US2020271657A1PendingUtilityA1
Articles and methods directed to personalized therapy of cancer
Assignee: STEPANOV ALEXEY VYACHESLAVOVICHPriority: Oct 4, 2017Filed: Oct 4, 2018Published: Aug 27, 2020
Est. expiryOct 4, 2037(~11.2 yrs left)· nominal 20-yr term from priority
Inventors:Alexey Vyacheslavovich StepanovDmitry Dmitrievich GenkinRichard A. LernerAlexey Anatolievich BelogurovAlexander Gabibovich GabibovJia Xie
G01N 33/5759G01N 33/57557A61K 40/4211A61K 40/11A61K 40/4204A61K 40/32A61K 40/4215A61K 40/421A61K 40/42A61K 40/31A61K 2239/48A61K 2239/31A61K 2239/38C12N 2510/00C07K 2317/73C07K 2317/53C07K 2319/33A61K 2039/6081C07K 2317/24C07K 2319/03C07K 2317/622C07K 2319/70C12Q 2600/156A61P 35/00C12Q 1/6886G01N 33/543G01N 33/505A61K 35/17A61K 47/643C07K 14/7051C07K 16/2863C07K 16/2803C12N 5/0636A61K 39/0011A61K 2039/5156A61K 2039/5158A61K 2300/00A61K 2121/00A61K 2039/545A61K 2039/572A61K 2039/54G01N 33/57492
52
PatentIndex Score
0
Cited by
0
References
0
Claims
Abstract
Described are methods for providing personalized medicine for the treatment of B cell malignancies including lymphoma. The methods make use of Chimeric Antigen Receptor (CAR) technology.
Claims
exact text as granted — not AI-modifiedWhat is claimed is:
1 . A method of treating lymphoma in a subject comprising:
identifying a unique B cell receptor expressed in lymphoma cells of the subject; expressing the unique B cell receptor in a cell; contacting the cell with a putative unique B cell receptor ligand from a library; detecting binding of said unique B cell receptor to a putative unique B cell receptor ligand, thereby identifying a unique B cell receptor ligand; and administering to the subject a therapeutically effective amount of the B cell receptor ligand coupled to a therapeutic agent.
2 . A method of treating lymphoma in a subject comprising:
identifying a unique B cell receptor expressed in lymphoma cells of the subject; contacting unique B cell receptor with a putative unique B cell receptor ligand from a library; detecting binding of said unique B cell receptor to a putative unique B cell receptor ligand, thereby identifying a unique B cell receptor ligand; and administering to the subject a therapeutically effective amount of the B cell receptor ligand coupled to a therapeutic agent.
3 . The method of claim 1 or 2 , wherein the putative unique B cell receptor ligand comprises a peptide, a cyclopeptide, a peptoid, a cyclopeptoid, a polysaccharide, a lipid, or a small molecule.
4 . The method of claim 1 , wherein the unique B cell receptor and the putative unique B cell receptor ligand are co-expressed in T cells.
5 . The method of any of claims claim 1 - 4 , wherein the cell comprises a CAR comprising the putative unique B cell receptor ligand.
6 . The method of claim 5 , wherein said detection method comprises identifying activation of the T cell.
7 . The method of claim 6 , wherein identifying activation of the T cell comprises measuring expression of CD69 or CD25.
8 . The method of claim 2 or 3 , wherein the unique B cell receptor is contacted with a putative unique B cell receptor ligand from a library by phage display.
9 . The method of claim 8 , wherein the library comprises a library of putative B cell receptor ligands linked to a phage.
10 . The method of claim 8 or 9 , wherein the unique B cell receptor is attached to a solid support.
11 . The method of claim 10 , wherein contacting unique B cell receptor with a putative unique B cell receptor ligand from a library comprises panning the unique B cell receptor attached to a solid support with the library of putative B cell receptor ligands linked to a phage for one or more rounds.
12 . The method of claim 11 , wherein each round of the panning includes negative selection.
13 . The method of any of claims 1 - 12 , wherein the subject is determined to have lymphoma.
14 . The method of claim 13 , wherein the subject is determined to have one or more single-nucleotide polymorphisms (SNPs) associated with lymphoma.
15 . The method of any of claims 1 - 14 , wherein identifying a unique B cell receptor comprises:
obtaining cells from a biopsy; extracting RNA from the cells; synthesizing cDNA from the extracted RNA; and sequencing the cDNA.
16 . The method of any of claims 1 - 14 , wherein identifying a unique B cell receptor comprises cloning and sequencing circulating cell free DNA.
17 . The method of any of claims 1 - 16 , wherein the method is performed in 3 weeks or less.
18 . The method of any of claims 1 - 17 , wherein the therapeutic agent comprises a radioactive isotope.
19 . The method of any of claims 1 - 17 , wherein the B cell receptor ligand coupled to a therapeutic agent comprises a therapeutic CAR.
20 . The method of any of claims 1 - 17 , wherein the therapeutic agent comprises a chemotherapy.
21 . The method of any of claims 1 - 17 , wherein the therapeutic agent comprises an immunotherapy.
22 . The method of any of claims 1 - 21 , wherein the subject is administered the B cell receptor, or a fragment thereof, concomitantly with the therapeutic agent.
