{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Patrick Tan"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001000256"],"host":["EGA"],"description":["EGA DAC EGAC00001000256"],"repository":["EGA"],"email":["gmstanp@duke-nus.edu.sg"],"pubmed_abstract":["Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analyzed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined 4 CCA clusters-fluke-positive CCAs (clusters 1/2) are enriched in <i>ERBB2</i> amplifications and <i>TP53</i> mutations; conversely, fluke-negative CCAs (clusters 3/4) exhibit high copy-number alterations and <i>PD-1</i>/<i>PD-L2</i> expression, or epigenetic mutations (<i>IDH1/2, BAP1</i>) and <i>FGFR</i>/<i>PRKA</i>-related gene rearrangements. Whole-genome analysis highlighted <i>FGFR2</i> 3' untranslated region deletion as a mechanism of <i>FGFR2</i> upregulation. Integration of noncoding promoter mutations with protein-DNA binding profiles demonstrates pervasive modulation of H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores-mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Our results exemplify how genetics, epigenetics, and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer.<b>Significance:</b> Integrated whole-genome and epigenomic analysis of CCA on an international scale identifies new CCA driver genes, noncoding promoter mutations, and structural variants. CCA molecular landscapes differ radically by etiology, underscoring how distinct cancer subtypes in the same organ may arise through different extrinsic and intrinsic carcinogenic processes. <i>Cancer Discov; 7(10); 1116-35. ©2017 AACR.</i><i>This article is highlighted in the In This Issue feature, p. 1047</i>.","<h4>Background</h4>Aristolochic acid (AA) is a natural compound found in many plants of the Aristolochia genus, and these plants are widely used in traditional medicines for numerous conditions and for weight loss. Previous work has connected AA-mutagenesis to upper-tract urothelial cell carcinomas and hepatocellular carcinomas. We hypothesize that AA may also contribute to bladder cancer.<h4>Methods</h4>Here, we investigated the involvement of AA-mutagenesis in bladder cancer by sequencing bladder tumor genomes from two patients with known exposure to AA. After detecting strong mutational signatures of AA exposure in these tumors, we exome-sequenced and analyzed an additional 11 bladder tumors and analyzed publicly available somatic mutation data from a further 336 bladder tumors.<h4>Results</h4>The somatic mutations in the bladder tumors from the two patients with known AA exposure showed overwhelming AA signatures. We also detected evidence of AA exposure in 1 out of 11 bladder tumors from Singapore and in 3 out of 99 bladder tumors from China. In addition, 1 out of 194 bladder tumors from North America showed a pattern of mutations that might have resulted from exposure to an unknown mutagen with a heretofore undescribed pattern of A > T mutations. Besides the signature of AA exposure, the bladder tumors also showed the CpG > TpG and activated-APOBEC signatures, which have been previously reported in bladder cancer.<h4>Conclusions</h4>This study demonstrates the utility of inferring mutagenic exposures from somatic mutation spectra. Moreover, AA exposure in bladder cancer appears to be more pervasive in the East, where traditional herbal medicine is more widely used. More broadly, our results suggest that AA exposure is more extensive than previously thought both in terms of populations at risk and in terms of types of cancers involved. This appears to be an important public health issue that should be addressed by further investigation and by primary prevention through regulation and education. In addition to opportunities for primary prevention, knowledge of AA exposure would provide opportunities for secondary prevention in the form of intensified screening of patients with known or suspected AA exposure."],"pubmed_title":["Mutation signatures implicate aristolochic acid in bladder cancer development.","Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma."],"pubmed_authors":["Jusakul Apinya A, Cutcutache Ioana I, Yong Chern Han CH, Lim Jing Quan JQ, Huang Mi Ni MN, Padmanabhan Nisha N, Nellore Vishwa V, Kongpetch Sarinya S, Ng Alvin Wei Tian AWT, Ng Ley Moy LM, Choo Su Pin SP, Myint Swe Swe SS, Thanan Raynoo R, Nagarajan Sanjanaa S, Lim Weng Khong WK, Ng Cedric Chuan Young CCY, Boot Arnoud A, Liu Mo M, Ong Choon Kiat CK, Rajasegaran Vikneswari V, Lie Stefanus S, Lim Alvin Soon Tiong AST, Lim Tse Hui TH, Tan Jing J, Loh Jia Liang JL, McPherson John R JR, Khuntikeo Narong N, Bhudhisawasdi Vajaraphongsa V, Yongvanit Puangrat P, Wongkham Sopit S, Totoki Yasushi Y, Nakamura Hiromi H, Arai Yasuhito Y, Yamasaki Satoshi S, Chow Pierce Kah-Hoe PK, Chung Alexander Yaw Fui AYF, Ooi London Lucien Peng Jin LLPJ, Lim Kiat Hon KH, Dima Simona S, Duda Dan G DG, Popescu Irinel I, Broet Philippe P, Hsieh Sen-Yung SY, Yu Ming-Chin MC, Scarpa Aldo A, Lai Jiaming J, Luo Di-Xian DX, Carvalho André Lopes AL, Vettore André Luiz AL, Rhee Hyungjin H, Park Young Nyun YN, Alexandrov Ludmil B LB, Gordân Raluca R, Rozen Steven G SG, Shibata Tatsuhiro T, Pairojkul Chawalit C, Teh Bin Tean BT, Tan Patrick P","Poon Song Ling SL, Huang Mi Ni MN, Choo Yang Y, McPherson John R JR, Yu Willie W, Heng Hong Lee HL, Gan Anna A, Myint Swe Swe SS, Siew Ee Yan EY, Ler Lian Dee LD, Ng Lay Guat LG, Weng Wen-Hui WH, Chuang Cheng-Keng CK, Yuen John Sp JS, Pang See-Tong ST, Tan Patrick P, Teh Bin Tean BT, Rozen Steven G SG"],"additional_accession":[]},"is_claimable":false,"name":"DAC for Duke-NUS genomic sequencing projects","description":"Data Access Committee EGAC00001000256","dates":{"output":"2025-1-9"},"accession":"EGAC00001000256","cross_references":{"TAXONOMY":["9606"],"pubmed":["26015808","28667006"],"EGA":["EGAS00001000975","EGAS00001001653","EGAD00001001994","EGAD00001001036"]}}