Treatment of cancer using GFR alpha-4 chimeric antigen receptor

1. A chimeric antigen receptor (CAR) polypeptide comprising an antigen binding domain, a transmembrane domain, and an intracellular signaling domain, wherein the antigen binding domain binds to isoform a or isoform b of human Glycosyl-phosphatidylinositol (GPI)-linked GDNF family α-receptor 4 (GFRα4) cell-surface receptor and comprises:

(a) (i) a heavy chain variable region comprising a heavy chain complementary determining region 1 (HC CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 63, a heavy chain complementary determining region 2 (HC CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 65, and a heavy chain complementary determining region 3 (HC CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 67; and

(ii) a light chain complementary determining region 1 (LC CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 71, a light chain complementary determining region 2 (LC CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 73, and a light chain complementary determining region 3 (LC CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 75; or

(b) (i) a heavy chain variable region comprising a heavy chain complementary determining region 1 (HC CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 43, a heavy chain complementary determining region 2 (HC CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 45, and a heavy chain complementary determining region 3 (HC CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 47; and

(ii) a light chain complementary determining region 1 (LC CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 51, a light chain complementary determining region 2 (LC CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 53, and a light chain complementary determining region 3 (LC CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 55.

2. The CAR polypeptide of claim 1 , wherein the antigen binding domain is an antibody or an antigen-binding fragment thereof.

3. The CAR polypeptide of claim 2 , wherein the antigen-binding fragment is a scFv.

4. The CAR polypeptide of claim 2 , wherein the antibody or antigen-binding fragment is a human antibody or a fragment thereof.

5. The CAR polypeptide of claim 1 , wherein the CAR comprises:

a light chain variable region comprising an amino acid sequence having at least one, two or three modifications but not more than 20 or 10 modifications of the amino acid sequence set forth in SEQ ID NO: 69 or SEQ ID NO: 49; or

a light chain variable region comprising an amino acid sequence with about 95% up to about 99% identity to the amino acid sequence set forth in SEQ ID NO: 69 or SEQ ID NO: 49.

6. The CAR polypeptide of claim 1 , wherein the CAR comprises:

a heavy chain variable region comprising an amino acid sequence having at least one, two or three modifications but not more than 20 or 10 modifications of the amino acid sequence set forth in SEQ ID NO: 61 or SEQ ID NO: 41: or

a heavy chain variable region comprising an amino acid sequence with about 95 up to about 99% identity to the amino acid sequence set forth in SEQ ID NO: 61 or SEQ ID NO: 41.

7. The CAR polypeptide of claim 1 , wherein the CAR comprises

(a) the amino acid sequences set forth in SEQ ID NO: 61 and SEQ ID NO: 69; or

(b) the amino acid sequences set forth in SEQ ID NO: 41 and SEQ ID NO: 49.

8. The CAR polypeptide of claim 1 , wherein the antigen binding domain comprises:

(a) the amino acid sequence selected from SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 78, or SEQ ID NO: 79;

(b) an amino acid sequence having at least one, two or three modifications but not more than 30, 20, or 10 modifications of SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 78, or SEQ ID NO: 79; or

(c) an amino acid sequence with about 95 up to about 99% identity to SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 78, or SEQ ID NO: 79.

9. The CAR polypeptide of claim 1 , wherein the transmembrane domain comprises a transmembrane domain from 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.

10. The CAR polypeptide of claim 1 , wherein the transmembrane domain comprises:

(a) the amino acid sequence of SEQ ID NO: 6;

(b) an amino acid sequence comprising at least one, two or three modifications but not more than 5 modifications of the amino acid sequence of SEQ ID NO: 6; or

(c) a sequence with about 95 up to about 99% identity to the amino acid sequence of SEQ ID NO: 6.

11. The CAR polypeptide of claim 1 , wherein the antigen binding domain is connected to the transmembrane domain by a hinge region.

