Current omics-based biomarkers for cholangiocarcinoma

References

• Patel T. Cholangiocarcinoma. Nat Clin Pract Gastroenterol Hepatol. 2006;3(1):33–42.
   PubMedGoogle Scholar
• Nakeeb A, Pitt HA, Sohn TA, et al. Cholangiocarcinoma. A spectrum of intrahepatic, perihilar, and distal tumors. Ann Surg. 1996;224(4):463–473.
   PubMed Web of Science ®Google Scholar
• Sripa B, Kaewkes S, Sithithaworn P, et al. Liver fluke induces cholangiocarcinoma. Plos Med. 2007;4(7):e201.
   PubMed Web of Science ®Google Scholar
• Sripa B, Pairojkul C. Cholangiocarcinoma: lessons from Thailand. Curr Opin Gastroenterol. 2008;24(3):349–356.
   PubMed Web of Science ®Google Scholar
• IARC. A review of human carcinogens: Opisthorchis viverrini and Clonorchis sinensis. IARC Monogr Eval Carcinog Risks Hum. 2012;100B:341–370.
   Google Scholar
• Anderson CD, Pinson CW, Berlin J, et al. Diagnosis and treatment of cholangiocarcinoma. Oncologist. 2004;9(1):43–57.
   PubMed Web of Science ®Google Scholar
• Khan SA, Davidson BR, Goldin RD, et al. Guidelines for the diagnosis and treatment of cholangiocarcinoma: an update. Gut. 2012;61(12):1657–1669.
   PubMed Web of Science ®Google Scholar
• Nakeeb A, Lipsett PA, Lillemoe KD, et al. Biliary carcinoembryonic antigen levels are a marker for cholangiocarcinoma. Am J Surg. 1996;171(1):147–152.
   PubMed Web of Science ®Google Scholar
• Qin XL, Wang ZR, Shi JS, et al. Utility of serum CA19-9 in diagnosis of cholangiocarcinoma: in comparison with CEA. World J Gastroenterol. 2004;10(3):427–432.
   PubMed Web of Science ®Google Scholar
• Chen CY, Shiesh SC, Tsao HC, et al. The assessment of biliary CA 125, CA 19-9 and CEA in diagnosing cholangiocarcinoma–the influence of sampling time and hepatolithiasis. Hepatogastroenterology. 2002;49(45):616–620.
   PubMedGoogle Scholar
• Kongpetch S, Jusakul A, Ong CK, et al. Pathogenesis of cholangiocarcinoma: from genetics to signalling pathways. Best Pract Res Clin Gastroenterol. 2015;29(2):233–244.
   PubMed Web of Science ®Google Scholar
• Jusakul A, Kongpetch S, Teh BT. Genetics of Opisthorchis viverrini-related cholangiocarcinoma. Curr Opin Gastroenterol. 2015;31(3):258–263.
   PubMed Web of Science ®Google Scholar
• Ong CK, Subimerb C, Pairojkul C, et al. Exome sequencing of liver fluke-associated cholangiocarcinoma. Nat Genet. 2012;44(6):690–693.
   PubMed Web of Science ®Google Scholar
• Chan-On W, Nairismagi ML, Ong CK, et al. Exome sequencing identifies distinct mutational patterns in liver fluke-related and non-infection-related bile duct cancers. Nat Genet. 2013;45(12):1474–1478.
   PubMed Web of Science ®Google Scholar
• Jusakul A, Cutcutache I, Yong CH, et al. Whole-genome and epigenomic landscapes of etiologically distinct subtypes of cholangiocarcinoma. Cancer Discov. 2017;7(10):1116–1135.
   PubMed Web of Science ®Google Scholar
• Zou S, Li J, Zhou H, et al. Mutational landscape of intrahepatic cholangiocarcinoma. Nat Commun. 2014;5:5696.
   PubMed Web of Science ®Google Scholar
• Wardell CP, Fujita M, Yamada T, et al. Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations. J Hepatol. 2018;68(5):959–969.
