CD20 THERAPIES, CD22 THERAPIES, AND COMBINATION THERAPIES WITH A CD19 CHIMERIC ANTIGEN RECEPTOR (CAR)- EXPRESSING CELL

• US 20160362472A1
• Filed: 04/08/2016
• Published: 12/15/2016
• Est. Priority Date: 04/08/2015
• Status: Active Grant

• Current Assignee: Novartis Ag, Trustees Of The University Of Pennsylvania (University of Pennsylvania)
• Original Assignee: Lu Huang
• Inventors: Bitter, Hans, Bordeaux, Jennifer Mary, Dakappagari, Naveen Kumar, Highfill, Steven, Huang, Lu, Kim, Ju Young, Lei, Ming, Li, Na, Orlando, Elena, Tran, Thai, Zhang, Jimin, Brannetti, Barbara, Brogdon, Jennifer, Gill, Saar, June, Carl H., Loew, Andreas, Ruella, Marco, Zhou, Li
• Granted Patent: US 10,253,086 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: A61K 2039/70 Multivalent vaccine
• CPC Class Codes: A61K 2239/38 characterised by the dose, timing or administration schedule
• CPC Class Codes: A61K 2239/48 Blood cells, e.g. leukemia or lymphoma
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61K 39/4611 T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
• CPC Class Codes: A61K 39/4631 Chimeric Antigen Receptors [CAR]
• CPC Class Codes: A61K 39/4636 Immune checkpoint inhibitors
• CPC Class Codes: A61K 39/464412 CD19 or B4
• CPC Class Codes: A61K 39/464413 CD22, BL-CAM, siglec-2 or sialic acid binding Ig-related lectin 2
• CPC Class Codes: A61K 39/464419 Receptors for interleukins [IL]
• CPC Class Codes: A61K 39/464424 CD20
• CPC Class Codes: A61K 45/06 Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/02 specific for leukemia
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07K 14/7051 T-cell receptor (TcR)-CD3 complex
• CPC Class Codes: C07K 14/70596 Molecules with a "CD"-designation not provided for elsewhere
• CPC Class Codes: C07K 16/2803 against the immunoglobulin superfamily
• CPC Class Codes: C07K 16/2866 against receptors for cytokines, lymphokines, interferons
• CPC Class Codes: C07K 2317/24 containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
• CPC Class Codes: C07K 2317/622 : Single chain antibody (scFv)
• CPC Class Codes: C07K 2319/00 : Fusion polypeptide
• CPC Class Codes: C12N 5/0636 : T lymphocytes
• CPC Class Codes: C12N 5/0646 : Natural killers cells [NK], NKT cells

Abstract

The invention provides compositions and methods for treating diseases associated with expression of CD19, e.g., by administering a recombinant T cell comprising the CD19 CAR as described herein, in combination with one or more B-cell inhibitors, e.g., inhibitors of one or more of CD10, CD20, CD22, CD34, CD123, FLT-3, ROR1, CD79b, CD179b, or CD79a. The disclosure additionally features novel antigen binding domains and CAR molecules directed to CD20 and CD22, and uses, e.g., as monotherapies or in combination therapies. The invention also provides kits and compositions described herein.

Claims

1. (canceled)

2. A method of treating a subject having a disease associated with expression of CD19, comprising administering to the subject an effective number of one or more cells that express a CAR molecule that binds CD19 in combination with one or more B-cell inhibitors, wherein the B-cell inhibitor comprises an inhibitor of one or more of CD10, CD20, CD22, CD34, CD123, FLT-3, ROR1, CD79b, CD179b, or CD79a.

6. The method of claim 2, wherein the B-cell inhibitor comprises an effective number of one or more cells that express a CAR molecule that binds one or more of CD10, CD20, CD22, CD34, CD123, FLT-3, ROR1, CD79b, CD179b, or CD79a.

8. The method of claim 2, wherein the subject has relapsed or is identified as having relapsed after treatment with the one or more cells that express a CAR molecule that binds CD19.

9. The method of claim 8,

wherein the subject has relapsed or is identified as having relapsed based on one or more of reappearance of blasts in the blood, bone marrow (>

5%), or any extramedullary site, after a complete response;

or

wherein the subject has relapsed or is identified as having relapsed based on detection of CD19−

blasts above a predetermined threshold;

or

wherein the subject has relapsed or is identified as having relapsed based on an increase in RNA levels of one or more of MIR199A1, MIR1203, uc021ovp, ITM2C, or HLA-DQB1;

or

wherein the subject has relapsed or is identified as having relapsed based on a decrease in RNA levels of one or more of PPIAL4D, TTTY10, TXLNG2P, MIR4650-1, KDM5D, USP9Y, PRKY, RPS4Y2, RPS4Y1, NCRNA00185, SULT1E1, and EIF1AY.

