Genomic Profiling of Biliary Tract Cancers and Implications for Clinical Practice

Current Treatment Options in Oncology

Volumn 17, Issue 11, 2016, Pages

  Jain, Apurva ^a   Kwong, Lawrence N ^a   Javle, Milind ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

ARID1A; Biliary tract cancers; overall survival; FGFR2; IDH1 2; NGS; Targeted therapy

Indexed keywords

BILE DUCT CARCINOMA; BILIARY TRACT CANCER; CANCER IMMUNOTHERAPY; CANCER PROGNOSIS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CLINICAL PRACTICE; DNA REPAIR; FGFR GENE; GENE; GENE MUTATION; GENOMICS; HER2 GENE; HUMAN; IDH1 GENE; IDH2 GENE; MOLECULARLY TARGETED THERAPY; MUTATIONAL ANALYSIS; ONCOGENE K RAS; REVIEW; SIGNAL TRANSDUCTION; TUMOR SUPPRESSOR GENE; BILIARY TRACT NEOPLASMS; DISEASE MANAGEMENT; DRUG EFFECTS; GENE EXPRESSION PROFILING; GENETIC HETEROGENEITY; GENETICS; IMMUNOTHERAPY; INCIDENCE; METABOLISM; MUTATION; PROCEDURES; PROGNOSIS;

FIBROBLAST GROWTH FACTOR RECEPTOR; TUMOR MARKER;

BILIARY TRACT NEOPLASMS; BIOMARKERS, TUMOR; CHROMATIN ASSEMBLY AND DISASSEMBLY; DISEASE MANAGEMENT; DNA REPAIR; GENE EXPRESSION PROFILING; GENETIC HETEROGENEITY; GENOMICS; HUMANS; IMMUNOTHERAPY; INCIDENCE; MOLECULAR TARGETED THERAPY; MUTATION; PROGNOSIS; RECEPTORS, FIBROBLAST GROWTH FACTOR; SIGNAL TRANSDUCTION;

EID: 84988625202     PISSN: 15272729     EISSN: 15346277     Source Type: Journal    
DOI: 10.1007/s11864-016-0432-2     Document Type: Review

References (57)

