, respectively.
[0584] [ 0269] In some cases, T cells are separated from a PBMC sample by negative selection for markers expressed on non-T cells, such as B cells, monocytes, or other white blood cells, such as CD14. In some aspects, a CD4 + or CD8 + selection step is used to separate CD4 + helper T cells and CD8 + cytotoxic T cells. Such CD4 + and CD8 + populations can be further classified into subpopulations by positive or negative selection for markers expressed or expressed to a relatively greater degree in one or more subpopulations of naive, memory and / or effector T cells.
[0586] [ 0270] In some cases, CD8 + cells are further enriched or depleted for naïve core memory, effector memory and / or core memory stem cells, such as by positive or negative selection based on surface antigens associated with the respective subpopulation. In some cases, central memory (Tcm) T cell enrichment is carried out to increase efficiency, e.g. g., to improve long-term survival, expansion and / or grafting after administration, which in some respects is particularly robust in such subpopulations. See Terakura et al. (2012) Blood. 1: 72-82; Wang et al. (2012) J Immunother. 35 (9): 689-701. In some cases, the combination of Tcm-enriched CD8 + T cells and CD4 + T cells further improves efficacy.
[0588] [ 0271] In cases, memory T cells are present in the CD62L + and CD62L 'subsets of CD8 + peripheral blood lymphocytes. PBMC can be enriched or reduced in CD62L 'CD8 + and / or CD62L + CD8 + fractions, such as using anti-CD8 and anti-CD62L antibodies.
[0590] [ 0272] In some cases, the enrichment of the central memory T (Tcm) of cells is based on the positive surface or high expression of CD45RO, c D62L, CCR7, CD28, CD3, and / or CD 127; in some aspects, it is based on the negative selection of cells that express or highly express CD45RA and / or granzyme B. In some aspects, the isolation of a CD8 + population enriched for Tcm cells is done by depletion of cells expressing CD4, CD14, CD45RA and positive selection or enrichment for cells expressing CD62L. In one aspect, core memory T cell (Tcm) enrichment is carried out from a negative fraction of cells selected based on CD4 expression, which undergoes negative selection based on CD14 expression. and CD45RA, and a positive selection based on CD62L. Said selections in some respects are carried out simultaneously and in other respects they are carried out sequentially, in any order. In some respects, the same CD4 expression-based selection step that is used to prepare the population or subpopulation of CD8 + cells is also used to generate the population or subpopulation of CD4 + cells, such that both the positive and negative fractions of the CD4-based separation is retained and used in subsequent steps of the methods, optionally following one or more additional positive or negative selection steps.
[0592] [ 0273] In a particular example, a sample of PBMCs or another sample of white blood cells is subjected to CD4 + cell selection, where both negative and positive fractions are preserved. The negative fraction is then subjected to negative selection based on the expression of CD14 and CD45RA or CD19, and positive selection based on a marker characteristic of central memory T cells, such as CD62L or CCR7, where positive and negative selections are carried out. out in order.
[0594] [ 0274] CD4 + helper T cells are sorted into naïve, central memory, and effector cells by identifying cell populations that have cell surface antigens. CD4 + lymphocytes can be obtained by standard methods. In some cases, naive CD4 + T cells are CD45r O ', CD45RA +, CD62L +, CD4 + T cells. In some cases, the central memory CD4 + cells are CD62L + and CD45RO +. In some cases, the CD4 + effector cells are CD62L 'and CD45RO'.
[0596] [ 0275] In one example, to enrich for CD4 + cells by negative selection, a monoclonal antibody cocktail typically includes antibodies to CD14, CD20, CD11b, CD16, HLA-DR, and CD8. In some cases, the antibody or binding partner is attached to a solid support or matrix, such as a magnetic bead or a paramagnetic bead, to allow separation of cells for positive and / or negative selection. For example, in some cases, cells and cell populations are separated or isolated by immunomagnetic (or magnetic affinity) separation techniques (reviewed in Methods in Molecular Medicine, vol. 58: Metastasis Research Protocols, Vol. 2: Cell Behavior In Vitro and In Vivo, p. 17-25 Edited by: SA Brooks and U. Schumacher © Humana Press Inc., Totowa, NJ).
[0598] [ 0276] In some aspects, the sample or composition of cells to be separated is incubated with small, magnetizable or magnetically sensitive material, such as magnetically sensitive particles or microparticles, such as paramagnetic spheres (eg, as Dynalbeads or MACS beads ). Magnetically sensitive material, e.g. eg, a particle, generally binds directly or indirectly to a binding partner, e.g. eg, an antibody, which specifically binds to a molecule, e.g. eg, a surface marker, present in the cell, cells, or population of cells to be separated, e.g. For example, you want to select negatively or positively.
[0600] [ 0277] In some cases, the magnetic bead or particle comprises a magnetically sensitive material attached to a specific binding member, such as an antibody or other binding partner. There are many well-known magnetic response materials that are used in magnetic separation methods. Suitable magnetic particles include those described in Molday, US Patent 4,452,773, and in European Patent Specification EP 452342 B. Colloidal-sized particles, such as those described in US Pat. No. 4,795,698 and Liberti et al., US Patent 5,200,084 are other examples.
[0602] [ 0278] Incubation is generally carried out under conditions wherein antibodies or binding partners, or molecules, such as secondary antibodies or other reagents, that specifically bind to said antibodies or binding partners, that are attached to the particle magnetic or bead, specifically bind to cell surface molecules if they are present in the sample cells.
[0604] [ 0279] In some aspects, the sample is placed in a magnetic field, and cells having magnetically sensitive or magnetizable particles attached to it will be attracted to the magnet and separated from unlabeled cells. For positive selection, cells that are attracted to the magnet are retained; for negative selection, cells that are not attracted (unlabeled cells) are retained. In some respects, a combination of positive and negative selection during the same selection step, where the positive and negative fractions are retained and further processed or subjected to additional separation steps.
[0606] [ 0280] In certain cases, the magnetically sensitive particles are coated with primary antibodies or other binding partners, secondary antibodies, lectins, enzymes, or streptavidin. In certain cases, magnetic particles are attached to cells by a coating of primary antibodies specific for one or more markers. In certain cases, cells, instead of beads, are labeled with a primary antibody or binding partner, and then magnetic particles coated with a cell-type-specific secondary antibody or other binding partner (eg. , streptavidin). In certain cases, streptavidin-coated magnetic particles are used in conjunction with biotinylated primary or secondary antibodies.
[0608] [ 0281] In some cases, magnetically sensitive particles are left attached to cells to be subsequently incubated, cultured and / or modified; in some aspects, the particles are left attached to cells for administration to a patient. In some cases, magnetizable or magnetically responsive particles are removed from cells. Methods for removing magnetizable particles from cells are known and include, e.g. eg, the use of competing unlabeled antibodies, magnetizable particles or antibodies conjugated to cleavable linkers, etc. In some cases, the magnetizable particles are biodegradable.
[0610] [ 0282] In some cases, affinity-based selection is through cells activated by magnetic sorting (MACS) (Miltenyi Biotech, Auburn, CA). Magnetically Activated Cell Sorting Systems (MACS) are capable of high purity screening of cells that have magnetized particles attached to them. In certain cases, MACS operates in a mode in which target and non-target species are sequentially eluted after application of the external magnetic field. That is, the cells attached to the magnetized particles are held in place while the unbound species are eluted. Then after this first elution step is complete, the species that were trapped in the magnetic field and prevented from being eluted are released in some way so that they can be eluted and recovered. In certain cases, non-target cells are labeled and depleted from the heterogeneous population of cells.
[0612] [ 0283] In certain cases, isolation or separation is carried out using a system, device or apparatus that carries out one or more of the steps of isolation, cell preparation, separation, processing, incubation, culture and / or formulation of the method. In some aspects, the system is used to carry out each of these steps in a closed or sterile environment, e.g. For example, to minimize errors, user manipulation and / or contamination. In one example, the system is a system as described in International Patent Application, Publication Number WO2009 / 072003, or US 20110003380 A1.
[0614] [ 0284] In some cases, the system or apparatus performs one or more, eg. ie, the entirety of the isolation, processing, engineering, and formulation of steps in an integrated stand-alone system and / or in an automated system or programmable mode. In some aspects, the system or apparatus includes a computer and / or computer program in communication with the system or apparatus, which allows the user to program, control, evaluate the result and / or adjust various aspects of the processing, isolation, steps of engineering and formulation.
[0616] [ 0285] In some aspects, the separation and / or other steps are carried out using the CliniMACs system (Miltenyi biotic), e.g. eg, for automated cell separation on a large scale clinical level in a closed and sterile system. The components can include an integrated microcomputer, a magnetic separation unit, a peristaltic pump, and various pinch valves. In some respects, the integrated computer controls all components of the instrument and directs the system to perform repeated procedures in a standardized sequence. The magnetic separation unit in some respects includes a movable permanent magnet and a pick column holder. The peristaltic pump controls the flow rate throughout the tubing assembly and, together with the pinch valves, ensures controlled flow of buffer through the system and continuous suspension of cells.
[0618] [ 0286] The CliniMACs system in some respects utilizes magnetizable coupled antibody particles that are supplied in a sterile, non-pyrogenic solution. In some cases, after marking the cells with magnetic particles, the cells are washed to remove excess particles. A cell preparation bag is then connected to the tube set, which in turn is connected to a bag containing buffer and a cell collection bag. The tube set consists of preassembled sterile tubes, which include a guard column and a separation column, and are for single use only. Once the separation program has started, the system automatically applies the cell sample to the separation column. Labeled cells are retained within the column, while unlabeled cells are removed by a series of washing steps. In some cases, the cell populations for use with the methods described in this document are not labeled and are not retained on the column. In some cases, cell populations for use with the methods described herein are labeled and retained on the column. In some cases, cell populations for use with the methods described herein are eluted from the column after removal of the magnetic field and collected within the cell collection bag.
[0620] [ 0287] In certain cases, the separation and / or other steps are carried out using the CliniMACs Prodigy system. (Miltenyi Biotec). The CliniMACS Prodigy system, in some respects, is equipped with a cell processing unit that allows automatic washing and fractionation of cells by centrifugation. The CliniMACS Prodigy system can also include an integrated camera and image recognition software that determines the optimal cell fractionation end point by discerning the macroscopic layers of the product from the cell of origin. For example, peripheral blood is automatically separated into erythrocytes, white blood cells, and layers of plasma. The CliniMACS Prodigy system can also include an integrated cell culture chamber that achieves cell culture protocols such as, e.g. eg, cell differentiation and expansion, antigen loading, and long-term cell culture. Inlet ports can allow sterile removal and replenishment of media and cells can be monitored using an integrated microscope. See, p. eg, Klebanoff et al. (2012) J Immunother.
[0621] 35 (9): 651-660, Terakura et al. (2012) Blood. 1: 72-82 and Wang et al. (2012) J Immunother. 35 (9): 689-701.
[0623] [ 0288] In some cases, a population of cells described herein is collected and enriched (or depleted) via flow cytometry, in which cells stained for multiple cell surface markers are carried in a stream of fluid. . In some cases, a cell population described herein is harvested and enriched (or depleted) by preparative scale sorting (FACS). In certain cases, a cell population described herein is harvested and enriched (or depleted) through the use of microelectromechanical systems (MEMS) chips in combination with a FACS-based detection system (see, e.g., WO 2010 / 033140, Cho et al. (2010) Lab Chip 10, 1567-1573; and Godin et al. (2008) J Biophoton. 1 (5): 355-376. In both cases, cells can be marked with multiple markers , allowing the isolation of T cell subsets in high purity.
[0625] [ 0289] In some cases, antibodies or binding partners are labeled with one or more detectable markers, to facilitate separation for positive and / or negative selection. For example, the separation can be based on binding to fluorescently labeled antibodies. In some examples, cell sorting based on the binding of antibodies or other specific binding partners for one or more cell surface markers is carried out in a fluid stream, such as by fluorescence activated cell sorting (FACS), including the preparative scale (FACS) and / or microelectromechanical systems (MEMS) chips, e.g. eg, in combination with a flow cytometry detection system. Such methods allow positive and negative selection based on multiple markers simultaneously.
[0627] [0290] In some cases, preparation methods include steps to freeze, eg. eg, cryopreserve cells, before or after isolation, incubation, and / or engineering. In some cases, the subsequent freeze-thaw step removes granulocytes and, to some extent, monocytes from the cell population. In some cases, the cells are suspended in a freezing solution, e.g. eg, after a washing step to remove plasma and platelets. Any of a variety of solutions and freezing parameters known in some respects can be used. An example involves the use of PBS containing 20% DMSO and 8% human serum albumin (HSA) or other suitable cell freezing media. It is then diluted 1: 1 with medium so that the final concentration of DMSO and HSA is 10% and 4%, respectively. The cells are then frozen at -80 ° C at a rate of 1 ° per minute and stored in the vapor phase of a liquid nitrogen storage tank.
[0629] [ 0291] In some cases, the methods provided include cultivation, incubation, cultivation and / or genetic engineering steps. For example, in some instances, methods are provided for incubating and / or manipulating depleted cell populations and culture initiator compositions.
[0631] [ 0292] Therefore, in some cases, cell populations are incubated in a starter culture composition. Incubation and / or engineering can be carried out in a culture vessel, such as a unit, chamber, well, column, tube, tube set, valve, vial, culture plate, bag, or other container for culture or for culturing the cells.