10. The method of claim 2, further comprising performing lymphodepletion on that subject.

12. The method of claim 2, wherein the CD19 CAR comprises an antibody or antibody fragment which includes a CD19 binding domain, a transmembrane domain, and an intracellular signaling domain comprising a stimulatory domain, and wherein said CD19 binding domain comprises a light chain complementary determining region 1 (LC CDR1), a light chain complementary determining region 2 (LC CDR2), and a light chain complementary determining region 3 (LC CDR3) of any CD19 scFv or light chain binding domain amino acid sequence listed in Tables 2 or 3, and a heavy chain complementary determining region 1 (HC CDR1), a heavy chain complementary determining region 2 (HC CDR2), and a heavy chain complementary determining region 3 (HC CDR3) of any CD19 scFv or heavy chain binding domain amino acid sequence listed in Tables 2 or 3.

14. The method of claim 2, wherein the CD19 CAR comprises a CD19 binding domain which comprises a sequence selected from a group consisting of SEQ ID NO:

1, SEQ ID NO;

2, SEQ ID NO;

3, SEQ ID NO;

4, SEQ ID NO;

5, SEQ ID NO;

6, SEQ ID NO;

7, SEQ ID NO;

8, SEQ ID NO;

9, SEQ ID NO;

10, SEQ ID NO;

11 and SEQ ID NO;

12, or an amino acid sequence with at least 95% identity thereof, or a polypeptide of SEQ ID NO;

59, or a sequence with at least 95% identity thereof, or

wherein the CD19 CAR comprises a polypeptide selected from the group consisting of SEQ ID NOA;

31-42 or 58, or a sequence with at least 95% identity thereof.

15. The method of claim 2, wherein the B-cell inhibitor comprises a CD20 CAR which comprises an antibody or antibody fragment which includes a CD20 binding domain, a transmembrane domain, and an intracellular signaling domain comprising a stimulatory domain, and wherein said CD20 binding domain comprises a light chain complementary determining region 1 (LC CDR1), a light chain complementary determining region 2 (LC CDR2), and a light chain complementary determining region 3 (LC CDR3) of any CD20 light chain binding domain amino acid sequence listed in Table 13, and a heavy chain complementary determining region 1 (HC CDR1), a heavy chain complementary determining region 2 (HC CDR2), and a heavy chain complementary determining region 3 (HC CDR3) of any CD20 heavy chain binding domain amino acid sequence listed in Table 12A or 12B.

16. The method of claim 2, wherein the B-cell inhibitor comprises a CD22 CAR which comprises an antibody or antibody fragment which includes a CD22 binding domain, a transmembrane domain, and an intracellular signaling domain comprising a stimulatory domain, and wherein said CD22 binding domain comprises a light chain complementary determining region 1 (LC CDR1), a light chain complementary determining region 2 (LC CDR2), and a light chain complementary determining region 3 (LC CDR3) of any CD22 light chain binding domain amino acid sequence listed in Table 8A or 8B, and a heavy chain complementary determining region 1 (HC CDR1), a heavy chain complementary determining region 2 (HC CDR2), and a heavy chain complementary determining region 3 (HC CDR3) of any CD22 heavy chain binding domain amino acid sequence listed in Table 7A, 7B, or 7C.

17. The method of claim 16, wherein the CD22 CAR comprises any light chain variable region listed in Table 10A or 10B, any heavy chain variable region listed in Table 9A or 9B, or any light chain variable region listed in Table 10A or 10B and any heavy chain variable region listed Table 9A or 9B.

18. The method of claim 2, wherein the B-cell inhibitor comprises a CD123 CAR which comprises an antibody or antibody fragment which includes a CD123 binding domain, a transmembrane domain, and an intracellular signaling domain comprising a stimulatory domain, and wherein said CD123 binding domain comprises a light chain complementary determining region 1 (LC CDR1), a light chain complementary determining region 2 (LC CDR2), and a light chain complementary determining region 3 (LC CDR3) of any CD123 light chain binding domain amino acid sequence listed in Table 18 or Table 27, and a heavy chain complementary determining region 1 (HC CDR1), a heavy chain complementary determining region 2 (HC CDR2), and a heavy chain complementary determining region 3 (HC CDR3) of any CD123 heavy chain binding domain amino acid sequence listed in Table 17 or Table 26.