1. Rovigatti U. Cancer modelling in the NGS era—part I: emerging technology and initial modelling. Crit Rev Oncol Hematol. 2015;96(2):274–307. doi:10.1016/j.critrevonc.2015.05.017.
2. Churi CR, Shroff R, Wang Y, Rashid A, Kang HC, Weatherly J, et al. Mutation profiling in cholangiocarcinoma: prognostic and therapeutic implications. PLoS One. 2014;9(12):e115383. doi:10.1371/journal.pone.0115383.This article correlates clinical outcome with somatic mutations in BTC and is therefore of significance
3. Jiao Y, Pawlik TM, Anders RA, Selaru FM, Streppel MM, Lucas DJ, et al. Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas. Nat Genet. 2013;45(12):1470–3.First experience with exome sequening in BTC that idnitifies mutations in chromatin modulating genes
4. Siegel RL, Miller KD, Jemal A. Cancer statistics, 2016. A cancer journal for clinicians: CA; 2015.
5. Bragazzi MC, Cardinale V, Carpino G, Venere R, Semeraro R, Gentile R, et al. Cholangiocarcinoma: epidemiology and risk factors. Translational Gastrointestinal Cancer. 2011;1(1):21–32.
6. Rizvi S, Borad MJ, Patel T, Gores GJ, editors. Cholangiocarcinoma: molecular pathways and therapeutic opportunities. Seminars in liver disease; 2014: NIH Public Access.
7. Tyson GL, El-Serag HB. Risk factors for cholangiocarcinoma. Hepatology (Baltimore, Md). 2011;54(1):173–84.
8. Henley SJ, Weir HK, Jim MA, Watson M, Richardson LC. Gallbladder cancer incidence and mortality, United States 1999–2011. Cancer epidemiology, biomarkers & prevention: a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2015;24(9):1319–26. doi:10.1158/1055-9965.epi-15-0199.
9. Castro FA, Koshiol J, Hsing AW, Devesa SS. Biliary tract cancer incidence in the United States—demographic and temporal variations by anatomic site. Int J Cancer. 2013;133(7):1664–71.Description of changes in the incidnce of BTC over time. Cholangiocarcinoma may not be increasing as rapidly as previously described
10. Witjes CD, van den Akker SA, Visser O, Karim-Kos HE, de Vries E, Ijzermans JN, et al. Gallbladder cancer in the Netherlands: incidence, treatment and survival patterns since 1989. Dig Surg. 2012;29(2):92–8. doi:10.1159/000336217.
11. Everhart JE, Ruhl CE. Burden of digestive diseases in the United States Part III: liver, biliary tract, and pancreas. Gastroenterology. 2009;136(4):1134–44.
12. Patel T. Increasing incidence and mortality of primary intrahepatic cholangiocarcinoma in the United States. Hepatology (Baltimore, Md). 2001;33(6):1353–7.
13. Shaib YH, Davila JA, McGlynn K, El-Serag HB. Rising incidence of intrahepatic cholangiocarcinoma in the United States: a true increase? J Hepatol. 2004;40(3):472–7.
14. Tyson GL, Ilyas JA, Duan Z, Green LK, Younes M, El-Serag HB, et al. Secular trends in the incidence of cholangiocarcinoma in the USA and the impact of misclassification. Dig Dis Sci. 2014;59(12):3103–10.Description of changes in the incidnce of BTC over time. Cholangiocarcinoma may not be increasing as rapidly as previously described
15. Roa I, de Toro G, Schalper K, de Aretxabala X, Churi C, Javle M. Overexpression of the HER2/neu gene: a new therapeutic possibility for patients with advanced gallbladder cancer. Gastrointestinal cancer research: GCR. 2014;7(2):42–8.Largest experience with her2/neu IHC in GB Cancer suggesting a need for targeted therapy in this disease
16. Chan-On W, Nairismägi M-L, Ong CK, Lim WK, Dima S, Pairojkul C, et al. Exome sequencing identifies distinct mutational patterns in liver fluke-related and non-infection-related bile duct cancers. Nat Genet. 2013;45(12):1474–8.Exome sequencing of asian patients with BTC shows differences when compared with western population
17. Wang P, Dong Q, Zhang C, Kuan PF, Liu Y, Jeck WR, et al. Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas. Oncogene. 2013;32(25):3091–100. doi:10.1038/onc.2012.315.IDH1 and 2 mutations occur in cholangiocarcinoma and gliomas and may represent targets for therapy in both these diseases
18. Jang S, Chun S-M, Hong S-M, Sung CO, Park H, Kang HJ, et al. High throughput molecular profiling reveals differential mutation patterns in intrahepatic cholangiocarcinomas arising in chronic advanced liver diseases. Mod Pathol. 2014;27(5).
19. Ross JS, Wang K, Javle MM, Catenacci DVT, Shroff RT, Ali SM et al. Comprehensive genomic profiling of biliary tract cancers to reveal tumor-specific differences and frequency of clinically relevant genomic alterations. ASCO Meeting Abstracts. 2015; 33(15_suppl):4009.