[0633] [ 0293] In some cases, cells are incubated and / or cultured prior to or in connection with genetic engineering. The incubation steps can include culturing, growing, stimulating, activating and / or propagating. In some cases, the compositions or cells are incubated in the presence of stimulating conditions or a stimulating agent. Such conditions include those designed to induce proliferation, expansion, activation, and / or survival of cells in the population, to mimic antigen challenge, and / or prime cells for genetic engineering, such as for the introduction of an antigen receptor. recombinant.
[0635] [ 0294] Conditions can include one or more of certain media, temperature, oxygen content, carbon dioxide content, time, agents, e.g. eg, nutrients, amino acids, antibiotics, ions, and / or stimulating factors, such as cytokines, chemokines, antigens, binding partners, fusion proteins, recombinant soluble receptors, and any other agent designed to activate cells.
[0637] [ 0295] In some cases, the stimulating agents or conditions include one or more agents, e.g. eg, ligand, which is capable of activating an intracellular signaling domain of a TCR complex. In some aspects, the agent turns on or initiates the intracellular TCR / CD3 signaling cascade in a T cell. Such agents can include antibodies, such as those specific for a TCR component and / or costimulatory receptor, e.g. eg, anti-CD3, antiCD28, p. eg, attached to a solid support such as a bead and / or one or more cytokines. Optionally, the expansion method may further comprise the step of adding anti-CD3 and / or anti-CD28 antibody to the culture medium (eg, at a concentration of at least about 0.5 ng / ml). In some cases, stimulating agents include IL-2 and / or IL-15, e.g. eg, an IL-2 concentration of at least about 10 units / ml.
[0639] [0296] In some aspects, incubation is carried out according to techniques such as those described in US Patent No. 6,040,177 to Riddell et al., Klebanoff et al. (2012) J Immunother. 35 (9): 651-660, Terakura et al. (2012) Blood. 1: 72-82 and / or Wang et al. (2012) J Immunother. 35 (9): 689-701.
[0641] [0297] In some cases, the T cells are expanded by addition to the starter culture cells of the feeding composition, such as peripheral non-dividing blood mononuclear cells (PBMC), (eg. , such that the resulting population of cells contains at least about 5, 10, 20 or 40 or more PBMC feeder cells for each T lymphocyte in the initial population to be expanded); and incubating the culture (eg, long enough to expand the number of T cells). In some aspects, non-dividing feeder cells may comprise gamma-irradiated PBMC feeder cells. In some cases, PBMCs are gamma-irradiated in the range of about 3000 to 3600 rads to prevent cell division. In some aspects, the feeder cells are added to the culture medium prior to the addition of the T cell populations.
[0643] [0298] In some cases, stimulating conditions include temperature suitable for the growth of human T lymphocytes, eg. eg, at least about 25 degrees Celsius, generally at least about 30 degrees, and generally at or around 37 degrees Celsius. Optionally, the incubation may further comprise the addition of EBV-transformed lymphoblastoid cells (LCL) that do not divide as feeder cells. LCL can be irradiated with gamma rays in the range of about 6000 to 10,000 rads. LCL feeder cells in some respects are provided in any suitable amount, such as a ratio of LCL feeder cells to initial T lymphocytes of at least about 10: 1.
[0645] [0299] In cases, antigen-specific T cells, such as CD4 + and / or CD8 + T cell specific antigen, are obtained by stimulation of naive or antigen-specific T lymphocytes with the antigen. For example, antigen-specific T cell lines or clones for cytomegalovirus antigens can be generated by isolating T cells from infected subjects and stimulating the cells in vitro with the same antigen.
[0647] II. Compositions, methods and uses
[0649] [0300] Also provided are compositions that include the modified molecules and cells, including the pharmaceutical compositions and formulations, and methods of use and uses of the molecules and compositions, such as CD19 binding in the treatment of diseases, conditions and disorders in those that express CD19 and / or methods of detection, diagnosis and prognosis.
[0651] A. Compositions and pharmaceutical formulations
[0653] [0301] Pharmaceutical formulations are provided that include the CD19 binding molecule, e.g. g., the antibody or chimeric receptor, and / or cells modified by expressing the molecules. Pharmaceutical compositions and formulations generally include one or more optional pharmaceutically acceptable carriers or excipients. In some cases, the composition includes at least one additional therapeutic agent.
[0655] [0302] The term "pharmaceutical formulation" refers to a preparation that is in such a form that the biological activity of an active ingredient contained therein is allowed to be effective, and that does not contain additional components that are unacceptably toxic to a subject. for which the formulation would be administered.
[0657] [0303] A "pharmaceutically acceptable carrier" refers to an ingredient in a pharmaceutical formulation, other than an active ingredient, that is not toxic to a subject. A pharmaceutically acceptable carrier includes, but is not limited to, a buffer, excipient, stabilizer, or preservative.
[0659] [0304] In some aspects, the choice of carrier is determined in part by the particular cell, binding molecule, and / or antibody, and / or the method of administration. Accordingly, there are a variety of suitable formulations. For example, the pharmaceutical composition can contain preservatives. Suitable preservatives can include, e.g. eg, methyl paraben, propyl paraben, sodium benzoate, and benzalkonium chloride. In some aspects, a mixture of two or more preservatives is used. The preservative or mixtures thereof are typically present in an amount of from about 0.0001% to about 2% by weight of the total composition. Carriers are described, e.g. eg, in Remington's Pharmaceutical Sciences 16th Edition, Osol, A. Ed. (1980). Pharmaceutically acceptable carriers are generally non-toxic to recipients at the doses and concentrations employed, and include, but are not limited to: buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyl dimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride; benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and mcresol); low molecular weight polypeptides (less than about 10 residues); proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose, or sorbitol; salt-forming counter ions such as sodium; metal complexes (eg, Zn-protein complexes); and / or nonionic surfactants such as polyethylene glycol (PEG).
[0661] [0305] Buffering agents in some respects are included in the compositions. Suitable buffering agents include, e.g. eg, citric acid, sodium citrate, phosphoric acid, potassium phosphate, and various other acids and salts. In some aspects, a mixture of two or more buffering agents is used. The buffering agent or mixtures thereof are typically present in an amount of from about 0.001% to about 4% by weight of the total composition. Methods for preparing administrable pharmaceutical compositions are known. Exemplary methods are described in more detail in, p. eg, Remington: The Science and Practice of Pharmacy, Lippincott Williams &Wilkins; 21st ed. (May 1, 2005).
[0663] [0306] Antibody formulations can include lyophilized formulations and aqueous solutions.
[0665] [0307] The formulation or composition may also contain more than one active ingredient useful for the particular indication, disease, or condition being treated with the binding molecules or cells, preferably those with activities complementary to the binding cell or molecule, where the respective activities do not adversely affect each other. Said active ingredients are suitably present in combination in amounts that are effective for the intended purpose. Thus, in some cases, the pharmaceutical composition further includes other pharmaceutically active agents or drugs, such as chemotherapeutic agents, e.g. eg, asparaginase, busulfan, carboplatin, cisplatin, daunorubicin, doxorubicin, fluorouracil, gemcitabine, hydroxyurea, methotrexate, paclitaxel, rituximab, vinblastine, vincristine, etc. In some cases, the cells or antibodies are administered in the form of a salt, e.g. eg, a pharmaceutically acceptable salt. Suitable pharmaceutically acceptable acid addition salts include those derived from mineral acids, such as hydrochloric, hydrobromic, phosphoric, metaphosphoric, nitric, and sulfuric acids, and organic acids, such as tartaric, acetic, citric, malic, lactic, fumaric. , benzoic, glycolic, gluconic, succinic and arylsulfonic acids, e.g. eg, ptoluenesulfonic acid.
[0667] [0308] Active ingredients can be entrapped in microcapsules, in colloidal drug delivery systems (eg, liposomes, albumin microspheres, microemulsions, nanoparticles and nanocapsules) or in macroemulsions. In certain cases, the pharmaceutical composition is formulated as an inclusion complex, such as a cyclodextrin inclusion complex, or as a liposome. Liposomes can serve to direct host cells (eg, T cells or NK cells) to a particular tissue. There are many methods available to prepare liposomes, such as those described in, e.g. eg, Szoka et al., Ann. Rev. Biophys. Bioeng., 9: 467 (1980), and US Patents 4,235,871, 4,501,728, 4,837,028, and 5,019,369.
[0669] [0309] The pharmaceutical composition in some aspects may employ time-released, delayed-release, sustained, and release delivery systems such that delivery of the composition occurs prior to, and with sufficient time to cause sensitization of the site to be treated. There are many types of delivery systems available and known. Such systems can avoid repeated administrations of the composition, thus increasing comfort for the subject and the physician.
[0671] [0310] The pharmaceutical composition in some cases contains the binding molecules and / or cells in amounts effective to treat or prevent the disease or condition, such as a therapeutically effective or prophylactically effective amount. In some cases, therapeutic or prophylactic efficacy is monitored by periodic evaluation of treated subjects. For repeated administrations over several days or more, depending on the condition, the treatment is repeated until the desired suppression of the symptoms of the disease occurs. However, other dosage regimens may be useful and can be determined. The desired dose can be administered by the administration of a single bolus of the composition, by multiple bolus administrations of the composition, or by the administration of continuous infusion of the composition.
[0673] [0311] In certain cases, in the context of genetically engineered cells containing the binding molecules, a subject is administered the range of about one million to about 100 billion cells, such as, e.g. g., 1 million to about 50 billion cells (eg, about 5 million cells, about 25 million cells, about 500 million cells, about 1 billion cells, about 5 billion cells, about 20 billion cells, about 30 billion cells, about 40 billion cells, or a range defined by two of the above values), such as about 10 million to about 100 thousand million cells (eg, about 20 million cells, about 30 million cells, about 40 million cells, about 60 million cells, about 70 million cells, about 80 million cells , about 90 million cells), about 10 billion cells, about 25 billion cells, about 50 billion cells, about 75 billion cells, about 90 billion cells or a rank of defined by two of the above values) and, in some cases, around 100 million cells to around 50 billion cells (p. eg about 120 million of cells, 250 million cells, about 350 million cells, about 450 million cells, about 650 million cells, about 800 million cells, about 900 million cells, about 3 billion cells , about 30 billion cells, about 45 billion cells) or any value in between these ranges, and / or such number of cells per kilogram of the subject's body weight.
[0675] [ 0312] It can be administered using standard delivery techniques, formulations, and / or devices. Formulations and devices, such as syringes and vials, are provided for the storage and administration of the compositions. Administration of the cells can be autologous or heterologous. For example, immunoresponder cells or progenitors can be obtained from one subject and administered to the same subject or to a different compatible subject. Immune response cells derived from peripheral blood or their progeny (eg, in vivo, ex vivo, or derived in vitro) can be administered by localized injection, including catheter administration, systemic injection, localized injection, intravenous injection, or parenteral administration. When a therapeutic composition is administered (eg, a pharmaceutical composition containing a genetically modified immunoresponder cell), it will generally be formulated in an injectable unit dose form (solution, suspension, emulsion).
[0677] [ 0313] Formulations include those for oral, intravenous, intraperitoneal, subcutaneous, pulmonary, transdermal, intramuscular, intranasal, buccal, sublingual, or suppository administration. In some cases, the cell populations are administered parenterally. The term "parenteral" as used herein includes intravenous, intramuscular, subcutaneous, rectal, vaginal, and intraperitoneal administration. In some cases, cell populations are administered to a subject using peripheral systemic administration by intravenous, intraperitoneal, or subcutaneous injection.
[0679] [ 0314] The compositions in some cases are provided as sterile liquid preparations, e.g. eg, isotonic aqueous solutions, suspensions, emulsions, dispersions or viscous compositions, which may in some respects be buffered to a selected pH. Liquid preparations are normally easier to prepare than gels, other viscous compositions, and solid compositions. Furthermore, liquid compositions are somewhat more convenient to administer, especially by injection. Viscous compositions, on the other hand, can be formulated within the appropriate viscosity range to provide longer contact periods with specific fabrics. Liquid or viscous compositions may comprise carriers, which may be a solvent or dispersant medium containing, e.g. eg, water, saline, phosphate buffered saline, polyoi (eg, glycerol, propylene glycol, liquid polyethylene glycol), and suitable mixtures thereof.
[0681] [ 0315] Sterile injectable solutions can be prepared by incorporating the binding molecule in a solvent, such as in admixture with a suitable carrier, diluent, or excipient such as sterile water, physiological saline, glucose, dextrose, or the like. . The compositions can also be lyophilized. The compositions may contain auxiliary substances such as wetting, dispersing or emulsifying agents (eg, methyl cellulose), pH buffering agents, gelling additives or viscosity enhancers, preservatives, flavoring agents, coloring agents, and the like, depending on the route of administration and desired preparation. In some respects, standard texts can be consulted to prepare suitable preparations.
[0683] [ 0316] Various additives can be added that increase the stability and sterility of the compositions, including antimicrobial preservatives, antioxidants, chelating agents and buffers. Prevention of the action of microorganisms can be ensured by various antibacterial and antifungal agents, e.g. eg, parabens, chlorobutanol, phenol, sorbic acid, and the like. Prolonged absorption of the injectable dosage form can be achieved through the use of agents that delay absorption, e.g. eg, aluminum monostearate and gelatin.
[0685] [ 0317] Sustained release preparations can be prepared. Suitable examples of sustained release preparations include semipermeable matrices of solid hydrophobic polymers containing the antibody, matrices that are in the form of molded articles, e.g. eg, films or microcapsules.