23 . A method of treating lymphoma in a subject comprising:
identifying a unique B cell receptor expressed in lymphoma cells of the subject; co-expressing the unique B cell receptor and putative unique B cell receptor ligand from a library in a cell; detecting binding of said unique B cell receptor to a putative unique B cell receptor ligand, thereby identifying a unique B cell receptor ligand; and administering to the subject a therapeutically effective amount of the B cell receptor ligand coupled to a therapeutic agent.
24 . The method of claim 23 , wherein the unique B cell receptor and the putative unique B cell receptor ligand are co-expressed in T cells.
25 . The method of claim 24 , wherein the T cell comprises a CAR comprising the putative unique B cell receptor ligand.
26 . The method of claim 25 , wherein said detection method comprises identifying activation of the T cell.
27 . The method of claim 26 , wherein identifying activation of the T cell comprises measuring expression of CD69 or CD25.
28 . The method of any of claims 23 - 27 , wherein the subject is determined to have lymphoma.
29 . The method of claim 28 , wherein the subject is determined to have one or more single-nucleotide polymorphisms (SNPs) associated with lymphoma.
30 . The method of any of claims 23 - 29 , wherein identifying a unique B cell receptor comprises:
obtaining cells from a biopsy; extracting RNA from the cells; synthesizing cDNA from the extracted RNA; and sequencing the cDNA.
31 . The method of any of claims 23 - 29 , wherein identifying a unique B cell receptor comprises cloning and sequencing circulating cell free DNA.
32 . The method of any of claims 23 - 31 , wherein the method is performed in 3 weeks or less.
33 . The method of any of claims 23 - 32 , wherein the therapeutic agent comprises a radioactive isotope.
34 . The method of any of claims 23 - 32 , wherein the B cell receptor ligand coupled to a therapeutic agent comprises a therapeutic CAR.
35 . The method of any of claims 23 - 32 , wherein the therapeutic agent comprises a chemotherapy.
36 . The method of any of claims 23 - 32 , wherein the therapeutic agent comprises an immunotherapy.
37 . The method of any of claims 23 - 36 , wherein the putative B cell receptor ligand domain comprises a polypeptide from a cyclopeptide library.
38 . The method of claim 37 , wherein the putative B cell receptor ligand domain further comprises an Fc region.
39 . The method of any of claims 23 - 38 , wherein the subject is administered the B cell receptor, or a fragment thereof, concomitantly with the therapeutic agent.
40 . A method of identifying a B cell receptor ligand comprising:
providing to a population of T cells nucleic acid molecules encoding a B cell receptor and a library of chimeric antigen receptors (CARs), wherein each CAR within the library comprises a distinct putative B cell receptor ligand domain; coexpressing the B cell receptor and the library of CARs in T cells; measuring activation of the T cells, wherein the putative B cell receptor ligand domain of a CAR from the library of CARs comprises a ligand of the B cell receptor if a T cell expressing the B cell receptor and the CAR is activated; and isolating the nucleic acid molecule encoding the CAR from an activated T cell; and sequencing the putative B cell receptor ligand domain of the nucleic acid molecule encoding the CAR from the activated T cell; thereby identifying a B cell receptor ligand.
41 . The method of claim 40 , wherein the B cell receptor is from a cancer cell.
42 . The method of claim 41 , wherein the cancer cell is a lymphoma cell, e.g., from a patient determined to have lymphoma.
43 . The method of claim 42 , wherein the lymphoma cell is obtained from a tumor from a patient.
44 . The method of claim 43 , wherein the patient is determined to have one or more single-nucleotide polymorphisms (SNPs) associated with lymphoma.
45 . The method of any of claims 40 - 44 , wherein the putative B cell receptor ligand domain comprises a polypeptide of 30 amino acids or less.
46 . The method of any of claims 40 - 45 , wherein the putative B cell receptor ligand domain comprises a polypeptide from a cyclopeptide library.
47 . The method of claim 46 , wherein the putative B cell receptor ligand domain further comprises an Fc region.
48 . The method of any of claims 40 - 47 , wherein the CAR comprises a transmembrane domain.
49 . The method of claim 48 , wherein the transmembrane domain comprises alpha, beta or zeta chain of the T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137 and/or CD154.
50 . The method of any of claims 40 - 49 , wherein the CAR comprises an intracellular region.
51 . The method of claim 50 , wherein the intracellular region comprises a MHC class I molecule, a TNF receptor protein, an Immunoglobulin-like protein, a cytokine receptor, an integrin, a signaling lymphocytic activation molecule (SLAM protein), an activating NK cell receptor, BTLA, a Toll ligand receptor, OX40, CD2, CD7, CD27, CD28, CD30, CD40, CDS, ICAM-1, LFA-1 (CD25/CD18), 4-29B (CD137), B7-H3, CDS, ICAM-1, ICOS (CD278), GITR, BAFFR, LIGHT, HVEM (LIGHTR), KIRDS2, SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD423, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD129, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, NKG2C, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 304), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, CD123, a ligand that specifically binds with CD83, and/or CD3 zeta.
52 . The method of any of claims 40 - 51 , wherein the CAR comprises a hinge domain.