19. The composition for use or the method of claim 18, wherein the CD123 CAR comprises any light chain variable region listed in Table 16 or Table 25, any heavy chain variable region listed in Table 16 or Table 25, or any light chain variable region listed in Table 16 or Table 25 and any heavy chain variable region listed Table 16 or Table 25.

22. The method of claim 2, wherein, wherein the B-cell inhibitor comprises a CAR (a “

B-cell inhibitor CAR”

) which comprises an antibody or antibody fragment which includes an antigen binding domain, a transmembrane domain, and an intracellular signaling domain comprising a stimulatory domain.

24. The method of claim 22, wherein the B-cell inhibitor CAR or CAR molecule that binds CD19 comprises a transmembrane domain that comprises a transmembrane domain of a protein selected from the group consisting of the 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 CD154.

25. The method of claim 22, wherein the B-cell inhibitor CAR or CAR molecule that binds CD19 comprises an antigen binding domain that is connected to the transmembrane domain by a hinge region.

26. The method of claim 22, wherein the B-cell inhibitor CAR or CAR molecule that binds CD19 comprises a costimulatory domain which is a functional signaling domain obtained from a protein selected from the group consisting of OX40, CD2, CD27, CD28, CDS, ICAM-1, LFA-1 (CD11a/CD18), ICOS (CD278), and 4-1BB (CD137).

27. The method of claim 22, wherein the B-cell inhibitor CAR or CAR molecule that binds CD19 comprises an intracellular signaling domain that comprises a functional signaling domain of 4-1BB, a functional signaling domain of CD3 zeta, or a combination thereof;

or

wherein the intracellular signaling domain comprises the sequence of SEQ ID NO;

16 or the sequence of SEQ ID NO;

17 or SEQ ID NO;

43, or the sequence of SEQ ID NO;

16 and the sequence of SEQ ID NO;

17 or SEQ ID NO;

43.

30. The method of claim 2, wherein the disease associated with CD19 expression is selected from a proliferative disease such as a cancer, tumor, or malignancy or a precancerous condition such as a myelodysplasia, a myelodysplastic syndrome or a preleukemia, or is a non-cancer related indication associated with expression of CD19, or

wherein the disease is one or more of a hematologic cancer, acute leukemia, B-cell acute lymphoid leukemia (BALL), T-cell acute lymphoid leukemia (TALL), small lymphocytic leukemia (SLL), acute lymphoid leukemia (ALL);

chronic leukemia, chronic myelogenous leukemia (CML), chronic lymphocytic leukemia (CLL), non-Hodgkin lymphoma, multiple myeloma, or myeloma;

or

wherein the disease is a CD19-negative cancer.

31. The method of claim 2, further comprising administering:

an agent that increases the efficacy of a cell expressing a CAR molecule, or

an agent that ameliorates one or more side effects associated with administration of a cell expressing a CAR molecule, or

an agent that treats the disease associated with CD19;

or

a checkpoint inhibitor.

33. The method of claim 2, wherein the subject comprises a CD19-negative cancer cell, and a cancer cell that is positive for one or more of CD10, CD20, CD22, CD34, CD123, FLT-3, ROR1, CD79b, CD179b, or CD79a.

34. The method of claim 2, further comprises administering to the subject an inhibitor of one or more of the CD10, CD20, CD22, CD34, CD123, FLT-3, ROR1, CD79b, CD179b, or CD79a for which the cancer cell is positive.

45. The method of claim 2, wherein the cancer is DLBCL, wherein the method comprises administering to the subject an effective number of one or more cells that express a CAR molecule that binds CD19, in combination with a PD1 inhibitor, wherein the subject has, or is identified as having, at least 5% of DLBCL cells which are CD3+/PD1+.

46. The method of claim 2, wherein the cancer is DLBCL, wherein the method comprises administering to the subject an effective number of one or more cells that express a CAR molecule that binds CD19, wherein the subject has, or is identified as having, at least 5% of DLBCL cells which are CD3+/PD1+.

47. The method of claim 2, wherein the cancer is DLBCL, wherein the method comprises administering to the subject an effective number of one or more cells that express a CAR molecule that binds CD19, in combination with a PD-L1 inhibitor, wherein the subject has, or is identified as having, less than 20% of cells in the cancer are double positive for CD19 and PD-L1.

3. (canceled)

4. A method of treating a patient who is, or is identified as being, a non-responder, partial responder, or relapser to a CD19 inhibitor comprising administering to the subject a B-cell.