[0687] [ 0318] Formulations to be used for in vivo administration are generally sterile. Sterility can be easily achieved, e.g. eg, by filtration through sterile filtration membranes.
[0689] B. Therapeutic and prophylactic methods and uses
[0691] [0319] Also provided are methods of use and uses of CD19 binding molecules, including anti-CD19 antibodies, e.g. eg, antibody fragments and / or genetically modified cells expressing the recombinant receptors. Such methods and uses include therapeutic methods and uses, e.g. eg, involving the administration of molecules, cells, or compositions containing them, to a subject who has a disease, condition, or disorder that expresses or is associated with the expression of CD19, and / or in which the cells or tissues express CD19. In some cases, the molecule, cell, and / or composition is administered in an amount effective to effect treatment of the disease or disorder. The uses include uses of the antibodies and cells in such methods and treatments, and in the preparation of a medicament for carrying out such therapeutic methods. In some cases, the methods are carried out by administering the antibodies or cells, or compositions comprising them, to the subject who has or is suspected of having the disease or condition. In some cases, the methods treat the disease this way or condition or disorder in the subject.
[0693] [ 0320] As used herein, "treatment" (and grammatical variations thereof, such as "treat 'or" treatment ") refers to completing or partial amelioration or reduction of a disease or condition or disorder, or a symptom, adverse effect or outcome, or phenotype associated therewith Desirable effects of treatment include, but are not limited to, prevention of disease onset or recurrence, alleviation of symptoms, reduction of direct pathological consequences, or indirect disease, prevention of metastasis, slowing the rate of disease progression, improvement or palliation of disease state and remission or better prognosis. The terms do not imply complete cure of a disease or elimination complete information on any symptom or effect (s) on all symptoms or results.
[0695] [ 0321] As used herein, "delay the development of a disease" means to postpone, hinder, slow down, delay, stabilize, suppress and / or postpone the development of the disease (such as cancer). This delay can be of different periods of time, depending on the history of the disease and / or the individual treated. As is apparent to one of ordinary skill in the art, a sufficient or significant delay may indeed encompass prevention, since the individual does not develop the disease. For example, late-stage cancer, such as the development of metastases, may be delayed.
[0697] [ 0322] "Prevention", as used herein, includes providing prophylaxis with respect to the onset or recurrence of a disease in a subject who may be predisposed to the disease but has not yet been diagnosed with the disease. In some cases, the molecules and compositions provided are used to delay the development of a disease or delay the progression of a disease.
[0699] [ 0323] As used herein, "suppressing" a function or activity is to reduce the function or activity when compared to conditions that are otherwise the same except for a condition or parameter of interest, or alternatively, compared to an other state. For example, an antibody or composition or cell that suppresses tumor growth reduces the rate of tumor growth compared to the rate of tumor growth in the absence of the antibody or composition or cell.
[0701] [ 0324] An "effective amount" of an agent, eg. eg, a pharmaceutical formulation, molecule, antibody, or cells, or binding to the composition, in the context of administration, refers to an effective amount, dosages / amounts and for periods of time necessary to achieve a desired result , as a therapeutic or prophylactic outcome.
[0703] [ 0325] A "therapeutically effective amount" of an agent, eg. For example, a pharmaceutical formulation, antibody, or cell, refers to an effective amount, at dosages and for periods of time necessary to achieve a desired therapeutic result, such as for treatment of a disease, condition or disorder and / or pharmacokinetic or pharmacodynamic effect of the treatment. The therapeutically effective amount can vary depending on factors such as the disease state, the age, sex and weight of the subject, and the populations of cells administered. In some cases, the methods provided involve the administration of molecules, cells, and / or compositions in effective amounts, e.g. eg, therapeutically effective amounts.
[0705] [ 0326] A "prophylactically effective amount" refers to an effective amount, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically, but not necessarily, since a prophylactic dose is used in subjects before or earlier in the disease, the prophylactically effective amount will be less than the therapeutically effective amount.
[0707] [ 0327] As used herein, a "subject" is a mammal, such as a human or other animal, and is typically a human. Diseases and disorders include B-cell malignancies, such as B-cell leukemias and lymphomas, including B-cell chronic lymphocytic leukemia (CLL), acute lymphocytic leukemia (ALL), pro-lymphocytic leukemias, hairy cell leukemias, acute lymphocytic leukemias. common, acute null lymphoblastic leukemias, non-Hodgkin lymphomas, diffuse large B-cell lymphomas (LDCBG), multiple myelomas, follicular lymphoma, splenic marginal zone lymphoma, mantle cell lymphoma, indolent B-cell lymphoma, Hodgkin lymphoma. Also among the diseases and conditions are autoimmune and inflammatory diseases, including those associated with improper or improved B cell numbers and / or activation. Exemplary diseases and conditions include multiple sclerosis, rheumatoid arthritis, and systemic lupus erythematosus (SLE).
[0709] [ 0328] In some cases, the subject has a persistent or relapsing disease, eg. g., after treatment with another CD19-specific antibody and / or cells expressing a CD19-targeting chimeric receptor and / or other therapy, including chemotherapy, radiation, and / or hematopoietic stem cell transplantation (HSCT), e.g. eg, allogeneic HSCT. In some cases, administration effectively treats the subject even though the subject has become resistant to other CD19 targeted therapy. In some cases, the subject has not relapsed, but is determined to be at risk of relapse, such as a high risk of relapse, and therefore the compound or composition is administered prophylactically, e.g. For example, to reduce the likelihood of relapse or prevent it.
[0710] [0329] In some cases, the treatment does not induce an immune response on the part of the subject to therapy, and / or does not induce such a response to a degree that prevents effective treatment of the disease or condition. In some aspects, the degree of immunogenicity and / or graft versus host response is less than that seen with a different but comparable treatment. For example, in the case of adoptive cell therapy using cells that express CAR, including the provided anti-CD19 antibodies, the degree of immunogenicity is reduced compared to CARs that include a different antibody that binds to a similar epitope, p. g., overlapping and / or competing to bind CD19 with the provided antibody, such as a mouse antibody.
[0712] [0330] In some cases, methods include adoptive cell therapy, whereby genetically modified cells expressing the provided anti-CD19-containing receptors (eg, CD19-targeted CARs) are administered to subjects. Such administration can promote cell activation (eg, T cell activation) in a CD19-targeted manner, such that disease or disorder cells are targeted for destruction.
[0714] [0331] Therefore, the methods and uses provided include methods and uses for adoptive cell therapy. In some cases, the methods include administering the cells or a composition containing the cells to a subject, tissue, or cell, such as one who has, is at risk, or is suspected of having the disease, condition, or disorder. In some cases, the cells, populations, and compositions are administered to a subject having the particular disease or condition to be treated, e.g. eg, by adoptive cell therapy, such as adoptive T cell therapy. In some cases, the cells or compositions are administered to the subject, such as a subject who has or is at risk for the disease or condition. In some respects, the methods thus deal with, e.g. eg, improve one or more symptoms of the disease or condition, eg. eg, decreasing the tumor burden in a cancer that expresses CD19.
[0716] [0332] Methods for the administration of cells for adoptive cell therapy are known and can be used in conjunction with the provided methods and compositions. For example, methods of adoptive T-cell therapy are described, e.g. eg, in US Patent Application Publication No. 2003/0170238 to Gruenberg et al; US Patent No. 4,690,915 to Rosenberg; Rosenberg (2011) Nat Rev Clin Oncol. 8 (10): 577-85). See, p. eg, Themeli et al. (2013) Nat Biotechnol. 31 (10): 928-933; Tsukahara et al. (2013) Biochem Biophys Res Commun 438 (1): 84-9; Davila et al. (2013) PLoS ONE 8 (4): e61338.
[0718] [0333] In some cases, cell therapy, eg. eg, adoptive cell therapy, eg. For example, adoptive T-cell therapy is carried out by autologous transfer, in which the cells and / or preparations are isolated from the subject to receive the cell therapy, or from a sample derived from said subject. Thus, in some aspects, cells are derived from a subject, e.g. eg, a patient, in need of treatment, and the cells, after isolation and processing, are administered to the same subject.
[0720] [0334] In some cases, cell therapy, eg. eg, adoptive cell therapy, eg. For example, adoptive T-cell therapy is carried out by allogeneic transfer, in which cells are isolated and / or otherwise prepared from a subject other than a subject who is to receive or ultimately receives cell therapy. , p. eg, a first subject. In such cases, the cells are then administered to a different subject, e.g. eg, a second subject, of the same species. In some cases, the first and second subjects are genetically identical. In some cases, the first and second subjects are genetically similar. In some cases, the second subject expresses the same HLA class or supertype as the first subject.
[0722] [0335] In some cases, the subject, to which the cells, cell populations, or compositions are administered is a primate, such as a human. In some cases, the primate is a monkey or an ape. The subject can be male or female and can be of any suitable age, including lactating, juvenile, adolescent, adult, and geriatric subjects. In some cases, the subject is a non-primate mammal, such as a rodent. In some examples, the patient or subject is a validated animal model for disease, adoptive cell therapy, and / or for evaluating toxic outcomes such as cytokine release syndrome (CRS).
[0724] [0336] The molecule-binding CD19, such as antibodies and chimeric receptors containing the antibodies and cells expressing the same, can be administered by any suitable means, e.g. eg, by injection, eg. eg, intravenous or subcutaneous injections, intraocular injection, periocular injection, subretinal injection, intravitreal injection, trans-septal injection, subscleral injection, intrachoroidal injection, intracameral injection, subconjunctival injection, subconjunctival injection, sub-Tenon injection, retrobulbar injection, peribulbar injection or posterior juxtascleral administration. In some cases, they are administered parenterally, intrapulmonary and intranasally and, if desired for local treatment, by intralesional administration. Parenteral infusions include intramuscular, intravenous, intraarterial, intraperitoneal, or subcutaneous administration. Dosage and administration may depend in part on whether the administration is brief or chronic. Various dosing schedules include, but are not limited to, single or multiple administrations at various time points, bolus delivery, and pulse infusion.
[0726] [0337] For the prevention or treatment of a disease, the appropriate dose of the binding cell or molecule may depend on the type of disease to be treated, the type of binding molecule, the severity and the course of the disease, whether the binding molecule is administered for preventive or therapeutic purposes, prior therapy, the patient's medical history and response to the binding molecule, and the discretion of the treating physician. In some cases, the compositions, molecules, and cells are suitably administered to the patient at one time or over a series of treatments.
[0728] [ 0338] Depending on the type and severity of disease, antibody doses may include about 1 jg / kg to 15 mg / kg (eg, 0.1 mg / kg-10 mg / kg), about 1 jg / kg to 100 mg / kg or more, from about 0.05 mg / kg to about 10 mg / kg, 0.5 mg / kg, 2.0 mg / kg, 4.0 mg / kg, or 10 mg / kg. Multiple doses can be administered intermittently, e.g. eg, every week or every three weeks. A higher initial loading dose may be given, followed by one or more lower doses.
[0730] [ 0339] In certain cases, in the context of genetically modified cells containing the binding molecules, a subject is administered the range of about one million to about 100 billion cells and / or that number of cells per kilogram of body weight , like, p. eg, 1 million to approximately 50 billion cells (eg, approximately 5 million cells, approximately 25 million cells, approximately 500 million cells, approximately 1 billion cells, approximately 5 billion cells, about 20 billion cells, about 30 billion cells, about 40 billion cells, or a range defined by two of the above values), such as about 10 million to about 100 billion cells (p eg, about 20 million cells, about 30 million cells, about 40 million cells, about 60 million cells, about 70 million cells, about 80 million cells, about 90 million of cells, about 10 billion cells, about 25 billion cells, about 50 billion cells, about 75 billion cells, about 90 billion cells, or a range defined by two of the above values), and in some cases around 100 million cells to around 50 billion cells (eg. eg, about 120 million cells, about 250 million cells, about 350 million cells, about 450 million cells, about 650 million cells, about 800 million cells, about 900 million cells, about 3 billion cells, about 30 billion cells, about 45 billion cells) or any value in between these ranges and / or per kilogram of body weight. Again, dosages may vary depending on the particular attributes of the disease or disorder and / or the patient and / or other treatments.
[0732] [ 0340] In some cases, the cells or antibodies are administered as part of a combination treatment, such as concurrently with or sequentially with, in any order, another therapeutic intervention, such as another antibody or cell-engineered or receptor or agent. , such as a cytotoxic or therapeutic agent.
[0734] [ 0341] Cells or antibodies in some cases are co-administered with one or more additional therapeutic agents or in connection with another therapeutic intervention, either simultaneously or sequentially in any order. In some contexts, cells are co-administered with other therapy close enough in time that cell populations enhance the effect of one or more additional therapeutic agents, or vice versa. In some cases, the cells or antibodies are administered prior to the one or more additional therapeutic agents. In some cases, the cells or antibodies are administered after the one or more additional therapeutic agents.