53 . The method of any of claims 40 - 52 , wherein T cell activation is measured by an increase in expression of CD69 or CD25.
54 . The method of any of claims 40 - 52 , wherein T cell activation is measured by an increase in expression of a fluorescent protein reporter gene under the control of Jun, NF-κB and/or Rel.
55 . The method of any of claims 40 - 54 , further comprising treating a subject having lymphoma with the B cell receptor ligand wherein:
the B cell receptor is expressed in a tumor from the subject; and the B cell receptor ligand coupled to a therapeutic agent.
56 . A method of treating lymphoma comprising:
administering to a subject a therapeutically effective dose of a B cell receptor ligand coupled to a therapeutic agent, wherein the B cell receptor ligand comprises a putative B cell receptor ligand domain, and wherein a CAR comprising the putative B cell receptor ligand domain activates a T cell when co-expressed with the B cell receptor of the lymphoma cells.
57 . The method of claim 56 , wherein the therapeutic agent comprises a radioactive isotope.
58 . The method of claim 56 , wherein the B cell receptor ligand coupled to a therapeutic agent comprises a therapeutic CAR.
59 . The method of claim 56 , wherein the therapeutic agent comprises a chemotherapy.
60 . The method of claim 56 , wherein the therapeutic agent comprises an immunotherapy.
61 . The method of any of claims 56 - 60 , wherein the putative B cell receptor ligand domain comprises a polypeptide of 30 amino acids or less.
62 . The method of any of claims 56 - 61 , wherein the putative B cell receptor ligand domain comprises a polypeptide from a cyclopeptide library.
63 . The method of claim 62 , wherein the putative B cell receptor ligand domain further comprises an Fc region.
64 . The method of any of claims 56 - 63 , wherein the CAR comprising the putative B cell receptor ligand domain or the therapeutic CAR comprises a transmembrane domain.
65 . The method of claim 64 , wherein the transmembrane domain comprises alpha, beta or zeta chain of the T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137 and/or CD154.
66 . The method of any of claims 56 - 65 , wherein the CAR comprising the putative B cell receptor ligand domain or the therapeutic CAR comprises an intracellular region.
67 . The method of claim 66 , wherein the intracellular region comprises a MHC class I molecule, a TNF receptor protein, an Immunoglobulin-like protein, a cytokine receptor, an integrin, a signaling lymphocytic activation molecule (SLAM protein), an activating NK cell receptor, BTLA, a Toll ligand receptor, OX40, CD2, CD7, CD27, CD28, CD30, CD40, CDS, ICAM-1, LFA-1 (CD25/CD18), 4-29B (CD137), B7-H3, CDS, ICAM-1, ICOS (CD278), GITR, BAFFR, LIGHT, HVEM (LIGHTR), KIRDS2, SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD423, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD129, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, NKG2C, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 304), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, CD123, a ligand that specifically binds with CD83, and/or CD3 zeta.
68 . The method of any of claims 56 - 67 , wherein the CAR comprising the putative B cell receptor ligand domain or the therapeutic CAR comprises a hinge domain.
69 . The method of any of claims 56 - 68 , wherein T cell activation is measured by an increase in expression of CD69 or CD25.
70 . The method of any of claims 56 - 69 , wherein the subject is administered the B cell receptor, or a fragment thereof, concomitantly with the therapeutic agent.
71 . A method of treating lymphoma in a subject comprising:
identifying a unique B cell receptor expressed in lymphoma cells of the subject; co-expressing the unique B cell receptor and a chimeric antigen receptor (CAR) from a library of CARs in a T cell, wherein each CAR within the library comprises a distinct putative B cell receptor ligand domain; identifying a B cell receptor ligand by identifying an activated T cell, wherein the putative B cell receptor ligand domain of the CAR from the library of CARs comprises a ligand of the unique B cell receptor if the T cell expressing the B cell receptor and the CAR is activated; and administering to the subject a therapeutically effective dose of the B cell receptor ligand coupled to a therapeutic agent.
72 . The method of claim 71 , wherein the subject is determined to have lymphoma.
73 . The method of claim 72 , wherein the subject is determined to have one or more single-nucleotide polymorphisms (SNPs) associated with lymphoma.
74 . The method of any of claims 71 - 73 , wherein identifying a unique B cell receptor comprises:
obtaining cells from a biopsy; extracting RNA from the cells; synthesizing cDNA from the extracted RNA; and sequencing the cDNA.
75 . The method of any of claims 71 - 73 , wherein identifying a unique B cell receptor comprises cloning and sequencing circulating cell free DNA.
76 . The method of any of claims 71 - 75 , further comprising preparing the B cell receptor ligand coupled to a therapeutic agent.
77 . The method of any of claims 71 - 76 , wherein the method is performed in 3 weeks or less.
78 . The method of any of claims 71 - 77 , wherein the T cell is activated by autocrine-based activation of the CAR.
79 . The method of any of claims 71 - 78 , wherein identifying a B cell receptor ligand further comprises:
isolating the nucleic acid molecule encoding the CAR from the activated T cell; and sequencing the putative B cell receptor ligand domain of the nucleic acid molecule encoding the CAR from the activated T cell.
80 . The method of any of claims 71 - 79 , wherein the therapeutic agent comprises a radioactive isotope.
