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Hoskins JW, Ibrahim A, Emmanuel M, Manmiller S, Jia J, Parikh H, Collins I, Ylaya K, Altekruse SF, Hewitt SM, Petersen GM, Amundadottir LT. Abstract A1-09: Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression with prognostic implications. Cancer Res 2015. [DOI: 10.1158/1538-7445.transcagen-a1-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A genome-wide association study (GWAS) of pancreatic cancer conducted within the NCI Cohort Consortium (PanScan I and II) identified pancreatic cancer susceptibility loci on chromosomes 1q32.1/NR5A2, 5p15.33/CLPTM1L/TERT, 9q34.2/ABO, and 13q22.1. The most significant single-nucleotide polymorphism (SNP) identified on 13q22.1, rs9543325, lies in a ~600 kb gene desert; the nearest genes are KLF5, KLF12, PIBF1, DIS3, and BORA (265–586 kb away). Imputation using the 1000 Genomes and DCEG reference datasets did not improve the GWAS signal, but produced a set of highly correlated SNPs for functional follow-up. We performed eQTL analysis to test for association between the genotypes of these functional candidate variants and expression of nearby genes. Among 64 normal derived pancreatic tissue samples, DIS3 expression showed the strongest association with a 30 bp indel variant in the risk locus (P = 4.8 × 10-4), indicating risk alleles associate with reduced DIS3 expression. Mutations in DIS3 have previously been identified in acute myeloid leukemia and multiple myeloma, and its expression has been correlated with metastatic potential in colorectal cancer, suggesting DIS3 is relevant to cancer biology. Chromosome conformation capture identified a physical interaction between the indel-containing locus and a region near the DIS3 promoter. Luciferase assay for regulatory function of this indel-containing locus revealed allele-specific silencer activity for the insertion allele. Supershift electromobility shift assay (EMSA) demonstrated binding of LEF1 specifically to the insertion allele of the indel, which contains two in silico predicted LEF1 binding elements. Finally, through immunohistochemical analysis, high DIS3 protein levels associated with better survival for pancreatic cancer patients (hazard ratio = 2.87, 95% CI = 1.49–5.53, P = 0.001). Our results suggest that at least one target gene for the pancreatic cancer risk variants on chr13q22.1 may be DIS3, and that the underlying biology may be mediated by the novel indel through a long-range repressive effect on DIS3 expression.
Citation Format: Jason W. Hoskins, Abdisamad Ibrahim, Mickey Emmanuel, Sarah Manmiller, Jinping Jia, Hemang Parikh, Irene Collins, Kris Ylaya, Sean F. Altekruse, Stephen M. Hewitt, Gloria M. Petersen, Laufey T. Amundadottir. Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression with prognostic implications. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-09.
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Affiliation(s)
| | | | | | | | | | | | | | - Kris Ylaya
- 1National Cancer Institute, Bethesda, MD,
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Hoskins JW, Ibrahim A, Emmanuel M, Parikh H, Jia J, Collins I, Ylaya K, Altekruse SF, Hewitt SM, Petersen GM, Amundadottir LT. Abstract B111: Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression with prognostic implications. Cancer Res 2015. [DOI: 10.1158/1538-7445.panca2014-b111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A genome-wide association study (GWAS) of pancreatic cancer conducted within the NCI Cohort Consortium (PanScan I and II) identified pancreatic cancer susceptibility loci on chromosomes 1q32.1/NR5A2, 5p15.33/CLPTM1L/TERT, 9q34.2/ABO, and 13q22.1. The most significant single-nucleotide polymorphism (SNP) identified on 13q22.1, rs9543325, lies in a 600 kb gene desert; the nearest genes are KLF5, KLF12, PIBF1, DIS3, and BORA (265–586 kb). Imputation using the 1000 Genomes and DCEG reference datasets did not improve the GWAS signal, but produced a set of highly correlated SNPs for functional follow-up. We performed eQTL analysis to test for association between the genotypes of these functional candidate variants and expression of nearby genes. Among 100 normal derived pancreatic tissue samples, DIS3 expression showed the strongest association with a novel 30 bp indel variant in the risk locus (P = 4.0 × 104), indicating risk alleles associate with reduced DIS3 expression. Mutations in DIS3 have previously been identified in acute myeloid leukemia and multiple myeloma, and its expression has been correlated with metastatic potential in colorectal cancer, suggesting DIS3 is relevant to cancer biology. Chromosome conformation capture identified a physical interaction between the indel-containing locus and a region near the DIS3 promoter. Luciferase assay for regulatory function of this indel-containing locus revealed allele-specific silencer activity for the insertion allele. Supershift electromobility shift assay (EMSA) demonstrated binding of LEF1 specifically to the insertion allele of the indel, which contains two in silico predicted LEF1 binding elements. Finally, through immunohistochemical analysis, high DIS3 protein levels associated with better survival for pancreatic cancer patients (hazard ratio = 2.87, 95% CI = 1.49–5.53, P = 0.001). Our results suggest that at least one target gene for the pancreatic cancer risk variants on chr13q22.1 may be DIS3, and that the underlying biology may be mediated by the novel indel through a long-range repressive effect on DIS3 expression.