   PubMed Web of Science ®Google Scholar
• Sia D, Hoshida Y, Villanueva A, et al. Integrative molecular analysis of intrahepatic cholangiocarcinoma reveals 2 classes that have different outcomes. Gastroenterology. 2013;144(4):829–840.
   PubMed Web of Science ®Google Scholar
• Andersen JB, Thorgeirsson SS. Genomic decoding of intrahepatic cholangiocarcinoma reveals therapeutic opportunities. Gastroenterology. 2013;144(4):687–690.
   PubMed Web of Science ®Google Scholar
• Sawyers CL. The cancer biomarker problem. Nature. 2008;452(7187):548–552.
   PubMed Web of Science ®Google Scholar
• Roychowdhury S, Chinnaiyan AM. Translating cancer genomes and transcriptomes for precision oncology. CA Cancer J Clin. 2016;66(1):75–88.
   PubMed Web of Science ®Google Scholar
• Obama K, Ura K, Li M, et al. Genome-wide analysis of gene expression in human intrahepatic cholangiocarcinoma. Hepatology. 2005;41(6):1339–1348.
   PubMed Web of Science ®Google Scholar
• Jinawath N, Chamgramol Y, Furukawa Y, et al. Comparison of gene expression profiles between Opisthorchis viverrini and non-Opisthorchis viverrini associated human intrahepatic cholangiocarcinoma. Hepatology. 2006;44(4):1025–1038.
   PubMed Web of Science ®Google Scholar
• Sole C, Arnaiz E, Manterola L, et al. The circulating transcriptome as a source of cancer liquid biopsy biomarkers. Semin Cancer Biol. 2019;58:100–108.
   Web of Science ®Google Scholar
• Billatos E, Vick JL, Lenburg ME, et al. The airway transcriptome as a biomarker for early lung cancer detection. Clin Cancer Res. 2018;24(13):2984–2992.
   PubMed Web of Science ®Google Scholar
• Schwartz GW, Petrovic J, Zhou Y, et al. Differential integration of transcriptome and proteome identifies pan-cancer prognostic biomarkers. Front Genet. 2018;9:205.
   PubMed Web of Science ®Google Scholar
• Henikoff S, Greally JM. Epigenetics, cellular memory and gene regulation. Curr Biol. 2016;26(14):R644–648.
   PubMed Web of Science ®Google Scholar
• Weinhold B. Epigenetics: the science of change. Environ Health Perspect. 2006;114(3):A160–167.
   PubMed Web of Science ®Google Scholar
• Ghavifekr Fakhr M, Farshdousti Hagh M, Shanehbandi D, et al. DNA methylation pattern as important epigenetic criterion in cancer. Genet Res Int. 2013;2013:317569.
   PubMedGoogle Scholar
• Sharma S, Kelly TK, Jones PA. Epigenetics in cancer. Carcinogenesis. 2010;31(1):27–36.
   PubMed Web of Science ®Google Scholar
• Kurdyukov S, Bullock M. Methylation analysis: DNA. Choosing the right method. Biology (Basel). 2016;5(1):3.
   PubMedGoogle Scholar
• Harrison A, Parle-McDermott A. DNA methylation: a timeline of methods and applications. Front Genet. 2011;2:74.
   PubMedGoogle Scholar
• Andresen K, Boberg KM, Vedeld HM, et al. Novel target genes and a valid biomarker panel identified for cholangiocarcinoma. Epigenetics. 2012;7(11):1249–1257.
   PubMed Web of Science ®Google Scholar
• Vedeld HM, Andresen K, Eilertsen IA, et al. The novel colorectal cancer biomarkers CDO1, ZSCAN18 and ZNF331 are frequently methylated across gastrointestinal cancers. Int J Cancer. 2015;136(4):844–853.
   PubMed Web of Science ®Google Scholar
• Goeppert B, Konermann C, Schmidt CR, et al. Global alterations of DNA methylation in cholangiocarcinoma target the Wnt signaling pathway. Hepatology. 2014;59(2):544–554.