81 . The method of any of claims 71 - 79 , wherein the B cell receptor ligand coupled to a therapeutic agent comprises a therapeutic CAR.
82 . The method of any of claims 71 - 79 , wherein the therapeutic agent comprises a chemotherapy.
83 . The method of any of claims 71 - 79 , wherein the therapeutic agent comprises an immunotherapy.
84 . The method of any of claims 71 - 83 , wherein the putative B cell receptor ligand domain comprises a polypeptide of 30 amino acids or less.
85 . The method of any of claims 71 - 83 , wherein the putative B cell receptor ligand domain comprises a polypeptide from a cyclopeptide library.
86 . The method of claim 85 , wherein the putative B cell receptor ligand domain further comprises an Fc region.
87 . The method of any of claims 71 - 86 , wherein the CAR comprising the putative B cell receptor ligand domain or the therapeutic CAR comprises a transmembrane domain.
88 . The method of claim 87 , wherein the transmembrane domain comprises alpha, beta or zeta chain of the T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137 and/or CD154.
89 . The method of any of claims 71 - 88 , wherein the CAR comprising the putative B cell receptor ligand domain or the therapeutic CAR comprises an intracellular region.
90 . The method of claim 89 , wherein the intracellular region comprises a MHC class I molecule, a TNF receptor protein, an Immunoglobulin-like protein, a cytokine receptor, an integrin, a signaling lymphocytic activation molecule (SLAM protein), an activating NK cell receptor, BTLA, a Toll ligand receptor, OX40, CD2, CD7, CD27, CD28, CD30, CD40, CDS, ICAM-1, LFA-1 (CD25/CD18), 4-29B (CD137), B7-H3, CDS, ICAM-1, ICOS (CD278), GITR, BAFFR, LIGHT, HVEM (LIGHTR), KIRDS2, SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD423, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD129, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, NKG2C, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 304), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, CD123, and/or a ligand that specifically binds with CD83.
91 . The method of any of claims 71 - 90 , wherein the CAR comprising the putative B cell receptor ligand domain or the therapeutic CAR comprises a hinge domain.
92 . The method of any of claims 71 - 90 , wherein T cell activation is measured by an increase in expression of CD69 or CD25.
93 . The method of any of claims 71 - 91 , wherein the subject is administered the B cell receptor, or a fragment thereof, concomitantly with the therapeutic agent.
94 . A method of treating lymphoma in a subject comprising:
identifying a unique B cell receptor expressed in lymphoma cells of the subject; co-expressing the unique B cell receptor and a putative unique B cell receptor ligand from a library in a cell; identifying said unique B cell receptor ligand by a detection method, wherein a putative unique B cell receptor ligand is a unique B cell receptor ligand if it interacts with the unique B cell receptor; and administering to the subject a therapeutically effective amount of the B cell receptor ligand coupled to a therapeutic agent.
95 . The method of claim 94 , wherein the unique B cell receptor and a putative unique B cell receptor ligand are co-expressed in T cells.
96 . The method of claim 94 or 95 , wherein cell comprises a CAR comprising the putative unique B cell receptor ligand.
97 . The method of claim 96 , wherein said detection method comprises identifying activation of the T cell.
98 . The method of claim 97 , wherein identifying activation of the T cell comprises measuring expression of CD69 or CD25.
99 . The method of any of claims 94 - 98 , wherein the subject is determined to have lymphoma.
100 . The method of claim 99 , wherein the subject is determined to have one or more single-nucleotide polymorphisms (SNPs) associated with lymphoma.
101 . The method of any of claims 94 - 100 , wherein identifying a unique B cell receptor comprises:
obtaining cells from a biopsy; extracting RNA from the cells; synthesizing cDNA from the extracted RNA; and sequencing the cDNA.
102 . The method of any of claims 94 - 100 , wherein identifying a unique B cell receptor comprises cloning and sequencing circulating cell free DNA.
103 . The method of any of claims 94 - 102 , wherein the method is performed in 3 weeks or less.
104 . The method of any of claims 94 - 103 , wherein the therapeutic agent comprises a radioactive isotope.
105 . The method of any of claims 94 - 103 , wherein the B cell receptor ligand coupled to a therapeutic agent comprises a therapeutic CAR.
106 . The method of any of claims 94 - 103 , wherein the therapeutic agent comprises a chemotherapy.
107 . The method of any of claims 94 - 103 , wherein the therapeutic agent comprises an immunotherapy.
108 . The method of any of claims 94 - 107 , wherein the putative B cell receptor ligand domain comprises a polypeptide from a cyclopeptide library.
109 . The method of claim 108 , wherein the putative B cell receptor ligand domain further comprises an Fc region.
110 . The method of any of claims 94 - 109 , wherein the subject is administered the B cell receptor, or a fragment thereof, concomitantly with the therapeutic agent.
111 . A chimeric antigen receptor (CAR) comprising:
a putative B cell receptor ligand domain that comprises a polypeptide from a cyclopeptide library;
a transmembrane domain; and
an intracellular region.
112 . The CAR of claim 111 , wherein the CAR activates a T cell when co-expressed with a B cell receptor, wherein a B cell receptor ligand of the B cell receptor comprises the putative B cell receptor ligand domain.
