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Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues
Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review
Documents
- Zhang et al 2016_post print
Accepted manuscript, 4.8 MB, PDF document
DOI
- https://doi.org/10.1136/gutjnl-2016-313146
Final published version
- Mingfeng Zhang, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Soren Lykke-Andersen
- Bin Zhu, Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA. ,
- Wenming Xiao, Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, FDA, Jefferson, Missouri, USA. ,
- Jason W Hoskins, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Xijun Zhang, Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA. ,
- Lauren M Rost, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Irene Collins, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Martijn van de Bunt, Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK. ,
- Jinping Jia, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Hemang Parikh, Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA. ,
- Tongwu Zhang, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Lei Song, Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Ashley Jermusyk, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Charles C Chung, Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA. ,
- Bin Zhu, Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA. ,
- Weiyin Zhou, Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA. ,
- Gail L Matters, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA. ,
- Robert C Kurtz, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA. ,
- Meredith Yeager, Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA. ,
- Torben Heick Jensen
- Kevin M Brown, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Halit Ongen, Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland. ,
- William R Bamlet, Department of Health Sciences Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota, USA. ,
- Bradley A Murray, The Eli and Edythe L Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, Cambridge, Massachusetts, USA. ,
- Mark I. McCarthy, Oxford NIHR Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK. ,
- Stephen J Chanock, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Nilanjan Chatterjee, Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. ,
- Brian M Wolpin, 1] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA. ,
- Jill P Smith, Division of Gastroenterology and Hepatology, Georgetown University Hospital, Washington, D.C., USA. ,
- Sara H Olson, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, New York, USA. ,
- Gloria M Petersen, Department of Health Sciences Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota, USA. ,
- Jianxin Shi, Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA. ,
- Laufey Amundadottir, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Objective To elucidate the genetic architecture of gene expression in pancreatic tissues. Design We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. Results We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0.1), with the strongest effects seen near transcriptional start sites. Approximately 23% and 42% of genes with significant cis-eQTLs appeared to be specific for tumour-derived and normal-derived tissues, respectively. Significant enrichment of cis-eQTL variants was noted in non-coding regulatory regions, in particular for pancreatic tissues (1.53-fold to 3.12-fold, p≤0.0001), indicating tissue-specific functional relevance. A common pancreatic cancer risk locus on 9q34.2 (rs687289) was associated with ABO expression in histologically normal (p=5.8×10 â '8) and tumour-derived (p=8.3×10 -5 ) tissues. The high linkage disequilibrium between this variant and the O blood group generating deletion variant in ABO (exon 6) suggested that nonsense-mediated decay (NMD) of the O' mRNA might explain this finding. However, knockdown of crucial NMD regulators did not influence decay of the ABO O' mRNA, indicating that a gene regulatory element influenced by pancreatic cancer risk alleles may underlie the eQTL. Conclusions We have identified cis-eQTLs representing potential functional regulatory variants in the pancreas and generated a rich data set for further studies on gene expression and its regulation in pancreatic tissues.
| Original language | English |
|---|---|
| Journal | Gut |
| Volume | 67 |
| Issue | 3 |
| Pages (from-to) | 521-533 |
| Number of pages | 13 |
| ISSN | 0017-5749 |
| DOIs | |
| Publication status | Published - 1 Mar 2018 |
Bibliographical note
© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.
- allele specific expression., eQTL, Gene expression, pancreas, RNA-seq, Gene Expression, Genome-Wide Association Study, Humans, Regulatory Sequences, Nucleic Acid, Transcriptome, Genotype, Pancreatic Neoplasms/genetics, ABO Blood-Group System/genetics, Chromosomes, Human, Pair 9, Nonsense Mediated mRNA Decay, Sequence Analysis, RNA, RNA, Neoplasm/analysis, Alleles, Polymorphism, Single Nucleotide, Pancreas, Quantitative Trait Loci, SUSCEPTIBILITY LOCI, ENDOPLASMIC-RETICULUM STRESS, CANCER, MESSENGER-RNA DECAY, GENOME-WIDE ASSOCIATION, GENETIC-BASIS, VARIANTS, RISK, ABO BLOOD-GROUP, EXPRESSION
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