METHODS OF TREATING A NEUROENDOCRINE TUMOR

1 . A method of treating a neuroendocrine tumor (NET) in an individual in need thereof, comprising administering to the individual a therapeutically effective amount of an agent that inhibits a tropomyosin receptor kinase (Trk) protein, wherein the NET is associated with a Trk protein that has undergone a genetic translocation or is an NTRK gene fusion protein.

2 . The method of claim 1 , wherein the NTRK gene fusion protein comprises an NTRK1, NTRK2, or NTRK3 tyrosine kinase signaling domain.

3 . The method of claim 2 , wherein the NTRK gene fusion protein is constitutively active.

4 . The method of claim 1 , wherein the NTRK gene fusion protein comprises:

(a) an N-terminal polypeptide region comprising a polypeptide sequence other than a TrkA, TrkB, or TrkC polypeptide sequence; and

(b) a C-terminal polypeptide region comprising a TrkA, TrkB, or TrkC polypeptide sequence, wherein the C-terminal polypeptide region has TrkA, TrkB, or TrkC kinase activity.

5 . The method of claim 1 , wherein the NTRK gene fusion protein comprises a nucleic acid sequence comprising:

(a) a first region corresponding to a sequence from a MPRIP, CD74, RABGAP1L, TPM3, TPR, TFG, PPL, CHTOP, ARHGEF2, NFASC, BCAN, LMNA, TP53, QKI, NACC2, VCL, AGBL4, TRIM24, PAN3, AFAP1, SQSTM1, ETV6, BTBD1, LYN, RBPMS, RFWD2, IRF2BP2, SSBP2, C18ORF8, RNF213, TBC1, DNER, PLEKHA6, PEAR1, MRPL24, MDM4, GRIPAP1, EPS15, DYNC2H1, CEL, EPHB2, EML4, HOMER2, TEL, or FAT1 gene sequence; and

(b) a second region corresponding to a NTRK1, NTRK2, or NTRK3 gene sequence.

6 . The method of claim 5 , wherein the NTRK gene fusion protein is an ETV6-NTRK gene fusion protein.

7 . The method of claim 1 , wherein the NTRK gene fusion protein comprises:

(a) an N-terminal polypeptide region comprising the sequence of a MPRIP, CD74, RABGAP1L, TPM3, TPR, TFG, PPL, CHTOP, ARHGEF2, NFASC, BCAN, LMNA, TP53, QKI, NACC2, VCL, AGBL4, TRIM24, PAN3, AFAP1, SQSTM1, ETV6, BTBD1, LYN, RBPMS, RFWD2, IRF2BP2, SSBP2, C18ORF8, RNF213, TBC1, DNER, PLEKHA6, PEAR1, MRPL24, MDM4, GRIPAP1, EPS15, DYNC2H1, CEL, EPHB2, EML4, HOMER2, TEL, or FAT1 polypeptide sequence; and

(b) a C-terminal polypeptide region comprising a TrkA, TrkB, or TrkC polypeptide sequence, wherein the C-terminal polypeptide region has TrkA, TrkB, or TrkC kinase activity.

8 . The method of claim 7 , wherein the N-terminal polypeptide region comprises an ETV6 polypeptide sequence.

9 . The method of claim 8 , wherein the C-terminal polypeptide region comprises a TrkC polypeptide sequence.

10 . The method of claim 1 , wherein the NTRK gene fusion protein comprises:

(a) an N-terminal polypeptide region comprising a polypeptide sequence other than a TrkA, TrkB, or TrkC polypeptide sequence; and

(b) a C-terminal polypeptide region comprising a TrkA polypeptide sequence, wherein the C-terminal polypeptide comprises TrkA kinase activity;

wherein the fusion protein is a TP53-TrkA, LMNA-TrkA, CD74-TrkA, TFG-TrkA, TPM3-TrkA, NFASC-TrkA, BCAN-TrkA, MPRIP-TrkA, TPR-TrkA, RFWD2-TrkA, IRF2BP2-TrkA, SQSTM1-TrkA, SSBP2-TrkA, RABGAP1L-TrkA, C18ORF8-TrkA, RNF213-TrkA, TBC1D22A-TrkA, C200RF112-TrkA, DNER-TrkA, ARHGEF2-TrkA, CHTOP-TrkA, PPL-TrkA, PLEKHA6-TrkA, PEAR1-TrkA, MRPL24-TrkA, MDM4-TrkA, LRRC71-TrkA, GRIPAP1-TrkA, EPS15-TrkA, DYNC2H1-TrkA, CEL-TrkA, EPHB2-TrkA, or TGF-TrkA fusion protein.