Citation Format: Jason W. Hoskins, Abdisamad Ibrahim, Mickey Emmanuel, Hemang Parikh, Jinping Jia, Irene Collins, Kris Ylaya, Sean F. Altekruse, Stephen M. Hewitt, Gloria M. Petersen, Laufey T. Amundadottir. Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression with prognostic implications. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr B111.
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Affiliation(s)
| | | | | | | | | | | | - Kris Ylaya
- 1National Cancer Institute, Bethesda, MD,
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Hoskins JW, Flandez M, Jia J, Parikh H, Collins I, Emmanuel M, Ibrahim A, Xiao W, Powell J, Malats N, Petersen GM, Real FX, Amundadottir LT. Abstract B112: Transcriptome analysis in pancreatic cancer reveals a tumor suppressor function for HNF1A. Cancer Res 2015. [DOI: 10.1158/1538-7445.panca2014-b112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC), as with all cancer, is driven by dysregulation of genetic programs due to accumulation of somatic mutations, epigenetic modifications and changes in the micro-environment. Holistic views of perturbations in gene expression networks could illuminate key regulators and pathways for this highly lethal cancer. Toward this end, we performed massively-parallel mRNA-sequencing in normal (n = 10) and tumor (n = 8) derived pancreatic tissue samples as well as pancreatic cancer cell lines (n = 9), and determined differential gene expression (DE) patterns. Sub-network enrichment analyses of all expressed genes based on magnitude of DE identified HNF1A as the regulator of the most significantly and consistently dysregulated expression sub-network in our pancreatic tumor samples (median P = 7.56 x 10-7, median rank = 1, range = 1-25). To explore the effect of HNF1A expression in pancreatic tumor-derived cells we generated stable HNF1A-inducible clones in two pancreatic cancer cell lines. Induction of HNF1A overexpression caused severe growth inhibition (5.3-fold, P = 4.5x10-5 for MIA PaCa-2 clones; 7.2-fold, P = 2.2x10-5 for PANC-1 clones), and G0/G1 cell cycle arrest. This was accompanied by down-regulation of 49 out of 84 assayed cell cycle genes, while only 1 displayed increased expression. These data, combined with HNF1A’s direct regulation of pancreatic development and homeostasis genes (i.e. PDX1, PTF1A and NR5A2), suggest it may be an important tumor suppressor in pancreatic cells.
Citation Format: Jason W. Hoskins, Marta Flandez, Jinping Jia, Hemang Parikh, Irene Collins, Mickey Emmanuel, Abdisamad Ibrahim, Wenming Xiao, John Powell, Nuria Malats, Gloria M. Petersen, Fransisco X. Real, Laufey T. Amundadottir. Transcriptome analysis in pancreatic cancer reveals a tumor suppressor function for HNF1A. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr B112.
