Methods of treating a neuroendocrine tumor

1. 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 fusion protein comprising:

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

(b) a C-terminal polypeptide region comprising a sequence from a TrkA, TrkB, or TrkC polypeptide, wherein the TrkA, TrkB, or TrkC polypeptide comprises a TrkA, TrkB, or TrkC tyrosine kinase signaling domain comprising TrkA, TrkB, or TrkC kinase activity.

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

3. The method of claim 1 , wherein the Trk fusion protein is constitutively active.

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

(a) an N-terminal polypeptide region comprising a 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; and

(b) a C-terminal polypeptide region comprising a sequence of a TrkA, TrkB, or TrkC polypeptide, wherein the TrkA, TrkB, or TrkC polypeptide comprises a TrkA, TrkB, or TrkC tyrosine kinase signaling domain comprising TrkA, TrkB, or TrkC kinase activity.

5. The method of claim 4 , wherein the N-terminal polypeptide region comprises a sequence from an ETV6 polypeptide.

6. The method of claim 5 , wherein the C-terminal polypeptide region comprises a sequence from a TrkC polypeptide.

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

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

(b) a C-terminal polypeptide region comprising a sequence from a TrkA polypeptide, wherein the TrkA polypeptide comprises a TrkA tyrosine kinase signaling domain comprising TrkA kinase activity; and

wherein the Trk 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.

8. The method of claim 1 , wherein the Trk fusion protein comprises:

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

(b) a C-terminal polypeptide region comprising a sequence from a TrkB polypeptide, wherein the TrkB polypeptide comprises a TrkB tyrosine kinase signaling domain comprising 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.

9. The method of claim 1 , wherein the Trk fusion protein comprises:

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

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

wherein the Trk 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.

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

11. The method of claim 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.

12. The method of claim 11 , wherein the agent is entrectinib, or a pharmaceutically acceptable salt thereof.

13. The method of claim 1 , wherein the gastrointestinal NET is a small intestine, large intestine, pancreatic, appendix, gastric, or rectal NET.

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

15. The method of claim 14 , wherein the secondary tissue is a lymph node, mesentery, liver, bone, lung, or brain.

16. A method of treating a gastrointestinal neuroendocrine tumor (NET) in an individual in need thereof comprising: (a) providing a sample of NET genetic material from the individual; (b) determining whether the sample of NET genetic material comprises a NTRK gene fusion comprising a C-terminal region comprising a NTRK1, NTRK2, or NTRK3 tyrosine kinase signaling domain; and (c) administering to the individual a therapeutically effective amount of an agent that inhibits a tropomyosin receptor kinase (Trk) protein.

17. The method of claim 16 , wherein the sample of NET genetic material is total nucleic acid obtained from formalin-fixed paraffin-embedded (FFPE) tumor biopsy sample.

18. The method of claim 16 , further comprising sequencing the sample of NET genetic material to determine whether the sample of NET genetic material comprises the NTRK gene fusion.

19. The method of claim 16 , further comprising amplifying the sample of NET genetic material using NTRK1, NTRK2, or NTRK3-specific primers prior to determining whether the sample of NET genetic material comprises the NTRK gene fusion.