Hepatology International

, Volume 13, Issue 4, pp 490–500 | Cite as

Prognostic subclass of intrahepatic cholangiocarcinoma by integrative molecular–clinical analysis and potential targeted approach

  • Keun Soo Ahn
  • Daniel O’Brien
  • Yu Na Kang
  • Taofic Mounajjed
  • Yong Hoon Kim
  • Tae-Seok Kim
  • Jean-Pierre A. Kocher
  • Loretta K. Allotey
  • Mitesh J. BoradEmail author
  • Lewis R. RobertsEmail author
  • Koo Jeong KangEmail author
Original Article



Although molecular characterization of iCCA has been studied recently, integrative analysis of molecular and clinical characterization has not been fully established. If molecular features of iCCA can be predicted based on clinical findings, we can approach to distinguish targeted treatment. We analyzed RNA sequencing data annotated with clinicopathologic data to clarify molecular-specific clinical features and to evaluate potential therapies for molecular subtypes.


We performed next-generation RNA sequencing of 30 surgically resected iCCA from Korean patients and the clinicopathologic features were analyzed. The RNA sequences from 32 iCCA resected from US patients were used for validation.


Patients were grouped into two subclasses on the basis of unsupervised clustering, which showed a difference in 5-year survival rates (48.5% vs 14.2%, p = 0.007) and similar survival outcome in the US samples. In subclass B (poor prognosis), both data sets were similar in higher carcinoembryonic antigen and cancer antigen 19-9 levels, underlying cholangitis, and bile duct-type pathology; in subclass A (better prognosis), there was more frequent viral hepatitis and cholangiolar-type pathology. On pathway analysis, subclass A had enriched liver-related signatures. Subclass B had enriched inflammation-related and TP53 pathways, with more frequent KRAS mutations. CCA cell lines with similar gene expression patterns of subclass A were sensitive to gemcitabine.


Two molecular subtypes of iCCA with distinct clinicopathological differences were identified. Knowledge of clinical and pathologic characteristics can predict molecular subtypes, and knowledge of different subtype signaling pathways may lead to more rational, targeted approaches to treatment.


Cholangiocarcinoma RNA sequence Gene expression Pathway Mutation KRAS Target therapy 



The authors thank Li Li, Dehai Wu, Katsuyuki Miyabe, Tao Song, Ning Zhang, Jianbo Huang, Shaoqing Wang, Lin Yang, and Amy S Mauer (Mayo clinic, Rochester, MN) for their help in the experiment. The biospecimens and data used for this study were provided by the Biobank of Keimyung University Dongsan Medical Center, member of the Korea Biobank Network. This work was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MSIP) (No. 2018R1C1B3004435). This work was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea Government (MSIP) (No. 2014R1A5A2010008).

Compliance with ethical standards

Conflict of interest

Keun Soo Ahn, Daniel O’Brien, Yu Na Kang, Taofic Mounajjed4, Yong Hoon Kim, Tae-Seok Kim, Jean-Pierre A. Kocher, Loretta K. Allotey, Mitesh J. Borad, Lewis R. Roberts, and Koo Jeong Kang declare that they have no conflict of interest.

Availability of data and materials

RNA sequencing data of this manuscript is registered at Gene Expression Omnibus ( with GEO accession number of GSE107943

Ethics approval

This study was approved by institutional review boards at both institutions (Keimyung University Dongsan Medical Center: IRB No. 2014-12-066, Mayo clinic: IRB No. 16-007369) and included secondary use of human-derived materials.

Informed consent

Informed consent for the human-derived materials was obtained from all patients before surgery.