113 . The CAR of claim 111 or 112 , wherein the transmembrane domain comprises alpha, beta or zeta chain of the T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137 and/or CD154.
114 . The CAR of any of claims 111 - 113 , wherein the intracellular region comprises a MHC class I molecule, a TNF receptor protein, an Immunoglobulin-like protein, a cytokine receptor, an integrin, a signaling lymphocytic activation molecule (SLAM protein), an activating NK cell receptor, BTLA, a Toll ligand receptor, OX40, CD2, CD7, CD27, CD28, CD30, CD40, CDS, ICAM-1, LFA-1 (CD25/CD18), 4-29B (CD137), B7-H3, CDS, ICAM-1, ICOS (CD278), GITR, BAFFR, LIGHT, HVEM (LIGHTR), KIRDS2, SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD423, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD129, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, NKG2C, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 304), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, CD123, and/or a ligand that specifically binds with CD83.
115 . The CAR of any of claims 111 - 114 , wherein the CAR comprises a hinge domain.
116 . The CAR of any of claims 111 - 115 , wherein the B cell receptor ligand comprises the amino acid sequence of any of SEQ ID NO: 1-3.
117 . A method of treating cancer in a subject comprising concomitantly administering:
CAR-expressing T-cells, wherein the CAR comprises an antigen binding domain that specifically binds a cancer-specific antigen in a cancer-specific manner; and a vaccine comprising a polypeptide or a nucleic acid expressing the cancer-specific antigen, or a cancer-specific fragment thereof.
118 . The method of claim 117 , wherein the cancer-specific antigen is a B-cell receptor.
119 . The method of claim 118 , wherein the cancer is a lymphoma.
120 . The method of any of claims 117 - 119 , wherein the polypeptide or nucleic acid comprises a heavy or light chain variable region, or fragment thereof.
121 . The method of claim 117 , wherein the cancer-specific antigen is expressed in the cancer and comprises a somatic mutation.
122 . The method of claim 121 , wherein the non-cancerous cells of the subject do not have the somatic mutation.
123 . The method of claim 121 or 122 , wherein the mutation is a point mutation, a splice-site mutation, a frameshift mutation, a read-through mutation, or a gene-fusion mutation.
124 . The method of any of claims 121 - 123 , wherein the somatic mutation comprises a mutation in EGFRvIII, PSCA, BCMA, CD30, CEA, CD22, L1CAM, ROR1, ErbB, CD123, IL13Rα2, Mesothelin, FRα, VEGFR, c-Met, 5T4, CD44v6, B7-H4, CD133, CD138, CD33, CD28, GPC3, EphA2, CD19, ACVR2B, anaplastic lymphoma kinase (ALK), MYCN, BCR, HER2, NY-ESO1, MUC1, or MUC16.
125 . The method of any of claims 121 - 124 , wherein the cancer comprises a tumor.
126 . The method of any of claims 121 - 125 , wherein the polypeptide or nucleic acid comprises the somatic mutation.
127 . The method of any of claims 121 - 126 , wherein the concomitant administration occurs at least two times, at least three times, at least four times, at least five times, at least six times, at least seven times, at least eight times, at least nine times, or at least ten times in the subject.
128 . The method of any of claims 121 - 127 , wherein the CAR-expressing T-cells are administered before the vaccine.
129 . The method of any of claims 121 - 127 , wherein the CAR-expressing T-cells are administered after the vaccine.
130 . The method of any of claims 121 - 129 , further comprising identifying the cancer-specific antigen in the subject.
131 . The method of claim 130 , wherein identifying the cancer-specific antigen comprises:
(i) obtaining cancerous cells from a subject; (ii) extracting DNA from the cells; and (iii) sequencing the DNA.
132 . The method of claim 131 , wherein identifying the cancer-specific antigen further comprises comparing the DNA sequence obtained from the cancerous cells to a DNA sequence of the same gene obtained from non-cancerous cells.
133 . The method of claim 130 or 131 , wherein the DNA is isolated from tumor cells.
134 . The method of claim 130 , wherein identifying the cancer-specific antigen comprises isolating and sequencing circulating cell free DNA of the subject.
135 . The method of claim 130 , wherein identifying the cancer-specific antigen comprises:
(i) obtaining cancerous cells from a subject; (ii) extracting RNA from the cells; (iii) synthesizing cDNA from the extracted RNA; and (iv) sequencing the cDNA.
136 . The method of claim 135 , wherein identifying the cancer-specific antigen further comprises comparing the cDNA sequence obtained from the cancerous cells to a cDNA sequence of the same gene obtained from non-cancerous cells.
137 . The method of any of claims 121 - 136 , wherein the vaccine comprises two or more polypeptides having overlapping sequences, each expressing a fragment of the cancer-specific antigen.
138 . The method of any of claims 121 - 137 , further comprising providing CAR-expressing T-cells by:
(i) identifying an antigen binding domain that specifically binds the cancer-specific antigen in a cancer-specific manner; and (ii) expressing a CAR comprising the antigen binding domain in T-cells.
139 . The method of any of claims 121 - 138 , wherein the polypeptide is conjugated to KLH.
