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Labreche K, Daniau M, Sud A, Law PJ, Royer-Perron L, Holroyd A, Broderick P, Went M, Benazra M, Ahle G, Soubeyran P, Taillandier L, Chinot OL, Casasnovas O, Bay JO, Jardin F, Oberic L, Fabbro M, Damaj G, Brion A, Mokhtari K, Philippe C, Sanson M, Houillier C, Soussain C, Hoang-Xuan K, Houlston RS, Alentorn A. A genome-wide association study identifies susceptibility loci for primary central nervous system lymphoma at 6p25.3 and 3p22.1: a LOC Network study. Neuro Oncol 2021; 21:1039-1048. [PMID: 31102405 DOI: 10.1093/neuonc/noz088] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Primary central nervous system lymphoma (PCNSL) is a rare form of extra-nodal non-Hodgkin lymphoma. PCNSL is a distinct subtype of non-Hodgkin lymphoma, with over 95% of tumors belonging to the diffuse large B-cell lymphoma (DLBCL) group. We have conducted a genome-wide association study (GWAS) on immunocompetent patients to address the possibility that common genetic variants influence the risk of developing PCNSL. METHODS We performed a meta-analysis of 2 new GWASs of PCNSL totaling 475 cases and 1134 controls of European ancestry. To increase genomic resolution, we imputed >10 million single nucleotide polymorphisms using the 1000 Genomes Project combined with UK10K as reference. In addition we performed a transcription factor binding disruption analysis and investigated the patterns of local chromatin by Capture Hi-C data. RESULTS We identified independent risk loci at 3p22.1 (rs41289586, ANO10, P = 2.17 × 10-8) and 6p25.3 near EXOC2 (rs116446171, P = 1.95 x 10-13). In contrast, the lack of an association between rs41289586 and DLBCL suggests distinct germline predisposition to PCNSL and DLBCL. We found looping chromatin interactions between noncoding regions at 6p25.3 (rs11646171) with the IRF4 promoter and at 8q24.21 (rs13254990) with the MYC promoter, both genes with strong relevance to B-cell tumorigenesis. CONCLUSION To our knowledge this is the first study providing insight into the genetic predisposition to PCNSL. Our findings represent an important step in defining the contribution of common genetic variation to the risk of developing PCNSL.
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Affiliation(s)
- Karim Labreche
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK.,(i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France
| | - Mailys Daniau
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,ICM, iGenSeq Platform, Paris, France
| | - Amit Sud
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Louis Royer-Perron
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
| | - Amy Holroyd
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Molly Went
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Marion Benazra
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,ICM, iGenSeq Platform, Paris, France
| | - Guido Ahle
- Department of Neurology, Colmar Civil Hospitals, Colmar Cedex, France
| | - Pierre Soubeyran
- Department of Medical Oncology, Bergnoié Institute, Bordeaux, France.,Inserm Research Unit U1218, Bordeaux, France
| | - Luc Taillandier
- Neuro-oncology Department, Nancy University Hospital and The Center of Research in Automatic Control of Nancy, Joint Research Unit 7039, National Center for Scientific Research, SBS BEAM Department, Nancy University, Vandoeuvre-lès-Nancy, France
| | - Olivier L Chinot
- Department of Pathology and Neuropathology, Timone Hospital, Aix-Marseille University (AMU), Public Assistance-Hospitals of Marseille, Marseille, France.,AMU Research Center in Oncology Biology and Oncopharmacology, Marseille, France
| | | | - Jacques-Olivier Bay
- Department of Hematology, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Fabrice Jardin
- Department of Hematology, Henri Becquerel Cancer Center, Rouen, France and Inserm U1245, Henri Becquerel Cancer Center, Institute of Research and Innovation in Biomedicine, University of Normandy, Rouen, France
| | - Lucie Oberic
- Department of Hematology, University Cancer Institute of Toulouse-Oncopole, Toulouse, France
| | | | - Gandhi Damaj
- Department of Hematology, University Hospital of Caen, Caen, France
| | - Annie Brion
- Department of Hematology, Regional and University Hospitals Besançon, Besançon, France
| | - Karima Mokhtari
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Raymond Escourolle Department of Neuropathology, Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France.,OncoNeuroTek, ICM, Paris, France
| | | | - Marc Sanson
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France.,OncoNeuroTek, ICM, Paris, France
| | - Caroline Houillier
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France
| | - Carole Soussain
- Department of Hematology, René Huguenin Hospital, Curie Institute, Saint-Cloud, France
| | - Khê Hoang-Xuan