Supplementary material

12072_2019_9954_MOESM1_ESM.xlsx (213 kb)
Supplementary material 1 (XLSX 212 kb)
12072_2019_9954_MOESM2_ESM.pdf (1 mb)
Supplementary material 2 (PDF 1035 kb)


  1. 1.
    Blechacz BR, Gores GJ. Cholangiocarcinoma. Clin Liver Dis 2008;12:131–150, ixCrossRefPubMedGoogle Scholar
  2. 2.
    Patel T. Worldwide trends in mortality from biliary tract malignancies. BMC Cancer 2002;2:10CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Andersen JB, Spee B, Blechacz BR, Avital I, Komuta M, Barbour A, et al. Genomic and genetic characterization of cholangiocarcinoma identifies therapeutic targets for tyrosine kinase inhibitors. Gastroenterology 2012;142:1021–1031 e1015CrossRefPubMedGoogle Scholar
  4. 4.
    Jusakul A, Cutcutache I, Yong CH, Lim JQ, Huang MN, Padmanabhan N, et al. Whole-genome and epigenomic landscapes of etiologically distinct subtypes of cholangiocarcinoma. Cancer Discov 2017;7:1116–1135CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Sia D, Hoshida Y, Villanueva A, Roayaie S, Ferrer J, Tabak B, et al. Integrative molecular analysis of intrahepatic cholangiocarcinoma reveals 2 classes that have different outcomes. Gastroenterology 2013;144:829–840CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, et al. integrative genomic analysis of cholangiocarcinoma identifies distinct IDH-mutant molecular profiles. Cell Rep 2017;18:2780–2794CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Liau JY, Tsai JH, Yuan RH, Chang CN, Lee HJ, Jeng YM. Morphological subclassification of intrahepatic cholangiocarcinoma: etiological, clinicopathological, and molecular features. Mod Pathol 2014;27:1163–1173CrossRefPubMedGoogle Scholar
  8. 8.
    Akita M, Fujikura K, Ajiki T, Fukumoto T, Otani K, Azuma T, et al. Dichotomy in intrahepatic cholangiocarcinomas based on histologic similarities to hilar cholangiocarcinomas. Mod Pathol 2017;30:986–997CrossRefPubMedGoogle Scholar
  9. 9.
    Alvarellos ML, Lamba J, Sangkuhl K, Thorn CF, Wang L, Klein DJ, et al. PharmGKB summary: gemcitabine pathway. Pharmacogenet Genom 2014;24:564–574CrossRefGoogle Scholar
  10. 10.
    Kuper H, Ye W, Broome U, Romelsjo A, Mucci LA, Ekbom A, et al. The risk of liver and bile duct cancer in patients with chronic viral hepatitis, alcoholism, or cirrhosis. Hepatology 2001;34:714–718CrossRefPubMedGoogle Scholar
  11. 11.
    Zheng DL, Zhang L, Cheng N, Xu X, Deng Q, Teng XM, et al. Epigenetic modification induced by hepatitis B virus X protein via interaction with de novo DNA methyltransferase DNMT3A. J Hepatol 2009;50:377–387CrossRefPubMedGoogle Scholar
  12. 12.
    Sun HY, Li Y, Guo K, Kang XN, Sun C, Liu YK. Identification of metastasis-related osteopontin expression and glycosylation in hepatocellular carcinoma. Zhonghua Gan Zang Bing Za Zhi 2011;19:904–907PubMedGoogle Scholar
  13. 13.
    Borger DR, Tanabe KK, Fan KC, Lopez HU, Fantin VR, Straley KS, et al. Frequent mutation of isocitrate dehydrogenase (IDH)1 and IDH2 in cholangiocarcinoma identified through broad-based tumor genotyping. Oncologist 2012;17:72–79CrossRefPubMedGoogle Scholar
  14. 14.
    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:e115383CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Borad MJ, Gores GJ, Roberts LR. Fibroblast growth factor receptor 2 fusions as a target for treating cholangiocarcinoma. Curr Opin Gastroenterol 2015;31:264–268CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Maeda S, Morikawa T, Takadate T, Suzuki T, Minowa T, Hanagata N, et al. Mass spectrometry-based proteomic analysis of formalin-fixed paraffin-embedded extrahepatic cholangiocarcinoma. J Hepatobiliary Pancreat Sci 2015;22:683–691CrossRefPubMedGoogle Scholar
  17. 17.