140 . The method of any of claims 121 - 139 , wherein the vaccine is administered by intravenous, intraperitoneal, transmucosal, oral, subcutaneous, pulmonary, intranasal, intradermal or intramuscular administration.
141 . The method of any of claims 121 - 140 , wherein the vaccine is administered intratumorally.
142 . The method of any of claims 121 - 141 , wherein the CAR-expressing T-cells are administered by intravenous administration.
143 . The method of any of claims 121 - 142 , wherein the CAR comprises a transmembrane domain.
144 . The method of claim 143 , wherein the transmembrane domain comprises alpha, beta or zeta chain of the T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137 and/or CD154.
145 . The method of any of claims 121 - 144 , wherein the CAR comprises an intracellular region.
146 . The method of claim 145 , wherein the intracellular region comprises a MHC class I molecule, a TNF receptor protein, an Immunoglobulin-like protein, a cytokine receptor, an integrin, a signaling lymphocytic activation molecule (SLAM protein), an activating NK cell receptor, BTLA, a Toll ligand receptor, OX40, CD2, CD7, CD27, CD28, CD30, CD40, CDS, ICAM-1, LFA-1 (CD25/CD18), 4-29B (CD137), B7-H3, CDS, ICAM-1, ICOS (CD278), GITR, BAFFR, LIGHT, HVEM (LIGHTR), KIRDS2, SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD423, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD129, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, NKG2C, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 304), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, CD123, a ligand that specifically binds with CD83, and/or CD3 zeta.
147 . The method of any of claims 121 - 146 , wherein the CAR comprises a hinge domain.
148 . The method of any of claims 121 - 147 , further comprising administering a TLR9 agonist.
149 . The method of claim 148 , wherein the cancer-specific antigen is OX40.
150 . A composition for treating cancer in a subject comprising:
CAR-expressing T-cells, wherein the CAR comprises an antigen binding domain that specifically binds a cancer-specific antigen in a cancer-specific manner; and a polypeptide or a nucleic acid expressing the cancer-specific antigen, or a cancer-specific fragment thereof.
151 . The composition of claim 150 , wherein the cancer-specific antigen is a B-cell receptor.
152 . The composition of claim 150 or 151 , wherein the polypeptide or nucleic acid comprises a heavy or light chain variable region, or fragment thereof.
153 . The composition of claim 150 , wherein the cancer-specific antigen is expressed in the cancer and comprises a somatic mutation.
154 . The composition of claim 153 , wherein the non-cancerous cells of the subject do not have the somatic mutation.
155 . The composition of claim 153 or 154 , wherein the mutation is a point mutation, a splice-site mutation, a frameshift mutation, a read-through mutation, or a gene-fusion mutation.
156 . The composition of any of claims 153 - 155 , wherein the somatic mutation comprises a mutation in EGFRvIII, PSCA, BCMA, CD30, CEA, CD22, L1CAM, ROR1, ErbB, CD123, IL13Rα2, Mesothelin, FRα, VEGFR, c-Met, 5T4, CD44v6, B7-H4, CD133, CD138, CD33, CD28, GPC3, EphA2, CD19, ACVR2B, anaplastic lymphoma kinase (ALK), MYCN, BCR, HER2, NY-ESO1, MUC1, or MUC16.
157 . The composition of any of claims 153 - 156 , wherein the polypeptide or nucleic acid comprises the somatic mutation.
158 . The composition of any of claims 150 - 157 , wherein the vaccine comprises two or more polypeptides having overlapping sequences, each expressing a fragment of the cancer-specific antigen.
159 . The composition of any claims 150 - 158 , wherein the polypeptide is conjugated to KLH.
160 . The composition of any of claims 150 - 159 , wherein the CAR comprises a transmembrane domain.
161 . The composition of claim 160 , wherein the transmembrane domain comprises alpha, beta or zeta chain of the T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137 and/or CD154.
162 . The composition of any of claims 150 - 161 , wherein the CAR comprises an intracellular region.
163 . The composition of claim 162 , wherein the intracellular region comprises a MHC class I molecule, a TNF receptor protein, an Immunoglobulin-like protein, a cytokine receptor, an integrin, a signaling lymphocytic activation molecule (SLAM protein), an activating NK cell receptor, BTLA, a Toll ligand receptor, OX40, CD2, CD7, CD27, CD28, CD30, CD40, CDS, ICAM-1, LFA-1 (CD25/CD18), 4-29B (CD137), B7-H3, CDS, ICAM-1, ICOS (CD278), GITR, BAFFR, LIGHT, HVEM (LIGHTR), KIRDS2, SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD423, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11A, LFA-1, ITGAM, CD129, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, NKG2C, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 304), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, CD123, a ligand that specifically binds with CD83, and/or CD3 zeta.
164 . The composition of any of claims 150 - 163 , wherein the CAR comprises a hinge domain.
165 . The composition of any of claims 150 - 164 , further comprising administering a TLR9 agonist.
166 . The composition of claim 165 , wherein the cancer-specific antigen is OX40.