12. The CAR polypeptide of claim 11 , wherein the hinge region comprises the amino acid sequence of SEQ ID NO: 2, or a sequence with about 95 up to about 99% identity to SEQ ID NO: 2.

13. The CAR polypeptide of claim 1 , wherein the intracellular signaling domain comprises a functional signaling domain from a protein selected from the group consisting of an MHC class I molecule, a TNF receptor protein, an immunoglobulin-like proteins, 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 (CD11a/CD18), 4-1BB (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, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, NKG2C, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), 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, CD19a, and a ligand that specifically binds with CD83.

14. The CAR polypeptide of claim 1 , wherein the intracellular signaling domain comprises the amino acid sequence of SEQ ID NO: 7, or an amino acid sequence having at least one, two or three modifications but not more than 10 or 5 modifications of the amino acid sequence of SEQ ID NO: 7, or a sequence with about 95 up to about 99% identity to the amino acid sequence of SEQ ID NO: 7.

15. The CAR polypeptide of claim 1 , wherein the intracellular signaling domain comprises a functional signaling domain of 4-1BB and/or a functional signaling domain of CD3 zeta.

16. The CAR polypeptide of claim 1 , wherein the intracellular signaling domain comprises:

(a) the amino acid sequence of SEQ ID NO: 7 and/or the sequence of SEQ ID NO: 9 or SEQ ID NO: 10; or

(b) an amino acid sequence having at least 1, one, two or three modifications but not more than 10 or 5 modifications of the amino acid sequence of SEQ ID NO: 7 and/or the amino acid sequence of SEQ ID NO: 9 or SEQ ID NO: 10; or

(c) a sequence with about 95 up to about 99% identity to the amino acid sequence of SEQ ID NO: 7 and/or the amino acid sequence of SEQ ID NO: 9 or SEQ ID NO: 10.

17. The CAR polypeptide of claim 1 , wherein the intracellular signaling domain comprises the sequence of SEQ ID NO: 7 and the sequence of SEQ ID NO: 9 or SEQ ID NO: 10, wherein the sequences comprising the intracellular signaling domain are expressed as a single polypeptide chain.

18. The CAR polypeptide of claim 1 , further comprising a leader sequence comprising the amino acid sequence of SEQ ID NO: 1.

19. The CAR polypeptide of claim 1 , wherein the CAR comprises:

(a) the amino acid sequence of any of SEQ ID NOs: 85, 86, 90, 92, 94, 96, 98, 100, 102, or 104;

(b) an amino acid sequence having at least one, two or three modifications but not more than 30, 20 or 10 modifications to any of SEQ ID NOs: 85, 86, 90, 92, 94, 96, 98, 100, 102, or 104; or

(c) an amino acid sequence with about 95 up to about 99% identity to any of SEQ ID NOs: 85, 86, 90, 92, 94, 96, 98, 100, 102, or 104.

20. A chimeric antigen receptor (CAR) polypeptide, wherein the CAR comprises an antigen binding domain, a transmembrane domain, and an intracellular signaling domain, and wherein the antigen binding domain binds to both isoforms a and b of human Glycosyl-phosphatidylinositol (GPI)-linked GDNF family α-receptor 4 (GFRα4) cell-surface receptor and comprises:

(a) (i) a heavy chain variable region comprising a heavy chain complementary determining region 1 (HC CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 63, a heavy chain complementary determining region 2 (HC CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 65, and a heavy chain complementary determining region 3 (HC CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 67; and

(ii) a light chain complementary determining region 1 (LC CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 71, a light chain complementary determining region 2 (LC CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 73, and a light chain complementary determining region 3 (LC CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 75; or

(b) (i) a heavy chain variable region comprising a heavy chain complementary determining region 1 (HC CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 43, a heavy chain complementary determining region 2 (HC CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 45, and a heavy chain complementary determining region 3 (HC CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 47; and

(ii) a light chain complementary determining region 1 (LC CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 51, a light chain complementary determining region 2 (LC CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 53, and a light chain complementary determining region 3 (LC CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 55.