[0736] [ 0342] Once the cells are administered to a mammal (eg, a human), the biological activity of the modified cell populations and / or antibodies in some respects is measured by any of a number of known methods. Parameters to evaluate include the specific binding of a natural or engineered T cell or other immune cell to the antigen, in vivo, e.g. eg, by imaging, or ex vivo, eg. eg, by ELISA or flow cytometry. In certain cases, the ability of engineered cells to kill target cells can be measured using any suitable method known in the art, such as the cytotoxicity assays described in, e.g. eg, Kochenderfer et al., J. Immunotherapy, 32 (7): 689-702 (2009) and Herman et al. J. Immunological Methods, 285 (1): 25-40 (2004). In certain cases, the biological activity of cells can also be measured by testing the expression and / or secretion of certain cytokines, such as CD 107a, IFNy, IL-2, and TNF. In some aspects, biological activity is measured by evaluating the clinical outcome, such as reduction in tumor burden or burden.
[0738] [ 0343] In certain cases, the engineered cells are modified in various ways, so that their therapeutic or prophylactic efficacy is increased. For example, the genetically engineered CAR or TCR expressed by the population can be conjugated directly or indirectly through a linker to a targeting moiety. The practice of conjugating compounds, p. eg, the CAR or TCR, to targeting moieties is known in the art. See, p. eg, Wadwa et al., J. Drug Targeting 3: 111 (1995) and US Patent 5,087,616.
[0740] C. Methods of diagnosis and detection
[0742] [0344] Methods involving the use of the provided binding molecules are also provided, e.g. eg, antibodies, including antibody fragments, and molecules (such as conjugates and complexes) containing one or more of said antibodies, for detection, prognosis, diagnosis, staging, determination of the binding of a particular treatment to one or more tissues or cell types, and / or treatment decision information in a subject, such as by the detection of CD19 and / or the presence of an epitope thereof recognized by the antibody. In some cases, the methods are diagnostic and / or prognostic methods in association with a CD19-expressing disease or condition. The methods in some cases include incubating and / or probing a biological sample with the antibody and / or administering the antibody to a subject. In certain cases, a biological sample includes a cell or tissue or part thereof, such as tumor or cancer tissue or biopsy or section thereof. In certain cases, the contact is made under conditions permissive for the binding of the anti-CD19 antibody to CD19 present in the sample. In some cases, the methods further include detecting whether a complex is formed between the anti-CD 19 antibody and CD19 in the sample, such as detecting the presence or absence or the level of such binding. Such a method can be an in vitro or in vivo method. In one case, an anti-CD19 antibody is used to select subjects eligible for therapy with an anti-CD19 antibody or modified antigen receptor, e.g. eg, where CD19 is a biomarker for patient selection.
[0744] [0345] In some cases, a sample, such as a cell, tissue sample, lysate, composition, or other sample derived therefrom, is contacted with the anti-CD19 antibody and binds or forms a complex between the antibody and the sample (eg, CD19 in the sample) is determined or detected. When binding is demonstrated or detected in the test sample compared to a reference cell of the same tissue type, it may indicate the presence of an associated disease or condition, and / or that a therapeutic agent containing the antibody (e.g. g., an antibody fragment) bind specifically to a tissue or cell that is the same or is of the same type as the tissue or cell or other biological material from which the sample is derived. In some cases, the sample is from human tissue and may come from diseased and / or normal tissue, e.g. eg, from a subject having the disease or condition to be treated and / or from a subject of the same species as said subject but who does not have the disease or condition to be treated. In some cases, the normal tissue or cell comes from a subject who has the disease or condition to be treated, but is not itself a diseased cell or tissue, such as normal tissue from the same organ or from a different organ than the of a cancer that is present in a given subject.
[0746] [0346] Various methods known in the art can be used to detect specific binding of antibody-antigen. Exemplary immunoassays include fluorescence polarization immunoassay (FPIA), fluorescence immunoassay (FIA), enzyme immunoassay (EIA), nephelometric inhibition immunoassay (NIA), enzyme-linked immunosorbent assay (ELISA), and radioimmunoassay (RIA). A reporter moiety, or marker group, can be attached to the antibodies in question and selected to meet the needs of various uses of the method which are often determined by the availability of compatible assay equipment and immunoassay procedures. Exemplary labels include radionuclides ( e.g., 125I, 131I, 35S, 3H, or 32P and / or chromium (51Cr), cobalt (57Co), fluorine (18F), gadolinium (153Gd, 159Gd), germanium (68Ge), holmium (166Ho), indium (115In, 113In, 112In, 111In), iodine (125I, 123I 121I), lanthanum (140La), lutetium (177Lu), manganese (54Mn), molybdenum (99Mo), palladium (103Pd), phosphorus (32p), praseodymium (142Pr), promise (149Pm), rhenium (186Re, 188Re), rhodium (105Rh), rutheroium (97Ru), samarium (153Sm), scandium (47Sc), selenium (75Se), (85Sr), sulfur (35S), technetium (99Tc), thallium (201Ti), tin (113Sn, 117Sn), tritium (3H), xenon (133Xe), ytterbium (169Yb, 175Yb), yttrium (90Y), enzymes (eg. , alkaline phosphatase, horseradish peroxidase, luciferase, or p-glactosidase), fluorescent residues or proteins (eg, fluorescein, rhodamine, phycoerythrin, g Fp or BFP), or luminescent residues (eg, supplied Qdot ™ nanoparticles by Quantum Dot Corporation, Palo Alto, California) Several general techniques are known for use in performance of the various immunoassays indicated above.
[0748] [0347] For diagnostic purposes, antibodies can be labeled with a detectable moiety, including but not limited to radioisotopes, fluorescent labels, and various enzyme substrate labels known in the art. Methods for conjugating labels to an antibody are known in the art.
[0750] [0348] In some cases, the antibodies do not need to be labeled and the presence of the antibodies can be detected using a labeled antibody that binds to any of the antibodies.
[0752] [0349] The antibodies provided herein can be employed in any known assay procedure, such as competitive binding, direct and indirect sandwich assays, and immunoprecipitation assays. Zola, Monoclonal Antibodies: A Manual of Techniques, pp. 147-158 (CRC Press, Inc. 1987).
[0754] [0350] Antibodies and polypeptides can also be used for in vivo diagnostic assays, such as in vivo imaging. Generally, the antibody is labeled with a radionuclide (such as 111In, 99Tc, 14C, 1311, 125I, or 3H) so that cells or tissue of interest can be localized in vivo after administration to a subject.
[0756] [0351] The antibody can also be used as the reagent stain in pathology, e.g. eg, using known techniques.
[0758] 111. Articles of manufacture
[0760] [0352] Articles of manufacture containing the provided binding molecules are also provided, e.g. eg, antibodies and CAR and / or genetically modified cells and / or compositions. The articles of manufacture may include a container and a label or package insert on or associated with the container. Suitable containers include, e.g. eg, bottles, vials, syringes, IV bags, etc. The containers can be formed from a variety of materials such as glass or plastic. In some cases, the container contains a composition that is by itself or in combination with another composition effective to treat, prevent, and / or diagnose the condition. In some In cases, the container has a sterile access port. Exemplary containers include IV bags, vials, including those with needle pierceable caps for injection. The label or package insert may indicate that the composition is used to treat the disease or condition expressing or associating CD19. The article of manufacture may include (a) a first container with a composition contained therein, wherein the composition includes the engineered antibody or antigen receptor; and (b) a second container with a composition contained therein, wherein the composition includes an additional agent, such as a cytotoxic or therapeutic agent. The article of manufacture may further include a package insert stating that the compositions can be used to treat a particular condition. Alternatively or additionally, the article of manufacture may further include another or the same container comprising a pharmaceutically acceptable buffer. In addition, it can include other materials such as other buffers, diluents, filters, needles, and / or syringes.
[0762] [0353] As used herein, reference to a "corresponding form" of an antibody medium means that, when comparing a property or activity of two antibodies, the property is compared by the same form of antibody. For example, if an antibody is stated to have higher activity compared to the activity of the corresponding form of a first antibody, that means that a particular form, such as a scFv of that antibody, has higher activity compared to the scFv form of the first antibody.
[0764] [0354] As used herein, the mention that nucleotide or amino acid positions "correspond to" nucleotides or amino acid positions in a described sequence, as set forth in the sequence listing, refers to nucleotides or amino acid positions identified after alignment with the described sequence. sequence to maximize identity using a standard alignment algorithm, such as the GAP algorithm. For example, in some cases, exemplary corresponding residues of a CD19 protein, such as a human c D19 protein, can be identified by aligning a sequence with an exemplary Vpx sequence set forth in SEQ ID NO: 92. By aligning the sequences, one skilled in the art can identify the corresponding residues, e.g. eg, using conserved and identical amino acid residues as guides. In general, to identify the corresponding positions, the amino acid sequences are aligned so that the highest order match is obtained (see, for example: Computational Molecular Biology, Lesk, AM, ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, DW, ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, AM, and Griffin, HG, eds., Humana Press, New Jersey , 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; Carrillo et al. . (1988) SIAM J Applied Math 48: 1073).
[0766] [0355] "Effector functions" refers to those biological activities attributable to the Fc region of an antibody, which vary with the isotype of the antibody. Examples of effector functions of antibodies include: C1q binding and complement dependent cytotoxicity (CDC); binding to the Fc receptor; Antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down-regulation of cell surface receptors (eg, B cell receptor); and activation of B cells.
[0768] [0356] The term "Fc region" herein is used to define a C-terminal region of an immunoglobulin heavy chain that contains at least a portion of the constant region. The term includes native sequence Fc regions and variant Fc regions. In one case, a human IgG heavy chain Fc region extends from Cys226, or from Pro230, to the carboxyl terminal end of the heavy chain. However, the C-terminal lysine (Lys447) of the Fc region may or may not be present. Unless otherwise specified herein, the numbering of amino acid residues in the Fc region or constant region is performed according to the EU numbering system, also called the EU index, as described in Kabat et al. , Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD, 1991.
[0770] [0357] The terms "full-length antibody", "intact antibody" and "whole antibody" are used interchangeably herein to refer to an antibody that has a structure substantially similar to a native antibody structure or that has heavy chains that they contain an Fc region as defined herein.
[0772] [0358] An "isolated" antibody is one that has been separated from a component of its natural environment. In some cases, an antibody is purified to greater than 95% or 99% purity as determined, e.g. g., by electrophoresis (eg, SDS-PAGE, isoelectric focusing (IEF), capillary electrophoresis) or chromatography (eg, ion exchange or HPLC phase). For a review of methods for evaluating the purity of antibodies, see, p. eg, Flatman et al., J. Chromatogr. B 848: 79-87 (2007).
[0774] [0359] An "isolated" nucleic acid refers to a nucleic acid molecule that has been separated from a component of its natural environment. An isolated nucleic acid includes a nucleic acid molecule contained in cells that normally contain the nucleic acid molecule, but the nucleic acid molecule is present extrachromosomally or in a chromosomal location that is different from its natural chromosomal location.
[0776] [0360] "Isolated nucleic acid encoding an anti-CD 19 antibody" refers to one or more nucleic acid molecules encoding antibody heavy and light chains (or fragments thereof), including said (s) nucleic acid molecule (s) in a single vector or separate vectors and said nucleic acid molecule (s) present at one or more locations in a host cell.
[0778] [0361] The terms "host cell", "host cell line", and "host cell culture" are used interchangeably and refer to cells into which the exogenous nucleic acid has been introduced, including the progeny of such cells. Host cells include "transformants" and "transformed cells", which include the primary transformed cell and progeny derived therefrom regardless of the number of passages. Progeny may not be completely identical in nucleic acid content to a parent cell, but may contain mutations. Mutant progeny that have the same biological function or activity as screened or selected in the originally transformed cell are included herein.
[0780] [0362] As used herein, "percent (%) amino acid sequence identity" and "percent identity", when used relative to an amino acid sequence (reference polypeptide sequence) is defined as the percent of amino acid residues in a candidate sequence (e.g., the subject antibody or fragment) that are identical to amino acid residues in the reference polypeptide sequence, after aligning the sequences and introducing spaces, if necessary, to achieve the percentage of maximum sequence identity, and do not consider conservative substitutions as part of sequence identity. Alignment for the purpose of determining percent amino acid sequence identity can be accomplished in a number of ways that are within the skill of the art, e.g. eg, using publicly available computer software such as BLAST, BLAST-2, ALIGN, or Megalign (DNASTAR) software. Those skilled in the art can determine the appropriate parameters for aligning sequences, including the algorithms necessary to achieve maximum alignment over the full length of the sequences being compared.
[0782] [0363] An amino acid substitution can include the substitution of one amino acid in a polypeptide with another amino acid. Exemplary substitutions are shown in Table 1. Amino acid substitutions can be introduced into a binding molecule, e.g. g., an antibody, of interest and the products are selected for a desired activity, e.g. eg, retained / enhanced antigen binding, decreased immunogenicity, or enhanced ADCC or CDC.
[0784] [0364] Amino acids can generally be grouped according to the following common side chain properties:
[0786] (1) hydrophobic: norleucine, Met, Ala, Val, Leu, Ile;
[0787] (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln;
[0788] ( 3 ) acid: Asp, Glu;
[0789] (4) basic: His, Lys, Arg;
[0790] (5) residues that influence chain orientation: Gly, Pro;
[0791] (6) aromatic: Trp, Tyr, Phe.
[0793] [0365] Non-conservative amino acid substitutions will involve exchanging a member of one of these classes for another class.
[0795] [0366] The term "vector", as used herein, refers to a nucleic acid molecule capable of propagating another nucleic acid to which it is attached. The term includes the vector as a self-replicating nucleic acid framework, as well as the vector incorporated into the genome of a host cell into which it has been introduced. Certain vectors are capable of directing the expression of nucleic acids to which they are operably linked. Such vectors are referred to herein as "expression vectors."