167 . A method for treating lymphoma in a subject comprising administering to the subject a therapeutically effective amount of a CART cell expressing a first CAR, wherein:
(i) the first CAR comprises an antigen binding domain that comprises a polypeptide from a cyclopeptide library that binds a unique B cell receptor expressed in lymphoma cells of the subject, (ii) the antigen binding domain is identified by
(a) identifying the unique B cell receptor expressed in lymphoma cells of the subject;
(b) co-expressing the unique B cell receptor and a second CAR from a library of CARs in a T cell, wherein each CAR within the library comprises a distinct putative ligand domain that comprises a polypeptide from the cyclopeptide library; and
(c) identifying the antigen binding domain of the first CAR by identifying an activated T cell, wherein the putative B cell receptor ligand domain of the second CAR from the library of CARs comprises the antigen binding domain of the first CAR if the T cell expressing the B cell receptor and the second CAR is activated; and
(iii) the first CAR has greater specificity and/or activity than a control.
168 . The method of claim 167 , wherein the control comprises a CART cell.
169 . The method of claim 168 wherein the antigen binding domain of the CAR expressed by the CART cell binds a ligand other than a B-cell receptor.
170 . The method of claim 168 or 169 wherein the antigen binding domain binds CD-19.
171 . The method of any of claims 167 - 170 wherein the first CAR and the second CAR are the same CAR.
172 . The method of any of claims 169 - 170 wherein the first CAR and the second CAR are different CARs.
173 . The method of any of claims 169 - 172 , wherein activity comprises cytotoxicity towards cells expressing the unique B cell receptor relative to a control.
174 . The method of claim 173 , wherein the cytotoxicity of the CART towards cells expressing the unique B cell receptor is 0%-10% greater than the control, as measured by % lysis, at an effector:target ratio of 1:1-10:1.
175 . The method of claim 173 , wherein the cytotoxicity of the CART towards cells expressing the unique B cell receptor is at least 10% greater than the control, as measured by % lysis, at an effector:target ratio of 10:1 or greater.
176 . The method of any of claims 173 - 175 , wherein the control comprises a CAR comprising an antigen binding domain that binds a ligand other than the B-cell receptor expressed on the cells expressing the unique B cell receptor.
177 . The method of any of claims 169 - 176 , wherein specificity comprises cytotoxicity towards cells that do not express the unique B cell receptor.
178 . The method of claim 177 , wherein cytotoxicity of the CART towards cells that do not express the unique B cell receptor is less than 10%, as measured by % lysis.
179 . The method of claim 177 , wherein cytotoxicity of the CART towards cells that do not express the unique B cell receptor is 0-10% less than the cytotoxicity of a control that binds a ligand expressed on the cells at an effector:target ratio of less than 10:1.
180 . The method of claim 177 , wherein cytotoxicity of the CART towards cells that do not express the unique B cell receptor is at least 15% less than the cytotoxicity of a control that binds a ligand expressed on the cells at an effector:target ratio of 10:1 or greater.
181 . The method of any of claims 169 - 180 , wherein the treatment results in reduced cytokine release syndrome (CRS) relative to a subject treated with a control.
182 . A method for treating lymphoma in subject population comprising:
selecting subjects having lymphoma; and administering to each subject a therapeutically effective amount of a CART cell expressing a first CAR unique to the B cell receptor expressed on the lymphoma cells on each subject, wherein: (i) the first CAR comprises an antigen binding domain that comprises a polypeptide from a cyclopeptide library that binds a unique B cell receptor expressed in lymphoma cells of each subject, (ii) the antigen binding domain is identified by
(a) identifying the unique B cell receptor expressed in lymphoma cells of the subject;
(b) co-expressing the unique B cell receptor and a second CAR from a library of CARs in a T cell, wherein each CAR within the library comprises a distinct putative ligand domain that comprises a polypeptide from the cyclopeptide library; and
(c) identifying the antigen binding domain of the first CAR by identifying an activated T cell, wherein the putative B cell receptor ligand domain of the second CAR from the library of CARs comprises the antigen binding domain of the first CAR if the T cell expressing the B cell receptor and the second CAR is activated; and
(iii) the first CAR has greater specificity and/or activity than a control.
183 . The method of claim 182 , wherein the control comprises a CART cell.
184 . The method of claim 183 wherein the antigen binding domain of the CAR expressed by the CART cell binds a ligand other than a B-cell receptor.
185 . The method of claim 182 or 183 wherein the antigen binding domain binds CD-19.
186 . The method of any of claims 182 - 185 wherein the first CAR and the second CAR are the same CAR.
187 . The method of any of claims 182 - 185 wherein the first CAR and the second CAR are different CARs.
188 . The method of any of claims 182 - 187 , wherein activity comprises cytotoxicity towards cells expressing the unique B cell receptor relative to a control.
189 . The method of claim 188 , wherein the cytotoxicity of the CART towards cells expressing the unique B cell receptor is 0%-10% greater than the control, as measured by % lysis, at an effector:target ratio of 1:1-10:1.
190 . The method of claim 188 , wherein the cytotoxicity of the CART towards cells expressing the unique B cell receptor is at least 10% greater than the control, as measured by % lysis, at an effector:target ratio of 10:1 or greater.
191 . The method of any of claims 188 - 190 , wherein the control comprises a CAR comprising an antigen binding domain that binds a ligand other than the B-cell receptor expressed on the cells expressing the unique B cell receptor.