20. Goyal L, Govindan A, Sheth RA, Nardi V, Blaszkowsky LS, Faris JE, et al. Prognosis and clinicopathologic features of patients with advanced stage isocitrate dehydrogenase (IDH) mutant and IDH wild-type intrahepatic cholangiocarcinoma. Oncologist. 2015;20(9):1019–27. doi:10.1634/theoncologist.2015-0210.Description of patients with IDH mutant cholangiocarcinoma in the U.S
21. Arai Y, Totoki Y, Hosoda F, Shirota T, Hama N, Nakamura H, et al. Fibroblast growth factor receptor 2 tyrosine kinase fusions define a unique molecular subtype of cholangiocarcinoma. Hepatology (Baltimore, Md). 2014;59(4):1427–34. doi:10.1002/hep.26890.
22. Borger DR, Goyal L, Yau T, Poon RT, Ancukiewicz M, Deshpande V, et al. Circulating oncometabolite 2-hydroxyglutarate is a potential surrogate biomarker in patients with isocitrate dehydrogenase-mutant intrahepatic cholangiocarcinoma. Clinical cancer research: an official journal of the American Association for Cancer Research. 2014;20(7):1884–90. doi:10.1158/1078-0432.ccr-13-2649.Circulating 2HG may be an important PD biomarker for iDH-directed therapies in BTC
23. Javle M, Churi C, Kang HC, Shroff R, Janku F, Surapaneni R, et al. HER2/neu-directed therapy for biliary tract cancer. J Hematol Oncol. 2015;8:58. doi:10.1186/s13045-015-0155-z.
24. Ang C. Role of the fibroblast growth factor receptor axis in cholangiocarcinoma. J Gastroenterol Hepatol. 2015;30(7):1116–22.
25. Hierro C, Rodon J, Tabernero J. Fibroblast growth factor (FGF) receptor/FGF inhibitors: novel targets and strategies for optimization of response of solid tumors. Semin Oncol. 2015;42(6):801–19. doi:10.1053/j.seminoncol.2015.09.027.
26. Wesche J, Haglund K, Haugsten EM. Fibroblast growth factors and their receptors in cancer. The Biochemical journal. 2011;437(2):199–213. doi:10.1042/bj20101603.
27. Graham RP, Fritcher EGB, Pestova E, Schulz J, Sitailo LA, Vasmatzis G, et al. Fibroblast growth factor receptor 2 translocations in intrahepatic cholangiocarcinoma. Hum Pathol. 2014;45(8):1630–8.
28. Borad MJ, Champion MD, Egan JB, Liang WS, Fonseca R, Bryce AH, et al. Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma. PLoS Genet. 2014;10(2):e1004135.
29. Ross JS, Wang K, Gay L, Al-Rohil R, Rand JV, Jones DM, et al. New routes to targeted therapy of intrahepatic cholangiocarcinomas revealed by next-generation sequencing. Oncologist. 2014;19(3):235–42.
30. Wu YM, Su F, Kalyana-Sundaram S, Khazanov N, Ateeq B, Cao X, et al. Identification of targetable FGFR gene fusions in diverse cancers. Cancer discovery. 2013;3(6):636–47. doi:10.1158/2159-8290.cd-13-0050.First description of FGFR mutations in cholangiocarcinoma
31. Javle MM, Shroff RT, Zhu A, Sadeghi S, Choo S, Borad MJ et al. A phase 2 study of BGJ398 in patients (pts) with advanced or metastatic FGFR-altered cholangiocarcinoma (CCA) who failed or are intolerant to platinum-based chemotherapy. ASCO Meeting Abstracts. 2016; 34(4_suppl):335.
32. Kipp BR, Voss JS, Kerr SE, Barr Fritcher EG, Graham RP, Zhang L, et al. Isocitrate dehydrogenase 1 and 2 mutations in cholangiocarcinoma. Hum Pathol. 2012;43(10):1552–8. doi:10.1016/j.humpath.2011.12.007.
33. Grassian AR, Pagliarini R, Chiang DY. Mutations of isocitrate dehydrogenase 1 and 2 in intrahepatic cholangiocarcinoma. Curr Opin Gastroenterol. 2014;30(3):295–302.
34. Merla A, Liu KG, Rajdev L. Targeted therapy in biliary tract cancers. Curr Treat Options in Oncol. 2015;16(10):48. doi:10.1007/s11864-015-0366-0.
35. Burris H, Mellinghoff I, Maher E, Wen P, Beeram M, Touat M, et al. Abstract PL04-05: the first reported results of AG-120, a first-in-class, potent inhibitor of the IDH1 mutant protein, in a phase I study of patients with advanced IDH1-mutant solid tumors, including gliomas. Mol Cancer Ther. 2015;14(12 Supplement 2):PL04–5. doi:10.1158/1535-7163.targ-15-pl04-05.
36. Maletzki C, Schmidt F, Dirks WG, Schmitt M, Linnebacher M. Frameshift-derived neoantigens constitute immunotherapeutic targets for patients with microsatellite-instable haematological malignancies: frameshift peptides for treating MSI+ blood cancers. Eur J Cancer. 2013;49(11):2587–95. doi:10.1016/j.ejca.2013.02.035.
37. Goyal L, Deshpande V, Chung DC, Groeschl RT, Gamblin TC, Zhu AX. Mismatch repair protein loss and microsatellite instability in cholangiocarcinoma. ASCO Meeting Abstracts. 2014; 32(3_suppl):237.