[0797] [0367] The term "package insert" is used to refer to the instructions usually included in commercial packages of therapeutic products, which contain information on the indications, use, dosage, administration, combination therapy, contraindications and / or warnings on use. of such therapeutic products.
[0799] [0368] As used herein, the singular forms "a", "an", "the" and "she" include plural referents unless the context clearly dictates otherwise. For example, "one" or "one" means "at least one" or "one or more." Aspects and variations described herein are understood to include "consisting of" and / or "consisting essentially of" aspects and variations.
[0801] [0369] Throughout this description, various aspects of the claimed subject are presented in a rank format. The description in the range format should be understood to be merely for convenience and brevity and should not be construed as an inflexible limitation of the scope of the claimed object. Consequently, the description of a range should be considered to have specifically revealed all possible subranges as well as individual numerical values within that range. For example, when a range of values is provided, it is understood that each intermediate value, between the upper and lower limit of that range and any other established or intermediate value in that established range is encompassed within the claimed object. The upper and lower limits of these smaller ranges can be independently included in the smaller ranges, and are also encompassed within the claimed object, subject to any specifically excluded limits on the indicated range. When the indicated range includes one or both limits, ranges that exclude one or both of the included limits are also included in the claimed subject. This applies regardless of the width of the range.
[0803] [0370] The term "approximately" as used herein refers to the usual error range for the respective value readily known to the person skilled in this technical field. Reference to "about" a value or parameter in this document includes (and describes) instances that are directed to that value or parameter per se. For example, the description that refers to "about X" includes the description of "X".
[0805] [0371] As used herein, a composition refers to any mixture of two or more products, substances, or compounds, including cells. It can be a solution, a suspension, liquid, powder, paste, aqueous, non-aqueous, or any combination thereof.
[0807] [0372] As used herein, a statement that a cell or population of cells is "positive" for a particular marker refers to the detectable presence on or in the cell of a particular marker, typically a surface marker. When referring to a surface marker, the term refers to the presence of surface expression detected by flow cytometry, e.g. eg, by staining with an antibody that specifically binds to the marker and detecting said antibody, wherein the staining is detectable by flow cytometry at a level substantially above the staining detected by performing the same procedure with an isotype control coincident under identical conditions and / or at a level substantially similar to that of the cell known to be positive for the marker, and / or at a level substantially higher than that for a cell known to be negative for the marker.
[0809] [0373] As used herein, a statement that a cell or population of cells is "negative" for a particular marker refers to the absence of the substantial detectable presence on or in the cell of a particular marker, typically a marker. Of surface. When referring to a surface marker, the term refers to the absence of surface expression detected by flow cytometry, e.g. g., by staining with an antibody that specifically binds to the marker and detecting said antibody, wherein the staining is not detected by flow cytometry at a level substantially above the staining detected by performing the same procedure with a control of isotype matched under otherwise identical conditions, and / or at a level substantially lower than that of the cell known to be positive for the marker, and / or at a substantially similar level compared to that of a cell that is knows that it is negative for the scoreboard.
[0811] [0374] Unless defined otherwise, all art terms, notations, and other technical and scientific terms or terminology used herein are intended to have the same meaning as commonly understood by one of ordinary skill in the art. to which the claimed matter belongs. In some cases, terms with commonly understood meanings are defined herein for clarity and / or for quick reference, and the inclusion of such definitions herein should not necessarily be construed as a material difference from what is understood. generally in the art.
[0813] [0375] The section headings used in this document are for organizational purposes only and should not be construed as limiting the subject matter described.
[0815] V. EXAMPLES
[0817] [0376] The following examples are included for illustrative purposes only and are not intended to limit the scope of the invention.
[0819] Example 1: Generation and evaluation of anti-CD19 antibodies
[0821] [0377] Exemplary anti-CD 19 antibodies were generated and evaluated that specifically bind to CD19-expressing cells with similar binding properties to reference murine anti-CD 19 antibodies, and / or compete for binding with anti-CD antibodies. 19 murine reference.
[0823] 1A. Library selection, antibody generation
[0825] [0378] Examples of anti-CD19 antibodies (scFv) are generated through a series of selection steps carried out on dsDNA-encoded human naive antibody libraries displayed in a cell-free system. Members of a Vh library were selected to bind to live cells through three successive rounds, enriching for members that specifically bind to stably transfected CD19-expressing HEK293 cells, but not to parental HEK293 cells and / or CHOK1 cells that they do not express CD19. At the end of each round of selection, three separate elution pools were generated by (a) separation from the surface to recover the binders from the target cells, (b) competitive elution using a murine anti-CD19 antibody, FMC63 IgG, and ( c) competitive elution using another murine anti-CD19 antibody, SJ25C1 ((b) and (c) were carried out to enrich the ligands that compete with FMC63 and / or SJ25C1 for binding to CD19).
[0827] [0379] At the end of the 3 rounds of selections, these enriched Vh libraries then became the scFv libraries by scrambled Vh members of these respective groups and a naive human Vl library in Vh- (G4S) 3-Vl format. The resulting scFv libraries were subjected to a fourth round, enriching for members that specifically bound CD19-expressing HEK293 cells and not parental cells, followed by surface extraction.
[0829] [ 0380] A fifth round was carried out to further enrich for members that bound to other CD19-expressing cells (CD19 / K562). Selections were followed by generation of separate elution pools using (a) surface separation, (b) FMC63 competitive elution, or (c) SJ25C1 competitive elution. In a sixth round, these three groups were individually enriched by negative selection for members that did not bind to parental cells (HEK293, twice, K562), followed by positive selection for members that did bind to HEK293 cells. expressing CD19 and immunoprecipitation with an anti-Myc antibody that recognized a C-terminal tag in c D19 expressed in HEK293 cells.
[0831] [ 0381] In one study, forty-eight (48) clones from each of the three resulting R6 scFv pools were sequenced using forward and reverse primers to determine amino acid sequences. 130 of the scFv sequences determined showed a full length read. Convergence was observed between the sequences. Eighteen (18) replicas were identified among the 130 scFv sequences (representing forty-six (46) of the 130 clones). In this study, a Vh portion sequence containing CDR 1-3 and FR 1-3 was detected fourteen (14) times in two of the different groups (10 copies of one and 4 copies of the other), paired with 5 Vls different. Other replicas were identified between 2 and 5 times in different groups; others were single copy sequences. In another study, additional CD19-binding clones were identified and sequenced. The same Vh portion appeared between them, with different VL sequences.
[0833] 1 B. Specific binding to cells expressing CD19
[0835] [0382] Binding of sequenced clones to cells expressing CD19 and control cells HEK293, compared to cells not expressing CD19, was evaluated by flow cytometry, either with crude cell lysate translated in vitro or with supernatant produced by batteries. Briefly, the RNA from each clone was normalized and translated in vitro as crude scFv with a C-terminal FLAG tag. HEK293 cells expressing CD19 and control HEK293 cells (mock transfected) were used in the assay. Binding of individual scFvs to CD19 and control cells was measured with a secondary anti-FLAG-Alexa647 conjugate. Alternatively, the scFv binding sets were cloned into E. coli expression vectors and produced as HIS-labeled scFvs that were detected with the anti-HIS-Alexa647 conjugate in flow cytometry assays. Murine anti-CD19 antibodies (FMC63 scFv and FMC63 IgG) were used as positive controls; a control scFv was also used. The mean fluorescence intensity (MFI) was evaluated by flow cytometry. The results are shown in Figures 1A and 1B, which demonstrate the binding of identified clones to cells expressing CD19. Among the clones evaluated were scFv, including clones 5, 17, 18 (identified with in vitro translated lysates) and 76 (identified with bacterial supernatant), which showed a clear binding preference for CD19-expressing cells compared to negative cells. for CD19.
[0837] [ 0383] As shown in Figures 1A and 1B, for some clones, binding detects the fold change in the degree of binding, in this case as measured by mean fluorescence intensity, to CD19-expressing cells. Compared to cells not expressing CD 19, it was approximately as large, at least as large, or greater than the fold change observed for reference positive control antibodies, murine anti-CD19 FMC63 scFv and / or FMC63 IgG antibodies. In some cases, the total degree of binding observed to CD19-expressing cells was approximately the same, at least as great or greater than that observed for one or more of the positive control reference antibodies.
[0839] [ 0384] Four (4) scFv clones showing a clear binding preference for cells expressing CD19 compared to cells not expressing CD19 ("clone 18", "clone 17", "clone 5 "and" clone 76 ") .. Sequencing revealed that the clones shared common CDR sequences within their Vh sequences, with different Vl sequences and different CDR-Ls. The sequence identifiers corresponding to the sequences, including exemplary amino acid sequences of scFv, Vh, Vl, and CDR (Kabat) and nucleotide sequences encoding scFv, for the four clones are listed in Table 2. A variant of the line germline of clone 18 (considered "clone 18B") was generated by a substitution of cysteine (C) for serine (s) at position 89 of Kabat; the sequences of this clone are also listed in Table 2. Each of the clones had a Vh3 chain sequence. Clone 18 included a light chain framework derived from a VA2 sequence (clone 18B having the VA2 germline framework sequence); clones 17 and 76 had VA1 sequences and clone 5 included a VA3 sequence. Clones 18 and 17 were obtained from multiple branches and libraries, including the mixture of Vh-Vl and scFv. Clone 76 was derived from the competitive elution Vh-Vl SJ25C1 (Round 6); clone 5 was derived from the competitive elution Vh-Vl FMC63 (Round 6).
[0842] 1 C. Binding affinities, competition with reference antibodies
[0844] [0385] Clones 5, 17, 18, 18B, and 76, were purified by single step purification and purification evaluated by SDS gel. A gel from an exemplary study is shown in Figure 2 (lanes 1 and 2 = clone 5, not reduced, reduced; lanes 3 and 4 = clone 17, not reduced, reduced; lanes 5 and 6 = clone 18, not reduced and reduced; lanes 7 and 8 = clone 76, not reduced and reduced). In this study, isoelectric points were measured as 5.36, 5.32, 7.11, and 5.32, respectively for clones 5, 17, 18, and 76.
[0846] [ 0386] Melting temperature (Tm) measurements were performed using a BioTad CFX96 instrument to analyze sypro orange protein incorporation at incremental temperatures, revealing Tm values similar to those observed for the reference antibody FMC63 scFv. The results are presented in Table 3.
[0851] [ 0387] Clones were titered, and their binding affinities (EC50) to CD19-expressing K562 cells evaluated by flow cytometry, with a reference murine CD19 antibody, FMC63 scFv, used as a positive control. Results of three separate assays, each of which includes and compares other binding affinities with those of clone 18, are shown in Figures 3A-3C.
[0853] [ 0388] In the assay, the results of which are shown in Figure 3A, the EC50 values for clone 18, clone 17, another clone identified by the study (clone 192; see sequences in Table 6), and the reference antibody (FMC63 scFv). In the assay, the results of which are shown in Figure 3B, the EC50 values for clone 18, clone 18B, and clone 76 were measured as 7.1 nM and 9.3 nM, and 7.9 nM, respectively. In testing the results of those shown in Figure 3C, the EC50 values for clone 18 and clone 76 were measured as 4.1 nM and 8.8 nM respectively.
[0855] [ 0389] Thus, each of the clones tested specifically bound to cells expressing CD19 with affinities similar to those of the reference antibody, e.g. e.g., having EC50 approximately equal to or less than that of the reference antibody, or no more than approximately 1.5 times or no more than approximately 2 times, or no more than approximately 3 times greater than the EC50 of the reference antibody .
[0857] [ 0390] In another assay, clones 18, 5, 17, other identified clones (161, 170, 1 (see sequence information in Table 6)), and positive control reference antibody FMC63 scFv (one plate) and clone 18, other identified clones (177, 184, 192, 198) and the positive control reference antibody FMC63 scFv (another plate) were evaluated by the same assay. The results are presented in Figure 4. The EC50 values observed for the two plates are presented in Tables 4A and 4B. As shown, the clones were found to have binding affinities comparable to that of the reference antibody.
[0860] [ 0391] Competition binding assays were carried out to assess the competition of various antibodies for binding to cells expressing CD19. In one assay, the binding of 0.5 nM (~ EC50) FITC-labeled SJ25C1 to Ramos cells was assessed in the presence or absence of various concentrations of unconjugated FMC63 IgG competitor or an IgG control; binding was assessed by flow cytometry (mean fluorescence intensity). Results are shown in Figure 5A, indicating that FMC63 IgG competed for CD19 binding with SJ25C1 IgG1 in this study, suggesting that SJ25C1 and FMC63 bound overlapping epitopes, e.g. eg, a common epitope, from CD19. In another assay, cells expressing CD19 were incubated with labeled FMC63 IgG in the presence of various concentrations of (or absence of) clone 18 scFv, FMC63 scFv (positive control), and a control scFv (negative control). The results are shown in Figure 5B. As shown, both clone 18 scFv and FMC63 scFv (but not the negative control scFv) were observed to compete with FMC63 IgG for binding to cells expressing CD19, with comparable IC50 values (24.0 nM and 19.8 nM, respectively), indicating that clone 18 bound a CD19 epitope that overlaps the epitope recognized by FMC63, and competed to bind the reference antibody to a similar degree.
[0862] [ 0392] In another assay, 10 nM (Alexa647-labeled EC50) FMC63 scFv was incubated with cells expressing CD19-K562 in the presence or absence of varying concentrations of clone 18 scFv, clone 18B scFv, clone 17 scFv, clone 76 scFv, a reference antibody (FMC63 scFv) and a negative control antibody (R12). The results are presented in Figure 6. The clones and the reference antibody, but not the negative control antibody, showed competition for binding to CD19 with the FMC63 scFv, and the competition for the reference antibody with itself was similar to the competition observed for the clones tested.