11 . The method of claim 1 , wherein the NTRK gene fusion protein comprises:

(a) an N-terminal polypeptide region comprising a polypeptide sequence other than a TrkA, TrkB, or TrkC polypeptide sequence; and

(b) a C-terminal polypeptide region comprising a TrkB polypeptide sequence, wherein the C-terminal polypeptide comprises TrkB kinase activity;

wherein the fusion protein is a NACC2-TrkB, QKI-TrkB, AFAP1-TrkB, PAN3-TrkB, SQSTM1-TrkB, TRIM24-TrkB, VCL-TrkB, AGBL4-TrkB, or DAB2IP-TrkB fusion protein.

12 . The method of claim 1 , wherein the NTRK gene fusion protein comprises:

(a) an N-terminal polypeptide region comprising a polypeptide sequence other than a TrkA, TrkB, or TrkC polypeptide sequence; and

(b) a C-terminal polypeptide region comprising a TrkC polypeptide sequence, wherein the C-terminal polypeptide comprises TrkC kinase activity;

wherein the fusion protein is a ETV6-TrkC, BTBD1-TrkC, LYN-TrkC, RBPMS-TrkC, EML4-TrkC, HOMER2-TrkC, TFG-TrkC, FAT1-TrkC, or TEL-TrkC fusion protein.

13 . The method of claim 1 , wherein the agent that inhibits a Trk protein is a kinase inhibitor.

14 . The method of claims 1 , wherein the agent that inhibits a Trk protein is entrectinib, RXDX-102, altiratinib, larotrectinib, LOXO-195, sitravatinib, cabozantinib, merestinib, dovitinib, crizotinib, TSR-011, DS-6051, PLX7486, lestaurtinib, danusertib, F17752, AZD6918, AZD7451, or AZ-23, or a pharmaceutically acceptable salt thereof.

15 . The method of claim 14 , wherein the agent is entrectinib, or a pharmaceutically acceptable salt thereof.

16 . The method of claim 1 , wherein the NET is a foregut, midgut, or hindgut NET.

17 . The method of claim 1 , wherein the NET is a gastrointestinal NET.

18 . The method of claim 1 , wherein the NET is a small intestine NET (SI-NET).

19 . The method of claim 1 , wherein the NET is a large intestine NET.

20 . The method of claim 1 , wherein the NET is a rectal intestine NET.

21 . The method of claim 1 , wherein the NET is a gastric intestine NET.

22 . The method of claim 1 , wherein the NET is a pancreatic NET (PNET).

23 . The method of claim 1 , wherein the NET is a bronchial NET.

24 . The method of claim 1 , wherein the NET is an appendix, ovarian, or thyroid NET.

25 . The method of claim 1 , wherein the NET is of unknown primary origin.

26 . The method of claim 1 , wherein the primary NET has metastasized to a secondary tissue.

27 . The method of claim 26 , wherein the secondary tissue is a lymph node, mesentery, liver, bone, lung, or brain.

28 . The method of claim 1 , wherein the agent is utilized as a primary or frontline therapy.

29 . The method of claim 1 , wherein the agent is utilized as a secondary or salvage therapy.

30 . The method of claim 1 , wherein the individual has stable or progressive disease after a previous chemotherapy treatment regimen.

31 . The method of claim 30 , wherein the previous chemotherapy treatment regimen comprises treatment with capecitabine, 5-fluorouracil, doxorubicin, etoposide, dacarbazine, streptozocin, temozolomide, cisplatin, cyclophosphamide, thalidomide, or any combination thereof.

32 . The method of claim 1 , further comprising administering to the individual an additional therapy.

33 . The method of claim 32 , wherein the additional therapy is a second agent that inhibits a Trk protein.

34 . The method of claim 32 , wherein the additional therapy comprises a PI3K/Akt/mTOR pathway inhibitor, a TGF-β pathway inhibitors, a cell cycle inhibitor, a somatostatin analogue, an interferon, or an angiogenesis inhibitor.

35 . The method of claim 34 , wherein the somatostatin analogue is octreotide, octreotate, pasireotide, or lanreotide.

36 . The method of claim 34 , wherein the somatostatin analogue is radiolabeled.

37 . The method of claim 37 , wherein the radiolabeled somatostatin analogue is [DOTA 0 ,Tyr 3 ]octreotate (Lutathera).

38 . The method of claim 34 , wherein the interferon is a type I interferon.

39 . The method of claim 38 , wherein the type I interferon is IFN-α.

40 . The method of claim 34 , wherein the additional therapy is everolimus, temsirolimus, bevacizumab, sunitinib, or sorafenib.