192 . The method of any of claims 182 - 191 , wherein specificity comprises cytotoxicity towards cells that do not express the unique B cell receptor.
193 . The method of claim 192 , wherein cytotoxicity of the CART towards cells that do not express the unique B cell receptor is less than 10%, as measured by % lysis.
194 . The method of claim 192 , wherein cytotoxicity of the CART towards cells that do not express the unique B cell receptor is 0-10% less than the cytotoxicity of a control that binds a ligand expressed on the cells at an effector:target ratio of less than 10:1.
195 . The method of claim 192 , wherein cytotoxicity of the CART towards cells that do not express the unique B cell receptor is at least 15% less than the cytotoxicity of a control that binds a ligand expressed on the cells at an effector:target ratio of 10:1 or greater.
196 . A method of rapidly identifying a personalized antibody binding ligand specific for a B cell lymphoma, e.g., a B cell receptor ligand, comprising:
identifying a B cell receptor from a B cell lymphoma cell, providing to a population of T cells nucleic acid molecules encoding the B cell receptor and a library of chimeric antigen receptors (CARs), wherein each CAR within the library comprises a distinct putative B cell receptor ligand domain; coexpressing the B cell receptor and the library of CARs in T cells; measuring activation of the T cells, wherein the putative B cell receptor ligand domain of a CAR from the library of CARs comprises a ligand of the B cell receptor if a T cell expressing the B cell receptor and the CAR is activated; and isolating the nucleic acid molecule encoding the CAR from an activated T cell; and sequencing the putative B cell receptor ligand domain of the nucleic acid molecule encoding the CAR from the activated T cell; thereby identifying a B cell receptor ligand.
197 . The method of claim 196 , wherein the B cell receptor ligand is identified within 4 weeks, within 3 weeks, within 2 weeks, or within 1 week.
198 . The method of claim 197 , wherein the B cell receptor ligand is identified within 3 weeks.
199 . The method of any of claims 196 - 198 , wherein the B cell lymphoma cell is obtained from a tumor from a patient
200 . The method of any of claims 196 - 199 , wherein the putative B cell receptor ligand domain comprises a polypeptide of 30 amino acids or less.
201 . The method of any of claims 196 - 200 , wherein the putative B cell receptor ligand domain comprises a polypeptide from a cyclopeptide library.
202 . The method of claim 201 , wherein the putative B cell receptor ligand domain further comprises an Fc region.
203 . The method of any of claims 196 - 202 , wherein T cell activation is measured by an increase in expression of CD69 or CD25.
204 . The method of any of claims 196 - 202 , wherein T cell activation is measured by an increase in expression of a fluorescent protein reporter gene under the control of Jun, NF-κB and/or Rel.
205 . The method of any of claims 196 - 204 , further comprising treating a subject having lymphoma with the B cell receptor ligand, wherein the B cell receptor ligand coupled to a therapeutic agent.
206 . A method of treating lymphoma in a subject comprising:
identifying a unique B cell receptor expressed in lymphoma cells of the subject; contacting the unique B cell receptor with a phage display library, wherein the phage display library comprises a library of putative unique B cell receptor ligands linked to phages; detecting binding of said unique B cell receptor to a putative unique B cell receptor ligand, thereby identifying a unique B cell receptor ligand; and administering to the subject a therapeutically effective amount of the B cell receptor ligand coupled to a therapeutic agent.
207 . The method of claim 206 , wherein the putative unique B cell receptor ligand comprises a peptide, a cyclopeptide, a peptoid, a cyclopeptoid, a polysaccharide, a lipid, or a small molecule.
208 . The method of claim 206 or 207 , wherein the unique B cell receptor is attached to a solid support.
209 . The method of claim 197 , wherein contacting unique B cell receptor with a putative unique B cell receptor ligand from a library comprises panning the unique B cell receptor attached to a solid support with the library of putative B cell receptor ligands linked to a phage for one or more rounds.
210 . The method of claim 198 , wherein each round of the panning includes negative selection.
211 . The method of any of claims 195 - 200 , wherein the subject is determined to have lymphoma.
212 . The method of claim 200 , wherein the subject is determined to have one or more single-nucleotide polymorphisms (SNPs) associated with lymphoma.
213 . The method of any of claims 195 - 200 , wherein identifying a unique B cell receptor comprises:
obtaining cells from a biopsy; extracting RNA from the cells; synthesizing cDNA from the extracted RNA; and sequencing the cDNA.
214 . The method of any of claims 195 - 202 , wherein identifying a unique B cell receptor comprises cloning and sequencing circulating cell free DNA.
215 . The method of any of claims 195 - 203 , wherein the method is performed in 3 weeks or less.
216 . The method of any of claims 195 - 204 , wherein the therapeutic agent comprises a radioactive isotope.
217 . The method of any of claims 195 - 204 , wherein the B cell receptor ligand coupled to a therapeutic agent comprises a therapeutic CAR.
218 . The method of any of claims 195 - 204 , wherein the therapeutic agent comprises a chemotherapy.
219 . The method of any of claims 195 - 204 , wherein the therapeutic agent comprises an immunotherapy.Join the waitlist — get patent alerts
Track US2020271657A1 — get alerts on status changes and closely related new filings.
We store only your email — no account needed. See our privacy policy.