[0864] [ 0393] Taken together, in a series of studies, the following EC50 (binding affinity) and IC50 (competition) values were observed for the various clones, which are listed in Table 5. As shown, among human CD19 antibodies identified were those that have similar degrees of binding affinity for CD19 and similar degrees of competitive inhibition for a murine anti-CD19 reference antibody, compared to the reference antibody itself, e.g. eg, approximately equal, less than or not more than 1.5 times, 2 times or 3 times greater EC50 and / or IC50.
[0869] ID. Size Exclusion Chromatography
[0871] [0394] The biophysical properties of clone 18B were evaluated by size exclusion chromatography. A HiLoad 16/600 Superdex 200 column was calibrated and Bio-Rad gel filtration standard proteins of 150-1901 kDa were injected, and fractions were collected at 1.5 ml / min to generate references. 770 ug of scFv from clone 18B were injected onto the column and the fraction was collected under the same conditions. The results are shown in Figure 7 (Figure 7A = standard; Figure 7B = Clone 18B). Results for clone 18B scFv revealed a single peak, with minimal large aggregates observed.
[0873] Example 2: Generation and Evaluation of Additional Antibodies Against CD19
[0875] [0395] Among additional exemplary anti-CD19 antibodies (scFv fragments) having binding properties similar to (and / or competing for binding with) anti-CD19 murine reference antibodies were generated and evaluated.
[0877] 2A. Library selection, antibody generation
[0878] [0396] Additional examples of anti-CD 19 scFv were generated by two different selection approaches, each involving a series of selection steps carried out on dsDNA-encoded human antibody libraries displayed in a cell-free system. .
[0880] [ 0397] In one approach (considered "clone 18 CDR3 graft"), a heavy chain CDR3 sequence (CDR-H3) present in clones identified in Example 1 (SEQ ID NO: 20, DQGYHYYDSAEHAFDI) was grafted into frames of Vh naive human library. Members of the resulting CDR3-grafted Vh library were shuffled with members of a naive human Vl library to generate a scFv library as Vh- (G4S) 3-Vl format. The resulting scFv library was subjected to three rounds of selection, to enrich for members that specifically bind to CD19-expressing HEK293 cells and not to parental cells, followed by surface removal for round (R1), immunoprecipitation, and out of speed for round 2 (R2).
[0882] [ 0398] In another approach (considered "FMC63-guided selection"), two initial scFv libraries were generated, respectively, (a) shuffling members of a naive Vh library with the Vl region of FMC63 and (b) shuffling members of a library Vl naive with the Vh region of FMC63. After two and three rounds of selection, respectively, to enrich the library members of (a) and (b) for binding of CD19 with the parental FMC63 Vh or Vl guide. The binding molecules were eluted by separation from the surface of CD19 / HEK293 cells (R1) and elution of FMC63 from CD19 / K562 cells (r 2 and R3). A third scFv library was generated by mixing the Vh sequences from the selection in (a) with the Vl sequences resulting from the selection in (b). Three additional rounds of selection were performed on CD19 / HEK293 cells with surface separation (R1), followed by CD19 / K562 cells with FMC63 elution (R2) and CD19 / HEK293 cells with immunoprecipitation (R3). Binding of selected scFv clones to cells expressing CD19 was confirmed by flow cytometry using supernatant produced by bacteria. The selected scFv pools were cloned into E. coli expression vectors and produced as HIS-labeled scFvs. Binding of individual clones to c D19 transfected HEK293 cells was detected with conjugated anti-HIS-Alexa647 by flow cytometry. Clone 18 or clone 18B were used as positive controls, along with several negative controls. The results are shown in Figures 8A-C (MFI = mean fluorescence intensity).
[0884] [ 0399] The results shown in Figure 8D confirm specific binding to CD19 by a twenty-three (23) specimen of the accesses (marked with asterisks in Figures 8A-C, representing 4 prototypes identified through the CDR3 grafting approach and 19 through selection guided by FMC63). Binding of in vitro translated FLAG-tagged scFvs to CD19-expressing K562 cells, compared to control K562 cells (mock transfected), was assessed by flow cytometry as described in Example 1. As shown, the clones specifically bound to cells expressing CD19.
[0886] [ 0400] These and additional CD19-specific scFv clones generated by the selection approaches in Examples 1 and 2 were further evaluated. Sequencing revealed several CD19-specific binding antibodies (scFv) with several different light chain sequences and sharing a common CDR-H3 sequence (SEQ ID NO: 20) also present in the scFvs described in Example 1. Identifiers of Sequences corresponding to several additional CD19-binding scFv sequences are listed in Table 6, which includes amino acid sequences of scFv, Vh, Vl and CDR (Kabat) (and the nucleotide sequences encoding scFv). Among the CD19-specific scFv clones were those with several different CDR sequences and light chain variables, some of which had CDR-H1, CDR-H2 and / or CDR-H3 present in SEQ ID NO: 11, CDR-H1, CDR-H2 and / or CDR-H3 that have sequences of SEQ ID NO: 18, 19 and / or 20, and / or CDR-H1, CDR-H2 and / or CDR-H3 that have sequences of 18 , 72 and 20. Each of the clones listed in Table 6 is derived from a human Vh3 framework (with kappa and lambda gene V segments from which the clones are derived).
[0889] 2B. Purification and evaluation
[0891] [0401] Clones described above, including clones listed in Table 6 and / or described in Example 1, were purified by one-step purification and purification evaluated by SDS gel. The results are presented in Figure 9 (lane 1 = MW marker; lanes 2, 9 and 10 = clone 5 (1530, 2880, 1130 pg / mL); lane 3 = clone 18B (660 pg / mL); lanes 4 , 11, 12 and 13 = clone 17 (300, 1060, 180, 1440 pg / mL); lane 5 = clone 192B (1580pg / mL); lanes 6 and 14 = clone 76 (1340, 3220 pg / mL); lane 7 = clone 835 (470 pg / mL); lane 8 = clone 488 (340 pg / mL)). Melting temperature (Tm) measurements were made as described in Example 1, revealing similar Tm values as observed for the reference antibody and clones in Example 1 (Table 7).
[0896] [ 0402] Several clones were titrated and their binding affinity (EC50) for various CD19-expressing cells evaluated by flow cytometry. The reference antibody FMC63 scFv was used as a positive control. The results of five separate assays evaluating binding affinities for various CD19-specific scFv clones are shown in Figures 10A-10E. As shown, the selections resulted in several CD19-specific scFv clones with various binding affinities and a saturable range of binding activity.
[0898] [ 0403] Competition binding assays were carried out as described in Example 1 to assess the ability of various identified antibodies (scFv clones) to compete for binding with a murine reference antibody for binding to cells expressing CD19 . In one example, cells expressing CD19 were incubated with 10 nM labeled FMC63 scFv in the presence of various concentrations of the indicated scFv clones that have different light chain sequences and share a common heavy chain CDR3 (or FMC63 scFv (control positive)). The results, shown in Figure 11, demonstrated that the clones competed with FMC63 scFv for binding to cells expressing CD19, with various IC50 values. Similar studies were carried out to evaluate the properties of other clones identified in the screening approaches described in Examples 1 and 2. EC50 (binding affinity) and IC50 (competition) values observed for various CD19-binding antibodies (scFv) are listed in Table 8. The CDR-L3 sequences for clones 79, 835, 184, 505, 506 and 305 are set out as SEQ ID NO: 116, 117, 118, 119, 120, 121 and respectively.
[0901] [ 0404] Among the identified human CD19 antibodies (scFv fragments), many demonstrated similar or higher degrees of binding affinity (eg, similar or lower EC50 values) for CD19 compared to a reference anti-CD19 antibody. murine, FMC63. Many also demonstrated similar or greater degrees of competition (eg, similar or lower IC50 values) with a mouse anti-CD19 reference antibody to binding CD19, compared to the reference antibody's ability to compete with itself. .
[0903] [ 0405] For example, clones were observed with EC50 values that were less than, about equal to, or not more than or about 1.5 times greater, greater than 2 times, or greater than 3 times than those of the reference antibody. Likewise, several of the identified anti-CD19 antibodies (scFv) were found to compete with the FMC63-labeled scFv for binding to CD19-expressing cells with IC50 values that were lower than the IC50 values observed for FMC63 scFv, approximately the same as the IC50 values observed for FMC63, or not more than 1.5 times or 2 times or 3 times higher (e.g., a degree of competition that is not more than 1.5 times or 2 times or 3 times lower than the competition for the reference antibody). The results indicated that these studies identified a plurality of antibodies that bind to a CD19 epitope that overlaps the epitope specifically bound by FMC63.
[0905] Example 3: Generation of chimeric antigen receptors (CARs) against CD19 and engineering of cells expressing such CARs
[0907] [0406] Several exemplary chimeric antigen receptors (CARs), with antigen-binding regions containing human anti-CD 19 scFv, were generated as described in Example 1. Specifically, nucleic acid molecules encoding CAR were generated with scFv (in VH-VL format) derived from the following clones and having the amino acid sequences established in the indicated sequence identifiers: Clone 18 (SEQ ID NO: 2), Clone 18B (SEQ ID NO: 4), Clone 17 (SEQ ID NO: 6), Clone 76 (SEQ ID NO: 8) and Clone 5 (SEQ ID NO: 10). Furthermore, for each clone, constructs were also generated that encode a CAR having the same VH and VL sequences, but present in the reverse orientation (VL-VH). A CAR containing an FMC63-derived murine anti-CD19 scFv (in the VH-VL orientation) was used as a control. Each CAR further contained an Ig-derived spacer; a transmembrane domain derived from human CD28; an intracellular signaling domain derived from human 4-1BB; and a human CD3 zeta-derived signaling domain, a truncated EGFR sequence (EGFRt), for use as a transduction marker, separated from the CAR sequence by a self-cleaving T2A sequence.
[0909] [ 0407] Populations of primary human T cells expressing the various CARs were generated. The nucleic acid molecules encoding each CAR were individually cloned into a lentiviral vector, which was used to transduce CD4 + and CD8 + T cells into isolated populations of human PBMC samples obtained from healthy donors (essentially as described by Yam et al. ( 2002) Mol. Ther 5: 479; WO2015 / 095895).
[0911] [ 0408] After transduction and expansion, anti-EGFR antibody staining was used to verify the expression of the EGFRt transduction marker on the surface of CD4 + and CD8 + T cells by flow cytometry. Figure 12A provides representative results for the expression of the various CARs in CD8 + cells; Similar results were seen for CD4 + cells. The expression of the CAR protein was confirmed by Western blot using an anti-CD247 (CD3 zeta) antibody (which in each case detected a band of approximately 50 kD, representing CAR, and a band of approximately 18 kDa, representing the endogenous CD3 zeta chain present in cells ) (Figure 12B). The results demonstrated comparable degrees of CAR protein transduction and expression for each of the various CAR constructs containing human scFv (including the VH-VL and VL-VH orientations) and control CAR constructs (murine, derived from FMC63) in Primary populations of T cells. EGFRt expression was not detected in non-transduced cells. The results of the Western blot confirmed that the CAR derived from clone 76, in the VH-VL orientation, was present in different forms of glycosylation.
[0913] [ 0409] As shown in Figure 12A, T cell populations were successfully enriched for transduced cells (at or near 100% EGFRt + as confirmed by flow cytometry) by staining with an anti-EGFR antibody, sorting on a flow cytometer, and stimulation in the presence of irradiated cells (8,000 rad) of a CD19 + B lymphoblastoid cell line (B-LCL) essentially as described by Yam et al. (2002) Mol. Ther. 5: 479; WO2015 / 095895.
[0915] Example 4: Evaluation of the effector functions of T cells designed to express the anti-CD19 chimeric antigen receptor (CAR) in vitro
[0917] [0410] Genetically modified human T cells (CD8 + or CD4 +) expressing various CARs containing anti-human CD19 scFv, produced as described in Example 3, were evaluated for various responses after coculture with cells expressing CD19.
[0919] A. Cytolytic activity
[0921] [0411] Target cells expressing CD19 were incubated with CD8 + T cells expressing the various CARs and separately with cells transduced with EGFRt alone (negative control). After incubation, the lysis of the target cells was monitored. Specifically, lysis of CD19 transduced K562 cells (K562 / CD19), Raji cells (CD19 + B cell lymphoma line) and non-transduced K562 control cells (negative control) (Figure 13A) and human chronic lymphocytic leukemia cells were tested. primary (LLC; Figure 13B).
[0923] [ 0412] Target cells (K562 / CD19 Raji non-transduced control cells K562 or CLL) were labeled overnight with 51 Cr. The labeled cells were washed and incubated in triplicate with effector T cells (CD8 + cells negative control and expressing CAR) at an effector to target (E: T) ratio of 30: 1. To measure spontaneous lysis, the target cells were incubated with an equal volume of medium but without effector cells and the maximum lysis was determined after incubation of the target cells with detergent to completely lyse the target cells. The supernatants were collected for counting and after a 4 hour incubation. The percentage of specific lysis for the experimental conditions was calculated as:
[0925] [(Experimental release - spontaneous release) / (Maximum release - spontaneous release)] x 100.
[0927] [0413] The results are shown in Figure 13A and 13B. As shown in Figure 13A, genetically modified CD8 + T cells expressing the various CARs containing anti-human CD 19 scFv exhibited antigen-specific cytolytic activity against CD19 + cells, to a degree comparable to cells expressing CARs containing the murine anti-CD19 scFv (FMC63). This cytotoxic activity was not observed against control K562 cells that did not express CD19. The degree of cytolytic activity observed for cells expressing CAR with human scFvs in the VH-VL (HL) orientation was found to be comparable to or greater than that observed for cells expressing CAR containing murine scFv. The degree of cytolytic activity observed for cells expressing a CAR with a given human scFv in the VH-VL (HL) orientation was generally higher than that observed for cells expressing a CAR with the corresponding scFv in the VL-VH orientation. reverse (LH). As shown in Figure 13B, the results also demonstrated antigen-specific cytolytic activity against primary human CLL cells by engineered CD8 + cells expressing the various CARs containing anti-human CD19 scFv (VH-VL orientation).
[0929] B. Cytokine release
[0931] [0414] Cytokine release was assessed after incubation of CAR expressing cells with cells expressing the antigen and control target. CD8 + and CD4 + T cells transduced in triplicate were co-cultured with target cells (K562, K562 / CD19, Raji) in an effector to target (E: T) ratio of 2: 1. Cytokine secretion after coculture of transduced CD8 + cells with primary human chronic lymphocytic leukemia (CLL) cells was also assayed in a similar manner. The co-cultured cells were incubated for approximately 24 hours, and then supernatants were collected for measurement of IFN-y (CD8 + cells) or IFN-Y, TNF-α or IL-2 (CD4 + cells) using a multiplex cytokine immunoassay ( Luminex®).