   Web of Science ®Google Scholar
• Nakamoto S, Kumamoto Y, Igarashi K, et al. Methylated promoter DNA of CDO1 gene and preoperative serum CA19-9 are prognostic biomarkers in primary extrahepatic cholangiocarcinoma. PloS One. 2018;13(10):e0205864.
   PubMed Web of Science ®Google Scholar
• Andresen K, Boberg KM, Vedeld HM, et al. Four DNA methylation biomarkers in biliary brush samples accurately identify the presence of cholangiocarcinoma. Hepatology. 2015;61(5):1651–1659.
   PubMed Web of Science ®Google Scholar
• Branchi V, Schaefer P, Semaan A, et al. Promoter hypermethylation of SHOX2 and SEPT9 is a potential biomarker for minimally invasive diagnosis in adenocarcinomas of the biliary tract. Clin Epigenetics. 2016;8(1):133.
   PubMedGoogle Scholar
• Shin SH, Lee K, Kim BH, et al. Bile-based detection of extrahepatic cholangiocarcinoma with quantitative DNA methylation markers and its high sensitivity. J Mol Diagn. 2012;14(3):256–263.
   PubMed Web of Science ®Google Scholar
• Limpaiboon T, Khaenam P, Chinnasri P, et al. Promoter hypermethylation is a major event of hMLH1 gene inactivation in liver fluke related cholangiocarcinoma. Cancer Lett. 2005;217(2):213–219.
   PubMed Web of Science ®Google Scholar
• Chinnasri P, Pairojkul C, Jearanaikoon P, et al. Preferentially different mechanisms of inactivation of 9p21 gene cluster in liver fluke-related cholangiocarcinoma. Hum Pathol. 2009;40(6):817–826.
   PubMed Web of Science ®Google Scholar
• Ahrendt SA, Eisenberger CF, Yip L, et al. Chromosome 9p21 loss and p16 inactivation in primary sclerosing cholangitis-associated cholangiocarcinoma. J Surg Res. 1999;84(1):88–93.
   PubMed Web of Science ®Google Scholar
• Sriraksa R, Zeller C, El-Bahrawy MA, et al. CpG-island methylation study of liver fluke-related cholangiocarcinoma. Br J Cancer. 2011;104(8):1313–1318.
   PubMed Web of Science ®Google Scholar
• Amornpisutt R, Proungvitaya S, Jearanaikoon P, et al. DNA methylation level of OPCML and SFRP1: a potential diagnostic biomarker of cholangiocarcinoma. Tumour Biol. 2015;36(7):4973–4978.
   PubMedGoogle Scholar
• Wasenang W, Chaiyarit P, Proungvitaya S, et al. Serum cell-free DNA methylation of OPCML and HOXD9 as a biomarker that may aid in differential diagnosis between cholangiocarcinoma and other biliary diseases. Clin Epigenetics. 2019;11(1):39.
   PubMed Web of Science ®Google Scholar
• Graves PR, Haystead TA. Molecular biologist’s guide to proteomics. Microbiol Mol Biol Rev. 2002;66(1):39–63.
   PubMed Web of Science ®Google Scholar
• Seeree P, Pearngam P, Kumkate S, et al. An omics perspective on molecular biomarkers for diagnosis, prognosis, and therapeutics of cholangiocarcinoma. Int J Genomics. 2015;2015:179528.
   PubMedGoogle Scholar
• Darby IA, Vuillier-Devillers K, Pinault E, et al. Proteomic analysis of differentially expressed proteins in peripheral cholangiocarcinoma. Cancer Microenviron. 2010;4(1):73–91.
   PubMedGoogle Scholar
• Haonon O, Rucksaken R, Pinlaor P, et al. Upregulation of 14-3-3 eta in chronic liver fluke infection is a potential diagnostic marker of cholangiocarcinoma. Proteomics Clin Appl. 2016;10(3):248–256.