    Komuta M, Govaere O, Vandecaveye V, Akiba J, Van Steenbergen W, Verslype C, et al. Histological diversity in cholangiocellular carcinoma reflects the different cholangiocyte phenotypes. Hepatology 2012;55:1876–1888CrossRefPubMedGoogle Scholar
  18. 18.
    Arumugam T, Ramachandran V, Logsdon CD. Effect of cromolyn on S100P interactions with RAGE and pancreatic cancer growth and invasion in mouse models. J Natl Cancer Inst 2006;98:1806–1818CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Dumartin L, Whiteman HJ, Weeks ME, Hariharan D, Dmitrovic B, Iacobuzio-Donahue CA, et al. AGR2 is a novel surface antigen that promotes the dissemination of pancreatic cancer cells through regulation of cathepsins B and D. Cancer Res 2011;71:7091–7102CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Beauchemin N, Arabzadeh A. Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) in cancer progression and metastasis. Cancer Metastasis Rev 2013;32:643–671CrossRefPubMedGoogle Scholar
  21. 21.
    Akagi J, Takai E, Tamori Y, Nakagawa K, Ogawa M. CA19-9 epitope a possible marker for MUC-1/Y protein. Int J Oncol 2001;18:1085–1091PubMedGoogle Scholar
  22. 22.
    Ringel J, Lohr M. The MUC gene family: their role in diagnosis and early detection of pancreatic cancer. Mol Cancer 2003;2:9CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Yang S, Che SP, Kurywchak P, Tavormina JL, Gansmo LB, Correa-de-Sampaio P, et al. Detection of mutant KRAS and TP53 DNA in circulating exosomes from healthy individuals and patients with pancreatic cancer. Cancer Biol Ther 2017;18:158–165CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Moeini A, Sia D, Bardeesy N, Mazzaferro V, Llovet JM. Molecular pathogenesis and targeted therapies for intrahepatic cholangiocarcinoma. Clin Cancer Res 2016;22:291–300CrossRefPubMedGoogle Scholar
  25. 25.
    Kordes C, Haussinger D. Hepatic stem cell niches. J Clin Invest 2013;123:1874–1880CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Cardinale V, Bragazzi MC, Carpino G, Torrice A, Fraveto A, Gentile R, et al. Cholangiocarcinoma: increasing burden of classifications. Hepatobiliary Surg Nutr 2013;2:272–280PubMedPubMedCentralGoogle Scholar
  27. 27.
    Lee BS, Lee SH, Son JH, Jang DK, Chung KH, Paik WH, et al. Prognostic value of CA 19-9 kinetics during gemcitabine-based chemotherapy in patients with advanced cholangiocarcinoma. J Gastroenterol Hepatol 2016;31:493–500CrossRefPubMedGoogle Scholar
  28. 28.
    Ramachandran V, Arumugam T, Wang H, Logsdon CD. Anterior gradient 2 is expressed and secreted during the development of pancreatic cancer and promotes cancer cell survival. Cancer Res 2008;68:7811–7818CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    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:e1004135CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Yamamoto J, Kosuge T, Takayama T, Shimada K, Makuuchi M, Yoshida J, et al. Surgical treatment of intrahepatic cholangiocarcinoma: four patients surviving more than five years. Surgery 1992;111:617–622PubMedGoogle Scholar

Copyright information

© Asian Pacific Association for the Study of the Liver 2019

Authors and Affiliations

  1. 1.Department of Surgery, Dongsan Medical Center, School of MedicineKeimyung UniversityDaeguRepublic of Korea
  2. 2.Division of Biomedical Statistics and InformaticsMayo ClinicRochesterUSA
  3. 3.Department of Pathology, Dongsan Medical CenterKeimyung UniversityDaeguRepublic of Korea
  4. 4.Department of Laboratory Medicine and PathologyMayo ClinicRochesterUSA
  5. 5.Department of Gastroenterology and HepatologyMayo ClinicRochesterUSA
  6. 6.University of Minnesota Medical SchoolMinneapolisUSA
  7. 7.Division of Hematology and Medical OncologyMayo ClinicScottsdaleUSA

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