[0933] [ 0415] Results for CD8 + cells are set forth in Figures 14A and 14B. The engineered CD8 + T cells expressing the various CARs containing anti-human CD19 scFv were observed to secrete IFN- and in an antigen-specific manner after incubation with CD19 + cells, to a degree comparable to that observed for CAR-expressing cells containing the anti-CD19 (FMC63) scFv. Cytokine secretion was not observed after incubation of control K562 cells that did not express CD19. The levels of cytokine secretion observed for cells expressing CAR with the anti-human CD19 scFvs tested in the VH-VL orientation were comparable and in some cases higher than those observed for cells expressing the CAR containing murine anti-CD19 scFv. . The degree of IFNy secretion observed for cells expressing a CAR with a given human scFv in the VH-VL orientation was generally greater than that observed for cells expressing a CAR with the corresponding scFv in the reverse orientation (VL-VH ). As shown in Figure 14B, secretion of antigen-specific cytokines by modified CD8 + T cells expressing the various CARs containing human anti-CD19 scFv (VH-VL orientation) was also observed after coculture with CLL cells.
[0935] [ 0416] Results for CAR-expressing CD4 + T cells are set forth in Figure 15. Modified CD4 + T cells expressing the various scFv-containing human anti-CD19 CARs (VH-VL orientation) were observed at cytokines secreted by a specific antigen after incubation with CD19 + target cells, at levels comparable and generally higher than those observed for cells expressing CAR containing murine scFv (FMC63). No cytokine secretion was observed after CD19 negative control cells.
[0937] C. T cell proliferation
[0939] [0417] The proliferation of the various CAR-expressing T cells after incubation with the CD19-expressing target cells was assessed by flow cytometry. CAR-expressing CD8 + or CD4 + T cells were labeled with 0.2 µM carboxyfluorescein succinmidyl ester (CFSE). Cells were washed and incubated for 72 hours in triplicate with target cells (K562, K562 / CD19 or Raji) in medium containing serum without exogenous cytokines. Division of live T cells was indicated by CFSE dilution, as assessed by flow cytometry.
[0941] [ 0418] The results are set forth in Figure 16A and 16B for CAR CD8 + expressing T cells and CAR CD4 + expressing T cells, respectively. As shown in Figure 16A, CD8 + T cells expressing each of the tested anti-human CD19 scFv-containing CAR constructs proliferated after coculture with CD19-expressing K562 / CD19 or Raji target cells, but generally not cells. control K562. The degree of proliferation observed for CAR-expressing T cells with the tested anti-human CD19 scFv was comparable to that observed for cells expressing CAR-containing murine anti-CD19 scFv. The degree of proliferation of cells expressing a CAR with a given human scFv in the VH-VL orientation was generally observed to be greater than that observed for cells expressing a CAR with the corresponding scFv in the reverse orientation (VL-VH) .
[0943] [ 0419] Antigen-specific proliferation of CAR expressing T cells was also observed for CD4 + cells. As shown in Figure 16B, CD4 + T cells expressing each of the tested anti-human CD19 scFv-containing CAR constructs proliferated after coculture with CD19-expressing K562 / CD19 or Raji target cells. The degree of proliferation observed for CD4 + T cells expressing CAR with the tested anti-human CD19 scFv was comparable to that observed for cells expressing the murine anti-CD19 scFv containing CAR.
[0945] Example 5: Antitumor effect of CAR expressing T cells after adoptive transfer in vivo
[0946] [ 0420] The antitumor effects of engineered primary human T cells expressing CAR were evaluated by controlling tumors after adoptive transfer of cells to patient derived xenograft tumor model (PDX) animal subjects. Six to eight week old female mice NOD.Cg.PrkdcscidIL2RGtmW;, / SZJ (NSG) were injected intravenously (iv) with 0.5 x 10 6 Raji firefly luciferase transfected (Raji-ffluc) lymphoma tumor cells . Tumor grafting was allowed to occur for 6 days and was verified using bioluminescence imaging. On day 7, mice received a single intravenous injection (iv) of a suboptimal dose (1 x 106 CAR expression T cells in this study) of the various genetically engineered human primary T cells (CD8 + cells alone (Figure 17A) or CD4 + and CD8 + cells combined in a 1: 1 ratio (Figure 17B)) described in Example 3. As a control, cells that were transduced with EGFRt alone (negative control) were administered to the mice. The suboptimal dose was used to better visualize differences in antitumor effects.
[0948] [ 0421] The anti-tumor activity of adoptively transferred CAR expressing cells was monitored by bioluminescence imaging on days 6, 9, 13, 2 or 27, and 34. For bioluminescence imaging, mice received intraperitoneally (ip ) of the luciferin substrate (CaliperLife Sciences, Hopkinton, MA) resuspended in PBS (15 µg / g body weight). Mice were anesthetized and imaged essentially as described in WO2015 / 095895. The mean luminosity (p / s / cm2 / sr) was determined.
[0950] [ 0422] As shown in Figures 17A and 17B, tumors in control mice continued to grow during the course of the study after adoptive transfer of control T cells (CD8 + cells alone (Figure 17A) or combination of c D4 + cells and CD8 + (Figure 17B) transduced with EGFRt alone). Compared to control mice, it was observed that mice given adoptive T-cell transfer Manipulated cells expressing each of the various anti-CD19 scFv-containing CARs tested had a lower degree of bioluminescence signal, indicating a reduction in tumor size with time and / or a lower degree of tumor growth in the treated animals. Overall, as shown in Figure 17A, adoptive transfer of CD8 + T cells expressing human anti-CD 19 scFv CARs tested alone led to a comparative reduction in tumor size to at least the same degree as adoptive transfer. from cells expressing a CAR containing the mouse anti-CD19 scFv (FMC63). As shown in Figure 17B, adoptive transfer of the combination of CD8 + and CD4 + T cells expressing the tested anti-human CD19 CARs was observed to reduce tumor size over time. Tumor size (indicated by bioluminescence signal) after adoptive transfer of such anti-CD19 CAR-expressing human cells was observed to be comparatively smaller than that detected after adoptive transfer of scFv-derived CAR-expressing cells mouse.
[0952] EXAMPLE 6: Identification of the region in human CD19 recognized by anti-CD19 antibodies
[0954] [ 0423] CARs containing certain anti-CD19 antibodies (scFv) described in Example 1, or the murine anti-CD19 scFv (FMC63), were evaluated for binding to various CD19 molecules. K562 cells were designed to express (a) a human CD19 (having the amino acid sequence indicated in SEQ ID NO: 92), (b) a Macaca mulatta (rhesus macaque (rhesus)) CD19 (having the sequence of amino acids indicated in SEQ ID NO: 139; accession number F7F486), or (c) one of three different human / rhesus chimeric CD19 molecules, V1, V2, and V3, containing regions proximal to the membrane that had the sequences depicted in Figure 18A. Apart from the region depicted in Figure 18A, the remaining regions of each chimeric molecule were identical in sequence to the corresponding regions of rhesus CD19.
[0956] [ 0424] CD19 chimeric V1: The 74 amino acid proximal membrane region depicted in Figure 18A of the chimeric molecule designated V1 had the amino acid sequence set forth in SEQ ID NO: 140, which was identical to the sequence of the corresponding region . (residues 218 to 291) of the human CD19 molecule having the sequence set forth in SEQ ID NO: 92.
[0958] [ 0425] V2 chimeric CD19: The 75 amino acid proximal membrane region depicted in Figure 18A of the chimeric CD19 molecule designated V2 had the amino acid sequence set forth in SEQ ID NO: 141. Within this region, the proximal portion the 27 amino acid membrane was identical in sequence to the corresponding portion (residues 265 to 291) of human CD19. The remaining portion of the region shown was identical in sequence to the corresponding portion of the CD19 rhesus sequence set forth in SEQ ID NO: 139. The positions in this remaining portion that have a substitution or insertion compared to the corresponding human sequence are underlined.
[0960] [ 0426] Chimeric CD19 V3: The 74 amino acid region depicted in Figure 18A of the chimeric CD19 molecule designated V3 had the amino acid sequence set forth in SEQ ID NO: 142. Within this depicted region, a portion of 47 amino acids. identical in sequence to the corresponding portion (residues 218-264) of the human CD19 sequence set forth in SEQ ID NO: 92. The remaining 27 amino acid portion proximal to the membrane was identical in sequence to the corresponding portion of the set of sequences of CD19 rhesus in SEQ ID NO: 139. Positions in this remaining 27 amino acid portion that has a substitution compared to the corresponding human sequence are underlined.
[0962] [ 0427] Primary human T cells expressing various human CARs containing anti-CD19 scFv or a CAR containing murine anti-CD19 scFv (FMC63) were generated as described in Example 3 and co-cultured with the various K562 target cells transfected with nucleic acid molecules encoding the various CD19 molecules, in an effector to target (E: T) ratio of 2: 1. Cells were incubated for 24 hours and supernatants were collected for IFN-y measurement, using a cytokine immunoassay, as an indicator of functional binding of CARs containing anti-CD 19 scFv to the respective c D19 molecules in the surface of the target cells. The results are shown in Figure 18B.
[0964] [ 0428] Each of the anti CD19 CARs tested exhibited detectable levels of cytokines after co-culturing with cells expressing the human CD19 molecule (indicating functional binding to it), but not after co-culturing with cells expressing CD19. rhesus. For each of the anti-CD19 CARs tested, detectable levels of secretion were observed after coculture with cells expressing the rhesus / human chimeric molecules designated V1 (derived from humans from the 74 amino acid region proximal to the entire membrane) and V3. (derived from rhesus from the proximal 27 amino acid portion of the membrane), but not to cells expressing the human / rhesus chimeric molecule designated V2 (derived from humans from the proximal 27 amino acid region of the membrane).
[0966] [ 0429] These results indicated that at least part of a 32 amino acid portion (SEQ ID NO: 143 (HPKGPKSLLSLELKDDRPARDMWVMETGLLLP) of the human CD19 molecule (corresponding to residues 218 249 of SEQ ID NO: 92), was important for functional binding to CD19 for each of the anti-CD19 CARs tested. Specifically, while each of V1 and V3 contained this 32 amino acid sequence (shown in bold in Figure 18A), the corresponding portion of V2 contained this sequence of 33 residue amino acids set forth in SEQ ID NO: 144 (RPKGPKSSLLSLELKDDRPDRDMWVVDTGLLLT), which was identical in sequence to the corresponding portion of the rhesus CD19 molecule, but contained five amino acid substitutions (at positions 218, 236, 242, 243, and 249 of the Sequence of CD19 of SEQ ID NO: 92) and an insert (between positions 223 and 224 of the human CD19 sequence of SEQ ID NO: 92) compared to the corresponding human sequence, each underlined in Figure 18A. Therefore, the results indicate that the amino acids present at least one of these positions in the human sequence (positions 218, 236, 242, 243, 249 and / or 223-224 of SEQ ID NO: 92) was important for the ability to each CAR tested to specifically bind to human CD19. Thus, the results support the conclusion that each of the human scFv-containing CARs tested bound a similar and / or overlapping epitope compared to the CAR-containing mouse scFv, FMC63.
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权利要求:
Claims (15)
[1]
1. A CD19-binding antibody or its CD19-binding antigen-binding fragment comprising:
a VH region comprising the amino acid sequence of SEQ ID NO: 11, and a region comprising the amino acid sequence of SEQ ID NO: 13; or
a VH region comprising the amino acid sequence of SEQ ID NO: 11, and a VL region comprising the amino acid sequence of SEQ ID NO: 14; or
a VH region comprising the amino acid sequence of SEQ ID NO: 11, and a VL region comprising the amino acid sequence of SEQ ID NO: 16; or
a VH region comprising the amino acid sequence of SEQ ID NO: 12, and a VL region comprising the amino acid sequence of SEQ ID NO: 15; or
a VH region comprising the amino acid sequence of SEQ ID NO: 12, and a VL region comprising the amino acid sequence of SEQ ID NO: 17.
[2]
2. The antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or antigen-its binding fragment specifically binds human CD19.
[3]
3. The antibody or antigen-binding fragment thereof according to claim 1 or claim 2, wherein the antibody or antigen-binding fragment thereof is human.
[4]
4. The antibody or antigen-binding fragment thereof of any of claims 1-3, wherein the antibody or antigen-binding fragment thereof is monoclonal.
[5]
5. The antibody or antigen-binding fragment thereof of any of claims 1-4, wherein the antibody or antigen-binding fragment thereof is a single chain fragment comprising an scFv.
[6]
The antibody or antigen-binding fragment thereof of claim 5, wherein the scFv comprises the amino acid sequence set forth in SEQ ID NO: 2, 4, 6, 8, 10 or a sequence exhibiting at least 95% of sequence identity with the amino acid sequence set forth in SEQ ID NO: 2, 4, 6, 8, 10.
[7]
7. A conjugate, comprising the antibody or antigen-binding fragment thereof of any of claims 1-6 and a heterologous molecule or moiety.
[8]
8. A chimeric antigen receptor (CAR) comprising an extracellular portion comprising the antibody or antigen-binding fragment thereof of any of claims 1-6 and an intracellular signaling domain, wherein optionally the antibody or fragment comprises an scFv and the intracellular signaling domain comprises an ITAM, where optionally the intracellular signaling domain comprises a signaling domain from a CD3-zeta chain (CD3Z).
[9]
The chimeric antigen receptor of claim 8, further comprising a transmembrane domain linking the extracellular domain and the intracellular signaling domain and / or further comprising an intracellular signaling domain of a T cell costimulatory molecule, optionally in where the T cell costimulatory molecule is selected from the group consisting of 4-1BB or c D28.
[10]
10. A nucleic acid encoding the antibody or antigen-binding fragment thereof of any of claims 1-6, conjugate of claim 7 or the chimeric antigen receptor of claim 8 or claim 9.
[11]
11. Genetically modified cells expressing a receptor comprising the antibody or antigen-binding fragment thereof of any of claims 1-6, conjugate of claim 7 or the chimeric antigen receptor of claim 8 or claim 9.
[12]
The genetically modified cells of claim 11, wherein the genetically modified cells are T cells, optionally where the T cells are CD4 + and / or CD8 + T cells.
[13]
13. A composition, comprising the antibody or fragment thereof of any of claims 1-6, the conjugate of claim 7 or the chimeric antigen receptor of claim 8 or claim 9 or the cells of claim 11 or the claim 12, and a pharmaceutically acceptable excipient.
[14]
14. A composition of claim 13 for use in a method of treating a disease or disorder associated with CD19, wherein the disease or disorder is a B-cell malignancy.
[15]
The composition of claim 13 for use according to claim 14, wherein the B-cell malignancy is selected from the group consisting of B-cell chronic lymphocytic leukemia (CLL), acute lymphocytic leukemia (ALL), leukemias. prolymphocytic, hairy cell leukemias, acute lymphocytic leukemias, leukemias Null acute lymphoblastic lantern, non-Hodgkin lantern, diffuse large B-cell lantern (DLBCL), multiple myelomas, follicular lantern, marginal zone splenic lantern, mantle cell lantern, indolent B-cell lantern, and Hodgkin lantern.

