Methods of treating cholangiocarcinoma

1. A method of treating a subject having a cholangiocarcinoma, comprising:

administering to the subject an effective amount of a therapeutic agent that antagonizes or inhibits a fibroblast growth factor receptor 2 (FGFR2) gene or gene product, or a neurotrophic tyrosine receptor kinase, type 1 (NTRK1) gene or gene product,

thereby treating the cholangiocarcinoma in the subject.

2. The method of claim 1 , wherein said therapeutic agent comprises one or more of:

a kinase inhibitor;

a tyrosine kinase inhibitor;

a pan-FGFR2 inhibitor;

a pan-TRK inhibitor;

a multi-specific kinase inhibitor;

an FGF receptor inhibitor;

a reversible or an irreversible FGFR2 inhibitor;

a small molecule that binds to the FGFR2 gene product or the NTRK1 gene product;

an antibody molecule against the FGFR2 gene product or the NTRK1 gene product;

a kinase inhibitor that is selective for the FGFR2 gene product or the NTRK1 gene product; and

a siRNA, antisense RNA, or other nucleic acid based inhibitor of the FGFR2 gene or gene product or the NTRK1 gene or gene product.

3. The method of claim 1 , wherein said therapeutic agent comprises one or more of AZD-2171, AZD-4547, BGJ398, BIBF1120, Brivanib, Cediranib, Dovitinib, ENMD-2076, JNJ 42756493, Masitinib, Lenvatinib, LY2874455, Ponatinib, Pazopanib, R406, Regorafenib, PD173074, PD-173955, Danusertib, Dovitinib Dilactic Acid, TSU-68, Tyrphostin AG 1296, MK-2461, Brivanib Alaninate, Lestaurtinib, PHA-848125, K252a, AZ-23, Oxindole-3, AV369b, ACTB1003, Volasertib, R1530, Loxo-101, ARRY-470, ARRY-786, RXDX-101, RXDX-102, axitinib, bosutinib, dasatinib, erlotinib, gefitinib, imatinib, lapatinib, neratinib, nilotinib, semaxanib, sunitinib, toceranib, vandetanib, vatalanib, sorafenib, PCI-32765, AC220, dovitinib lactate, BIBW 2992, SGX523, PF-04217903, PF-02341066, PF-299804, BMS-777607, ABT-869, MP470, AP24534, JNJ-26483327, MGCD265, DCC-2036, BMS-690154, CEP-11981, tivozanib, OSI-930, MM-121, XL-184, XL-647, and XL228.

4. The method of claim 3 , wherein said therapeutic agent is Regorafenib or Ponatinib.

5. The method of claim 1 , wherein said therapeutic agent is an antibody molecule.

6. The method of claim 1 , wherein the therapeutic agent hybridizes to a nucleic acid molecule encoding an FGFR2 fusion polypeptide or an NTRK1 fusion polypeptide, or hybridizes to a transcription regulatory region that blocks or reduces mRNA expression of the FGFR2 fusion polypeptide or the NTRK1 fusion polypeptide, and

wherein the therapeutic agent comprises one or more of: an antisense molecule, a ribozyme, an RNAi, and a triple helix molecule.

7. The method of claim 1 , further comprising acquiring knowledge of the presence of a fusion polypeptide or a fusion nucleic acid molecule encoding the fusion polypeptide in a sample from the subject, wherein the fusion polypeptide is:

(a) an FGFR2-TACC3 fusion polypeptide encoded by a nucleic acid molecule comprising a fusion junction of exon 16 of SEQ ID NO: 1 and exon 11 of SEQ ID NO: 3;

(b) an FGFR2-KIAA1598 fusion polypeptide encoded by a nucleic acid molecule comprising a fusion junction of exon 16 of SEQ ID NO: 1 and exon 7 of SEQ ID NO: 5;

(c) a BICC1-FGFR2 fusion polypeptide encoded by a nucleic acid molecule comprising a fusion junction of exon 2 of SEQ ID NO: 7 and exon 17 of SEQ ID NO: 1;

(d) a PARK2-FGFR2 fusion polypeptide encoded by a nucleic acid molecule comprising a fusion junction of exon 9 of SEQ ID NO: 9 and exon 18 of SEQ ID NO: 11;

(e) an FGFR2-NOL4 fusion polypeptide encoded by a nucleic acid molecule comprising a fusion junction of exon 17 of SEQ ID NO: 11 and exon 7 of SEQ ID NO: 13;

(f) a ZDHHC6-FGFR2 fusion polypeptide encoded by a nucleic acid molecule comprising a fusion junction of exon 5 of SEQ ID NO: 15 and exon 18 of SEQ ID NO: 11; or

(g) a RABGAP1L-NTRK1 fusion polypeptide.