38. Liengswangwong U, Karalak A, Morishita Y, Noguchi M, Khuhaprema T, Srivatanakul P, et al. Immunohistochemical expression of mismatch repair genes: a screening tool for predicting mutator phenotype in liver fluke infection-associated intrahepatic cholangiocarcinoma. World journal of gastroenterology: WJG. 2006;12(23):3740–5.
39. Lee H, Wang K, Johnson A, Jones DM, Ali SM, Elvin JA, et al. Comprehensive genomic profiling of extrahepatic cholangiocarcinoma reveals a long tail of therapeutic targets. J Clin Pathol. 2016;69(5):403–8. doi:10.1136/jclinpath-2015-203394.
40. Philip PA, Mahoney MR, Allmer C, Thomas J, Pitot HC, Kim G, et al. Phase II study of erlotinib in patients with advanced biliary cancer. J Clin Oncol Off J Am Soc Clin Oncol. 2006;24(19):3069–74. doi:10.1200/jco.2005.05.3579.
41. Lee J, Park SH, Chang HM, Kim JS, Choi HJ, Lee MA, et al. Gemcitabine and oxaliplatin with or without erlotinib in advanced biliary-tract cancer: a multicentre, open-label, randomised, phase 3 study. The Lancet Oncology. 2012;13(2):181–8. doi:10.1016/s1470-2045(11)70301-1.
42. Malka D, Cervera P, Foulon S, Trarbach T, de la Fouchardière C, Boucher E, et al. Gemcitabine and oxaliplatin with or without cetuximab in advanced biliary-tract cancer (BINGO): a randomised, open-label, non-comparative phase 2 trial. The lancet oncology. 2014;15(8):819–28.
43. Wu RC, Wang TL, Shih IM. The emerging roles of ARID1A in tumor suppression. Cancer biology & therapy. 2014;15(6):655–64. doi:10.4161/cbt.28411.
44. Chiang NJ, Shan YS, Hung WC, Chen LT. Epigenetic regulation in the carcinogenesis of cholangiocarcinoma. Int J Biochem Cell Biol. 2015;67:110–4. doi:10.1016/j.biocel.2015.06.012.
45. Ong CK, Subimerb C, Pairojkul C, Wongkham S, Cutcutache I, Yu W, et al. Exome sequencing of liver fluke-associated cholangiocarcinoma. Nat Genet. 2012;44(6):690–3. doi:10.1038/ng.2273.Exome sequencing of population of cholangiocarcinoma, particularly in Thailand suggests a different disease biology
46. Murali R, Wiesner T, Scolyer RA. Tumours associated with BAP1 mutations. Pathology. 2013;45(2):116–26. doi:10.1097/PAT.0b013e32835d0efb.
47. Dudley JC, Lin MT, Le DT, Eshleman JR. Microsatellite instability as a biomarker for PD-1 blockade. Clinical cancer research: an official journal of the American Association for Cancer Research. 2016;22(4):813–20. doi:10.1158/1078-0432.CCR-15-1678.
48. Tran E, Turcotte S, Gros A, Robbins PF, Lu YC, Dudley ME, et al. Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science. 2014;344(6184):641–5. doi:10.1126/science.1251102.
49. Schumacher T, Bunse L, Pusch S, Sahm F, Wiestler B, Quandt J, et al. A vaccine targeting mutant IDH1 induces antitumour immunity. Nature. 2014;512(7514):324–7. doi:10.1038/nature13387.
50. Bang YJ, Doi T, Braud FD, Piha-Paul S, Hollebecque A, Razak ARA, et al. 525 safety and efficacy of pembrolizumab (MK-3475) in patients (pts) with advanced biliary tract cancer: interim results of KEYNOTE-028. Eur J Cancer. 51:S112. doi:10.1016/S0959-8049(16)30326-4.
51. Nakamura H, Arai Y, Totoki Y, Shirota T, Elzawahry A, Kato M et al. Genomic spectra of biliary tract cancer. Nat Genet 2015; 47(9):1003–10. doi: 10.1038/ng.3375http://www.nature.com/ng/journal/v47/n9/abs/ng.3375.html#supplementary-information.
52. Zou S, Li J, Zhou H, Frech C, Jiang X, Chu JS, et al. Mutational landscape of intrahepatic cholangiocarcinoma. Nat Commun. 2014;5:5696. doi:10.1038/ncomms6696.
53. Simbolo M, Fassan M, Ruzzenente A, Mafficini A, Wood LD, Corbo V, et al. Multigene mutational profiling of cholangiocarcinomas identifies actionable molecular subgroups. Oncotarget. 2014;5(9):2839–52. doi:10.18632/oncotarget.1943.
54. https://tcgadata.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=CHOL&diseaseName=Cholangiocarcinoma.
55. Lee H, Wang K, Johnson A, Jones DM, Ali SM, Elvin JA, et al. Comprehensive genomic profiling of extrahepatic cholangiocarcinoma reveals a long tail of therapeutic targets. J Clin Pathol. 2015. doi:10.1136/jclinpath-2015-203394.
56. Li M, Zhang Z, Li X, Ye J, Wu X, Tan Z, et al. Whole-exome and targeted gene sequencing of gallbladder carcinoma identifies recurrent mutations in the ErbB pathway. Nat Genet. 2014;46(8):872–6. doi:10.1038/ng.3030.
57. Stephens P, Wang K, Palma NA, Chmielecki J, Shroff RT, Churl C et al., editors. Comprehensive genomic profiling of gallbladder adenocarcinoma and frequent genomic-derived targets of therapy. JOURNAL OF CLINICAL ONCOLOGY; 2014: AMER SOC CLINICAL ONCOLOGY 2318 MILL ROAD, STE 800, ALEXANDRIA, VA 22314 USA.