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Affiliation(s)
| | - Marta Flandez
- 2CNIO-Spanish National Cancer Research Centre, Madrid, Spain,
| | | | | | | | | | | | | | - John Powell
- 3National Institutes of Health, Bethesda, MD,
| | - Nuria Malats
- 2CNIO-Spanish National Cancer Research Centre, Madrid, Spain,
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Bonani M, Brockmann J, Cohen CD, Fehr T, Nocito A, Schiesser M, Serra AL, Blum M, Struker M, Frey DF, Wuthrich RP, Kim YW, Park SJ, Kim TH, Kim YH, Kang SW, Webb L, Casula A, Tomson C, Ben-Shlomo Y, Webb L, Casula A, Ben-Shlomo Y, Tomson C, Mansour H, Akl A, Wafa E, El Shahawy M, Palma R, Swaminathan S, Irish AB, Kolonko A, Chudek J, Wiecek A, Vanrenterghem Y, Kuypers D, Katrien DV, Evenepoel P, Claes K, Bammens B, Meijers B, Naesens M, Kolonko A, Chudek J, Wiecek A, Lo S, Chan CK, Yong D, Wong PN, Kwan TH, Cheng YL, Fung KS, Choy BY, Chau KF, Leung CB, Ebben J, Liu J, Chen SC, Collins A, Ho YW, Abelli M, Ferrario DI Torvajana A, Ticozzelli E, Maiga B, Ferrario DI Torvajana A, Patane A, Albrizio P, Gregorini M, Libetta C, Rampino T, Albrizio P, Geraci P, Dal Canton A, Rotter MT, Jacobi J, Pressmar K, Amann K, Eckardt KU, Weidemann A, Muller K, Stein M, Diezemann C, Sefrin A, Babel N, Reinke P, Schachtner T, Costa C, Touscoz GA, Sidoti F, Sinesi F, Mantovani S, Simeone S, Balloco C, Piasentin Alessio E, Messina M, Segoloni G, Cavallo R, Sharma R.K, Kaul DA, Gupta RK, Gupta A, Prasad N, Bhadhuria D, Suresh KJ, Benaboud S, Prie D, Thervet E, Urien S, Legendre C, Souberbielle JC, Hirt D, Friedlander G, Treluyer JM, Courbebaisse M, Arias M, Arias M, Campistol J, Pascual J, Grinyo JM, Hernandez D, Morales JM, Pallardo LM, Seron D, Senecal L, Boucher A, Dandavino R, Boucher A, Colette S, Vallee M, Lafrance JP, Tung-Min Y, Min-Ju W, Cheng-Hsu C, Chi-Hung C, Kuo-Hsiung S, Mei-Chin W, Direkze S, Khorsavi M, Khorsavi M, Stuart S, Goode A, Jones G, Chudek J, Kolonko A, Wiecek A, Massimetti C, Napoletano I, Imperato G, Muratore MT, Fazio S, Pessina G, Brescia F, Feriozzi S, Tanaka K, Sakai K, Futaki A, Hyoudo Y, Muramatsu M, Kawamura T, Shishido S, Hara S, Kushiyama A, Aikawa A, Jankowski K, Gozdowska J, Lewandowska D, Kwiatkowski A, Durlik M, Pruszczyk P, Obi Y, Ichimaru N, Kato T, Okumi M, Kaimori J, Yazawa K, Nonomura N, Isaka Y, Takahara S, Aimele M, Christophe R, Geraldine D, Eric R, Alexandre H, Masson I, Nicolas M, Ivan T, Acil J, Lise T, Aoumeur HA, Laurence D, Pierre D, Etienne C, Lionel R, Nassim K, Emmanuel M, Eric A, Christophe M, Webb L, Casula A, Tomson C, Ben-Shlomo Y, Alexandre K, Pierre B, Jean-Philippe H, Dominique P, Christophe L, Alexei G, Michel D, Shah P, Kute VB, Vanikar A, Gumber M, Modi P, Trivedi H, GoIebiewska J, Debska-Slizien A, Rutkowski B, Domanski L, Dutkiewicz G, Kloda K, Pawlik A, Ciechanowicz A, Binczak-Kuleta A, Rozanski J, Myslak M, Safranow K, Ciechanowski K, Aline CS, Basset T, Delavenne X, Alamartine E, Mariat C, Kloda K, Domanski L, Pawlik A, Bobrek-Lesiakowska K, Wisniewska M, Romanowski M, Safranow K, Kurzawski M, Rozanski J, Myslak M, Ciechanowski K, De Borst M, Baia L, Navis G, Bakker S, Ranghino A, Tognarelli G, Basso E, Messina M, Manzione AM, Daidola G, Segoloni GP, Kimura T, Yagisawa T, Ishikawa N, Sakuma Y, Hujiwara T, Nukui A, Yashi M, Kim JH, Kim SS, Han DJ, Park SK, Randhawa G, Gumber M, Kute VB, Shah P, Patel H, Vanikar A, Modi P, Trivedi H, Taheri S, Goker-Alpan O, Ibrahim J, Nedd K, Shankar S, Lein H, Barshop B, Boyd E, Holida M, Hillman R, Ibrahim J, Mardach R, Wienreb N, Rever B, Forte R, Desai A, Wijatyk A, Chang P, Martin R. Transplantation - clinical I. Nephrol Dial Transplant 2012. [DOI: 10.1093/ndt/gfs230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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