   PubMed Web of Science ®Google Scholar
• Shi Y, Deng X, Zhan Q, et al. A prospective proteomic-based study for identifying potential biomarkers for the diagnosis of cholangiocarcinoma. J Gastrointest Surg. 2013;17(9):1584–1591.
   PubMed Web of Science ®Google Scholar
• Onsurathum S, Haonon O, Pinlaor P, et al. Proteomics detection of S100A6 in tumor tissue interstitial fluid and evaluation of its potential as a biomarker of cholangiocarcinoma. Tumour Biol. 2018;40(4):1010428318767195.
   Google Scholar
• Shimonishi T, Miyazaki K, Kono N, et al. Expression of endogenous galectin-1 and galectin-3 in intrahepatic cholangiocarcinoma. Hum Pathol. 2001;32(3):302–310.
   PubMed Web of Science ®Google Scholar
• Junking M, Wongkham C, Sripa B, et al. Decreased expression of galectin-3 is associated with metastatic potential of liver fluke-associated cholangiocarcinoma. Eur J Cancer. 2008;44(4):619–626.
   PubMed Web of Science ®Google Scholar
• Dechaphunkul A, Kanngurn S, Dechsukhum C, et al. The significance of galectin-3 immunohistochemistry, clinical characteristics and liver imaging in differentiating intrahepatic cholangiocarcinoma from adenocarcinoma liver metastasis. J Med Assoc Thai. 2010;93(5):523–528.
   PubMedGoogle Scholar
• Iguchi T, Aishima S, Taketomi A, et al. Fascin overexpression is involved in carcinogenesis and prognosis of human intrahepatic cholangiocarcinoma: immunohistochemical and molecular analysis. Hum Pathol. 2009;40(2):174–180.
   PubMed Web of Science ®Google Scholar
• Mao X, Chen D, Wu J, et al. Differential expression of fascin, E-cadherin and vimentin: proteins associated with survival of cholangiocarcinoma patients. Am J Med Sci. 2013;346(4):261–268.
   PubMed Web of Science ®Google Scholar
• Onodera M, Zen Y, Harada K, et al. Fascin is involved in tumor necrosis factor-alpha-dependent production of MMP9 in cholangiocarcinoma. Lab Invest. 2009;89(11):1261–1274.
   PubMed Web of Science ®Google Scholar
• Yonglitthipagon P, Pairojkul C, Chamgramol Y, et al. Up-regulation of annexin A2 in cholangiocarcinoma caused by Opisthorchis viverrini and its implication as a prognostic marker. Int J Parasitol. 2010;40(10):1203–1212.
   PubMed Web of Science ®Google Scholar
• Yonglitthipagon P, Pairojkul C, Bhudhisawasdi V, et al. Proteomics-based identification of alpha-enolase as a potential prognostic marker in cholangiocarcinoma. Clin Biochem. 2012;45(10–11):827–834.
   PubMed Web of Science ®Google Scholar
• Yonglitthipagon P, Pairojkul C, Chamgramol Y, et al. Prognostic significance of peroxiredoxin 1 and ezrin-radixin-moesin-binding phosphoprotein 50 in cholangiocarcinoma. Hum Pathol. 2012;43(10):1719–1730.
   PubMed Web of Science ®Google Scholar
• Hongsrichan N, Rucksaken R, Chamgramol Y, et al. Annexin A1: A new immunohistological marker of cholangiocarcinoma. World J Gastroenterol. 2013;19(16):2456–2465.
   PubMed Web of Science ®Google Scholar
• Pavlou MP, Diamandis EP, Blasutig IM. The long journey of cancer biomarkers from the bench to the clinic. Clin Chem. 2013;59(1):147–157.
   PubMed Web of Science ®Google Scholar
• Liu L, Wang J, Liu B, et al. Serum levels of variants of transthyretin down-regulation in cholangiocarcinoma. J Cell Biochem. 2008;104(3):745–755.