41 . The method of claim 32 , wherein the additional therapy comprises surgery, chemotherapy, or radiation therapy.

42 . The method of claim 1 , wherein the individual has a carcinoid syndrome.

43 . The method of claim 42 , further comprising administering to the individual a treatment for the carcinoid syndrome.

44 . The method of claim 43 , wherein the treatment for the carcinoid syndrome is an anti-serotonin agent.

45 . The method of claim 44 , wherein the anti-serotonin agent is a somatostatin analogue.

46 . The method of claim 45 , wherein the somatostatin analogue is octreotide, octreotate, pasireotide, or lanreotide.

47 . A method of treating a neuroendocrine tumor (NET) in an individual in need thereof comprising: (a) obtaining a sample of NET genetic material from the individual; (b) determining whether the NET tumor comprises a NTRK translocation or gene fusion; and (c) administering to the individual an agent that inhibits a tropomyosin receptor kinase (Trk) protein.

48 . The method of claim 47 , wherein the sample of NET genetic material is total nucleic acid obtained from formalin-fixed paraffin-embedded (FFPE) tumor biopsy sample.

49 . The method of claim 47 , further comprising sequencing the NET genetic material to determine whether the tumor sample comprises a NTRK translocation or gene fusion.

50 . The method of claim 49 , wherein the NET genetic material is sequenced by whole genome DNA sequencing, whole exome sequencing, targeted DNA sequencing, targeted RNA sequencing, or whole transcriptome RNA sequencing.

51 . The method of claim 47 , further comprising amplifying the NET genetic material using NTRK1, NTRK2, or NTRK3-specific primers prior to determining whether the NET tumor comprises a NTRK translocation or gene fusion.

52 . The method of claim 48 , further comprising detecting the amount of NTRK expression or Trk protein levels in a NET tumor sample, wherein elevated levels of NTRK expression or Trk protein levels is indicative of a NTRK translocation or gene fusion.

53 . A method of treating a gastrointestinal neuroendocrine tumor (NET) in an individual in need thereof, comprising administering to the individual a therapeutically effective amount of an agent that inhibits a tropomyosin receptor kinase (Trk) protein, wherein the NET is associated with a Trk protein that has undergone a genetic translocation or is an NTRK gene fusion protein.

54 . The method of claim 53 , wherein the NTRK gene fusion protein comprises an NTRK1, NTRK2, or NTRK3 tyrosine kinase signaling domain.

55 . The method of claim 54 , wherein the NTRK gene fusion protein is constitutively active.

56 . The method of claim 53 , wherein the NTRK gene fusion protein comprises:

(a) an N-terminal polypeptide region comprising a polypeptide sequence other than a TrkA, TrkB, or TrkC polypeptide sequence; and

(b) a C-terminal polypeptide region comprising a TrkA, TrkB, or TrkC polypeptide sequence, wherein the C-terminal polypeptide region has TrkA, TrkB, or TrkC kinase activity.

57 . The method of claim 53 , wherein the NTRK gene fusion protein comprises:

(a) an N-terminal polypeptide region comprising the sequence of a MPRIP, CD74, RABGAP1L, TPM3, TPR, TFG, PPL, CHTOP, ARHGEF2, NFASC, BCAN, LMNA, TP53, QKI, NACC2, VCL, AGBL4, TRIM24, PAN3, AFAP1, SQSTM1, ETV6, BTBD1, LYN, RBPMS, RFWD2, IRF2BP2, SSBP2, C18ORF8, RNF213, TBC1, DNER, PLEKHA6, PEAR1, MRPL24, MDM4, GRIPAP1, EPS15, DYNC2H1, CEL, EPHB2, EML4, HOMER2, TEL, or FAT1 polypeptide sequence; and

(b) a C-terminal polypeptide region comprising a TrkA, TrkB, or TrkC polypeptide sequence, wherein the C-terminal polypeptide region has TrkA, TrkB, or TrkC kinase activity.

58 . The method of claim 57 , wherein the N-terminal polypeptide region comprises an ETV6 polypeptide sequence.

59 . The method of claim 58 , wherein the C-terminal polypeptide region comprises a TrkC polypeptide sequence.