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同族专利:

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公开号 | 公开日

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RU2741105C2|2021-01-22|

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AU2015308648A1|2017-03-02|

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RU2020144342A|2021-02-18|

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SA517380971B1|2021-04-19|

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MA40497A|2017-07-05|

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PH12017500268A1|2017-07-03|

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RU2020144342A3|2021-06-25|

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IL250831D0|2017-04-30|

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US20160152723A1|2016-06-02|

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RU2017110044A|2018-09-28|

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EP3186280A1|2017-07-05|

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KR20170057298A|2017-05-24|

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CU20170023A7|2017-08-08|

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SG11201701297WA|2017-03-30|

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US20200172630A1|2020-06-04|

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RU2017110044A3|2019-03-27|

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WO2016033570A1|2016-03-03|

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AU2021203056A1|2021-06-24|

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ES2833010T3|2021-06-14|

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JP2020182454A|2020-11-12|

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EP3186280B1|2020-09-23|

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US10533055B2|2020-01-14|

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CN114106181A|2022-03-01|

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BR112017003505A2|2017-12-12|

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JP2017526370A|2017-09-14|

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CN106922147B|2021-12-21|

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EP3805267A1|2021-04-14|

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EP3186280B9|2021-03-31|

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CA2962915A1|2016-03-03|

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CN106922147A|2017-07-04|

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AU2015308648B2|2021-06-10|

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CU24494B1|2021-01-12|

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TW201625686A|2016-07-16|

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MX2017002459A|2017-05-19|

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JP6727192B2|2020-07-22|

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法律状态:

优先权:

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申请号 | 申请日 | 专利标题

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US201462043273P| true| 2014-08-28|2014-08-28|

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US201462078942P| true| 2014-11-12|2014-11-12|

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PCT/US2015/047606|WO2016033570A1|2014-08-28|2015-08-28|Antibodies and chimeric antigen receptors specific for cd19|

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