   PubMed Web of Science ®Google Scholar
• Wang X, Dai S, Zhang Z, et al. Characterization of apolipoprotein A-I as a potential biomarker for cholangiocarcinoma. Eur J Cancer Care (Engl). 2009;18(6):625–635.
   PubMed Web of Science ®Google Scholar
• Tolek A, Wongkham C, Proungvitaya S, et al. Serum alpha1beta-glycoprotein and afamin ratio as potential diagnostic and prognostic markers in cholangiocarcinoma. Exp Biol Med (Maywood). 2012;237(10):1142–1149.
   PubMed Web of Science ®Google Scholar
• Rucksaken R, Khoontawad J, Roytrakul S, et al. Proteomic analysis to identify plasma orosomucoid 2 and kinesin 18A as potential biomarkers of cholangiocarcinoma. Cancer Biomark. 2012;12(2):81–95.
   PubMed Web of Science ®Google Scholar
• Rucksaken R, Charoensuk L, Pinlaor P, et al. Plasma orosomucoid 2 as a potential risk marker of cholangiocarcinoma. Cancer Biomark. 2017;18(1):27–34.
   PubMed Web of Science ®Google Scholar
• Khoontawad J, Hongsrichan N, Chamgramol Y, et al. Increase of exostosin 1 in plasma as a potential biomarker for opisthorchiasis-associated cholangiocarcinoma. Tumour Biol. 2014;35(2):1029–1039.
   PubMedGoogle Scholar
• Kristiansen TZ, Bunkenborg J, Gronborg M, et al. A proteomic analysis of human bile. Mol Cell Proteomics. 2004;3(7):715–728.
   PubMed Web of Science ®Google Scholar
• Koopmann J, Thuluvath PJ, Zahurak ML, et al. Mac-2-binding protein is a diagnostic marker for biliary tract carcinoma. Cancer. 2004;101(7):1609–1615.
   PubMed Web of Science ®Google Scholar
• Shen J, Wang W, Wu J, et al. Comparative proteomic profiling of human bile reveals SSP411 as a novel biomarker of cholangiocarcinoma. PloS One. 2012;7(10):e47476.
   PubMed Web of Science ®Google Scholar
• Laohaviroj M, Potriquet J, Jia X, et al. A comparative proteomic analysis of bile for biomarkers of cholangiocarcinoma. Tumour Biol. 2017;39(6):1010428317705764.
   Google Scholar
• Zhang Z, Oyesanya RA, Campbell DJ, et al. Preclinical assessment of simultaneous targeting of epidermal growth factor receptor (ErbB1) and ErbB2 as a strategy for cholangiocarcinoma therapy. Hepatology. 2010;52(3):975–986.
   PubMed Web of Science ®Google Scholar
• Ramanathan RK, Belani CP, Singh DA, et al. A phase II study of lapatinib in patients with advanced biliary tree and hepatocellular cancer. Cancer Chemother Pharmacol. 2009;64(4):777–783.
   PubMed Web of Science ®Google Scholar
• Javle M, Churi C, Kang HC, et al. HER2/neu-directed therapy for biliary tract cancer. J Hematol Oncol. 2015;8:58.
   PubMed Web of Science ®Google Scholar
• Rizvi S, Yamada D, Hirsova P, et al. A hippo and fibroblast growth factor receptor autocrine pathway in cholangiocarcinoma. J Biol Chem. 2016;291(15):8031–8047.
   PubMed Web of Science ®Google Scholar
• Simile MM, Bagella P, Vidili G, et al. Targeted therapies in cholangiocarcinoma: emerging evidence from clinical trials. Medicina (Kaunas). 2019;55(2):42.
   Web of Science ®Google Scholar
• Borger DR, Zhu AX. IDH mutations: new genetic signatures in cholangiocarcinoma and therapeutic implications. Expert Rev Anticancer Ther. 2012;12(5):543–546.
   PubMed Web of Science ®Google Scholar