5. (canceled)

7. (canceled)

11. (canceled)

13. (canceled)

20-21. -21. (canceled)

23. (canceled)

28-29. -29. (canceled)

32. (canceled)

35. (canceled)

36. A composition comprising, separately or admixed:

(i) one or more cells that express a CAR molecule that binds CD19, and

(ii) one or more B-cell inhibitors chosen from inhibitors of one or more of CD10, CD20, CD22, CD34, CD123, FLT-3, or ROR1.

37. A composition comprising:

(i) a first nucleic acid encoding a CAR molecule that binds CD19, and

(ii) a second nucleic acid encoding a CAR molecule that binds a B-cell antigen chosen from one or more of CD10, CD20, CD22, CD34, CD123, FLT-3, ROR1, CD79b, CD179b, or CD79a, wherein the first nucleic acid and second nucleic acid are in the same or a separate nucleic acid molecule.

40. A cell comprising a nucleic acid composition of claim 37.

38-39. -39. (canceled)

41-44. -44. (canceled)

48. An isolated nucleic acid molecule encoding a chimeric antigen receptor (CAR), wherein the CAR comprises an antibody or antibody fragment which includes a CD20 binding domain, a transmembrane domain, and an intracellular signaling domain, and wherein said CD20 binding domain comprises one or more of light chain complementary determining region 1 (LC CDR1), light chain complementary determining region 2 (LC CDR2), and light chain complementary determining region 3 (LC CDR3) of any CD20 light chain binding domain amino acid sequence listed in Table 13, 15A, or 15B, and one or more of heavy chain complementary determining region 1 (HC CDR1), heavy chain complementary determining region 2 (HC CDR2), and heavy chain complementary determining region 3 (HC CDR3) of any CD20 heavy chain binding domain amino acid sequence listed in Table 12A, 12B, 14A, or 14B.

49. An isolated CAR molecule comprising a CD20 binding domain, a transmembrane domain, and an intracellular signaling domain, wherein the CD20 binding domain comprises one or more light chain complementary determining region 1 (LC CDR1), light chain complementary determining region 2 (LC CDR2), and light chain complementary determining region 3 (LC CDR3) of any CD20 binding domain listed in Table 13, 15A, or 15B, and one or more heavy chain complementary determining region 1 (HC CDR1), heavy chain complementary determining region 2 (HC CDR2), and heavy chain complementary determining region 3 (HC CDR3) of any CD20 binding domain listed in Table 12A, 12B, 14A, or 14B.

50. A method of treating a mammal having a disease associated with expression of CD20 comprising administering to the mammal an effective amount of the cell of comprising a CAR molecule of claim 49.

51. An isolated nucleic acid molecule encoding a chimeric antigen receptor (CAR), wherein the CAR comprises an antibody or antibody fragment which includes a CD22 binding domain, a transmembrane domain, and an intracellular signaling domain, and wherein said CD22 binding domain comprises one or more of light chain complementary determining region 1 (LC CDR1), light chain complementary determining region 2 (LC CDR2), and light chain complementary determining region 3 (LC CDR3) of any CD22 light chain binding domain amino acid sequence listed in Table 8A, 8B, 10A or 10B, and one or more of heavy chain complementary determining region 1 (HC CDR1), heavy chain complementary determining region 2 (HC CDR2), and heavy chain complementary determining region 3 (HC CDR3) of any CD22 heavy chain binding domain amino acid sequence listed in Table 7A, 7B, 7C, 9A, or 9B.

52. An isolated CAR molecule comprising a CD22 binding domain, a transmembrane domain, and an intracellular signaling domain, wherein the CD22 binding domain comprises one or more light chain complementary determining region 1 (LC CDR1), light chain complementary determining region 2 (LC CDR2), and light chain complementary determining region 3 (LC CDR3) of any CD22 binding domain listed in Table 8A, 8B, 10A or 10B, and one or more heavy chain complementary determining region 1 (HC CDR1), heavy chain complementary determining region 2 (HC CDR2), and heavy chain complementary determining region 3 (HC CDR3) of any CD22 binding domain listed in Table 7A, 7B, 7C, 9A, or 9B.

53. A method of treating a mammal having a disease associated with expression of CD22 comprising administering to the mammal an effective amount of the cell of comprising a CAR molecule of claim 52.

54. A cell comprising a CAR that comprises a bispecific antibody that comprises a CD19 antigen-binding domain and an antigen-binding domain directed to a second antigen, wherein the second antigen is selected from CD10, CD20, CD22, CD34, CD123, FLT-3, ROR1, CD79b, CD179b, or CD79a.