8. The method of claim 7 , comprising directly acquiring knowledge of the presence of the fusion polypeptide or the fusion nucleic acid molecule encoding the fusion polypeptide in the sample from the subject.

9. The method of claim 7 , wherein determination of the presence of the fusion polypeptide or the fusion nucleic acid molecule encoding the fusion polypeptide comprises sequencing.

10. The method of claim 7 , wherein the therapeutic agent is administered responsive to determination of the presence of the fusion polypeptide or the fusion nucleic acid molecule encoding the fusion polypeptide in the sample.

11. The method of claim 7 , wherein the subject is undergoing or has undergone treatment with a different therapeutic agent or therapeutic modality.

12. The method of claim 11 , wherein responsive to determination of the presence of the fusion polypeptide or the fusion nucleic acid molecule encoding the fusion polypeptide in the sample, the method further comprises discontinuing the different therapeutic agent or therapeutic modality.

13. The method of claim 11 , wherein the different therapeutic agent or therapeutic modality is a chemotherapy, immunotherapy, or a surgical procedure.

14. The method of claim 11 , wherein the different therapeutic agent or therapeutic modality comprises one or more of a surgical procedure, fluorouracil, doxorubicin, gemcitabine, or cisplatin.

15. The method of claim 7 , wherein:

(a) the FGFR2-TACC3 fusion polypeptide is encoded by a nucleic acid molecule comprising exons 1-16 of SEQ ID NO: 1 and exons 11-16 of SEQ ID NO: 3;

(b) the FGFR2-KIAA1598 fusion polypeptide is encoded by a nucleic acid molecule comprising exons 1-16 of SEQ ID NO: 1 and exons 7-17 of SEQ ID NO: 5;

(c) the BICC1-FGFR2 fusion polypeptide is encoded by a nucleic acid molecule comprising exons 1-2 of SEQ ID NO: 7 and exon 17 of SEQ ID NO: 1;

(d) the PARK2-FGFR2 fusion polypeptide is encoded by a nucleic acid molecule comprising exons 1-9 of SEQ ID NO: 9 and exon 18 of SEQ ID NO: 11;

(e) the FGFR2-NOL4 fusion polypeptide is encoded by a nucleic acid molecule comprising exons 1-17 of SEQ ID NO: 11 and exons 7-11 of SEQ ID NO: 13; or

(f) the ZDHHC6-FGFR2 fusion polypeptide is encoded by a nucleic acid molecule comprising exons 1-5 of SEQ ID NO: 15 and exon 18 of SEQ ID NO: 11.

16. The method of claim 15 , wherein the fusion polypeptide comprises an FGFR2 receptor tyrosine kinase domain or a functional fragment thereof.

17. The method of claim 7 , wherein the fusion nucleic acid molecule encoding the RABGAP1L-NTRK1 fusion polypeptide comprises a breakpoint within the encoded tyrosine kinase domain of NTRK1.

18. The method of claim 1 , further comprising administering to the subject an effective amount of a second therapeutic agent or a different therapeutic modality.

19. The method of claim 18 , wherein the second therapeutic agent comprises an anti-cancer agent, and/or the different therapeutic modality comprises a surgical and/or radiation procedure.

20. The method of claim 1 , wherein the cholangiocarcinoma comprises one or more mutated cells that originate in the bile duct.

21. The method of claim 1 , wherein the cholangiocarcinoma is intrahepatic carcinoma or extrahepatic carcinoma.

22. The method of claim 1 , wherein the cholangiocarcinoma is a perihilar cancer, a Klatskin tumor, or a distal cholangiocarcinoma.

23. The method of claim 1 , wherein the cholangiocarcinoma is an adenocarcinoma.

24. The method of claim 1 , wherein the cholangiocarcinoma is:

a Stage I, Stage II, Stage IIIA-IIIC, or Stage IV intrahepatic cholangiocarcinoma; or

a Stage 0, Stage IA-IB, Stage IIA-JIB, Stage III, or Stage IV extrahepatic cholangiocarcinoma.

25. The method of claim 1 , wherein the cholangiocarcinoma is metastatic cholangiocarcinoma.

26. The method of claim 7 , wherein the sample is a nucleic acid sample.

27. The method of claim 7 , wherein the sample is a blood, serum or plasma sample.

28. The method of claim 7 , wherein the sample comprises a tumor biopsy or a circulating tumor cell or nucleic acid.

29. The method of claim 1 , wherein the subject is a human.