60 . The method of claim 53 , wherein the NTRK gene fusion protein comprises:

(a) an N-terminal polypeptide region comprising a polypeptide sequence other than a TrkA, TrkB, or TrkC polypeptide sequence; and

(b) a C-terminal polypeptide region comprising a TrkA polypeptide sequence, wherein the C-terminal polypeptide comprises TrkA kinase activity;

wherein the fusion protein is a TP53-TrkA, LMNA-TrkA, CD74-TrkA, TFG-TrkA, TPM3-TrkA, NFASC-TrkA, BCAN-TrkA, MPRIP-TrkA, TPR-TrkA, RFWD2-TrkA, IRF2BP2-TrkA, SQSTM1-TrkA, SSBP2-TrkA, RABGAP1L-TrkA, C18ORF8-TrkA, RNF213-TrkA, TBC1D22A-TrkA, C200RF112-TrkA, DNER-TrkA, ARHGEF2-TrkA, CHTOP-TrkA, PPL-TrkA, PLEKHA6-TrkA, PEAR1-TrkA, MRPL24-TrkA, MDM4-TrkA, LRRC71-TrkA, GRIPAP1-TrkA, EPS15-TrkA, DYNC2H1-TrkA, CEL-TrkA, EPHB2-TrkA, or TGF-TrkA fusion protein.

61 . The method of claim 53 , wherein the NTRK gene fusion protein comprises:

(a) an N-terminal polypeptide region comprising a polypeptide sequence other than a TrkA, TrkB, or TrkC polypeptide sequence; and

(b) a C-terminal polypeptide region comprising a TrkB polypeptide sequence, wherein the C-terminal polypeptide comprises TrkB kinase activity;

wherein the fusion protein is a NACC2-TrkB, QKI-TrkB, AFAP1-TrkB, PAN3-TrkB, SQSTM1-TrkB, TRIM24-TrkB, VCL-TrkB, AGBL4-TrkB, or DAB2IP-TrkB fusion protein.

62 . The method of claim 53 , wherein the NTRK gene fusion protein comprises:

(a) an N-terminal polypeptide region comprising a polypeptide sequence other than a TrkA, TrkB, or TrkC polypeptide sequence; and

(b) a C-terminal polypeptide region comprising a TrkC polypeptide sequence, wherein the C-terminal polypeptide comprises TrkC kinase activity;

wherein the fusion protein is a ETV6-TrkC, BTBD1-TrkC, LYN-TrkC, RBPMS-TrkC, EML4-TrkC, HOMER2-TrkC, TFG-TrkC, FAT1-TrkC, or TEL-TrkC fusion protein.

63 . The method of claim 53 , wherein the agent that inhibits a Trk protein is a kinase inhibitor.

64 . The method of claim 53 , wherein the agent that inhibits a Trk protein is entrectinib, RXDX-102, altiratinib, larotrectinib, LOXO-195, sitravatinib, cabozantinib, merestinib, dovitinib, crizotinib, TSR-011, DS-6051, PLX7486, lestaurtinib, danusertib, F17752, AZD6918, AZD7451, or AZ-23, or a pharmaceutically acceptable salt thereof.

65 . The method of claim 64 , wherein the agent is entrectinib, or a pharmaceutically acceptable salt thereof.

66 . The method of claim 53 , wherein the gastrointestinal NET is a small intestine, large intestine, pancreatic, appendix, gastric, rectal, or unknown primary origin NET.

67 . The method of claim 53 , wherein the primary NET has metastasized to a secondary tissue.

68 . The method of claim 67 , wherein the secondary tissue is a lymph node, mesentery, liver, bone, lung, or brain.

69 . A method of treating a gastrointestinal neuroendocrine tumor (NET) in an individual in need thereof comprising: (a) obtaining a sample of NET genetic material from the individual; (b) determining whether the NET tumor comprises a NTRK translocation or gene fusion; and (c) administering to the individual a therapeutically effective amount of an agent that inhibits a tropomyosin receptor kinase (Trk) protein.

70 . The method of claim 69 , wherein the sample of NET genetic material is total nucleic acid obtained from formalin-fixed paraffin-embedded (FFPE) tumor biopsy sample.

71 . The method of claim 69 , further comprising sequencing the NET genetic material to determine whether the tumor sample comprises a NTRK translocation or gene fusion.

72 . The method of claim 71 , wherein the NET genetic material is sequenced by whole genome DNA sequencing, whole exome sequencing, targeted DNA sequencing, targeted RNA sequencing, or whole transcriptome RNA sequencing.

73 . The method of claim 69 , further comprising amplifying the NET genetic material using NTRK1, NTRK2, or NTRK3-specific primers prior to determining whether the NET tumor comprises a NTRK translocation or gene fusion.

74 . The method of claim 69 , further comprising detecting the amount of NTRK expression or Trk protein levels in a NET tumor sample, wherein elevated levels of NTRK expression or Trk protein levels is indicative of a NTRK translocation or gene fusion.