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Agusti Alentorn
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
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Large-Scale Profiling of Signaling Pathways Reveals a Distinct Demarcation between Normal and Extended Liver Resection. Cells 2020; 9:cells9051149. [PMID: 32392745 PMCID: PMC7290735 DOI: 10.3390/cells9051149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 12/20/2022] Open
Abstract
Despite numerous studies addressing normal liver regeneration, we still lack comprehensive understanding of the biological processes underlying failed liver regeneration. Therefore, we analyzed the activity of 271 intracellular signaling pathways (ISPs) by genome wide profiling of differentially expressed RNAs in murine liver tissue biopsies after normal hepatectomy (nHx; 68% of liver removed) and extended hepatectomy (eHx; 86% of liver removed). Comprehensive, genome-wide transcriptome profiling using RNAseq was performed in liver tissue obtained from mice (sham, nHx, and eHx) harvested 1, 8, 16, 32, and 48 h after operation (n = 3 per group) and the OncoFinder toolkit was used for an unsupervised, unbiased identification of intracellular signaling pathways (ISP) activity. We observed that the normal regenerative process requires a transient activation and silencing of approximately two dozen of ISPs. After nHx, the Akt Pathway represented with 13 branches, the Chromatin Pathway and the DDR Pathways dominated. After eHx, the ATM main pathway and two of its branches (Cell Survival; G2_M Checkpoint Arrest) dominated, as well as the Hypoxia Pathways. Further, 14 ISPs demonstrated a strong inverse regulation, with the Hedgehog and the Brca1 Main Pathways as chief activators after nHx, and the ATM Pathway(G2_M Checkpoint Arrest) as the dominating constraining response after eHx.
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Borger P, Schneider M, Frick L, Langiewicz M, Sorokin M, Buzdin A, Kachaylo E, Graf R, Humar B, Clavien PA. Exploration of the Transcriptional Landscape of ALPPS Reveals the Pathways of Accelerated Liver Regeneration. Front Oncol 2019; 9:1206. [PMID: 31824837 PMCID: PMC6882302 DOI: 10.3389/fonc.2019.01206] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/23/2019] [Indexed: 12/16/2022] Open
Abstract
Background and Aims: ALPPS (associating liver partition and portal vein ligation for staged hepatectomy), a novel 2-staged hepatectomy, dramatically accelerates liver regeneration and thus enables extensive liver tumor resection. The signaling networks underlying the ALPPS-induced accelerated regeneration process are largely unknown. Methods: We performed transcriptome profiling (TP) of liver tissue obtained from a mouse model of ALPPS, standard hepatectomy (68% model), and additional control surgeries (sham, PVL and Tx). We also performed TP using human liver biopsies (n = 5) taken from the occluded lobe and the future liver remnant (FLR) during the first step of ALPPS surgery (4–5 h apart). We used Oncofinder computational tools, which covers 378 ISPs, for unsupervised, unbiased quantification of ISP activity. Results: Gene expression cluster analysis revealed an ALPPS specific signature: the IGF1R Signaling Pathway (Cell survival), the ILK Pathway (Induced cell proliferation), and the IL-10 Pathway (Stability determination) were significantly enriched, whereas the activity of the Interferon Pathway (Transcription) was reduced (p < 0.05). Further, the PAK- and ILK-associated ISPs were activated at an earlier time point, reflecting significant acceleration of liver regeneration (p < 0.001). These pathways, which were also recovered in human liver biopsies, control cell growth and proliferation, inflammatory response, and hypoxia-related processes. Conclusions: ALPPS is not a straightforward addition of portal vein ligation (PVL) plus transection—it is more. The early stages of normal and accelerated liver regeneration are clearly discernible by a significantly increased and earlier activation of a small number of signaling pathways. Compounds mimicking these responses may help to improve the ALPPS method and further reduce the hospitalization time of the patient.
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Affiliation(s)
- Pieter Borger
- Laboratory of the Swiss Hepato-Pancreato-Biliary (HPB) and Transplantation Center, Department of Surgery, University Hospital Zürich, Zurich, Switzerland
| | - Marcel Schneider
- Laboratory of the Swiss Hepato-Pancreato-Biliary (HPB) and Transplantation Center, Department of Surgery, University Hospital Zürich, Zurich, Switzerland
| | - Lukas Frick
- Laboratory of the Swiss Hepato-Pancreato-Biliary (HPB) and Transplantation Center, Department of Surgery, University Hospital Zürich, Zurich, Switzerland
| | - Magda Langiewicz
- Laboratory of the Swiss Hepato-Pancreato-Biliary (HPB) and Transplantation Center, Department of Surgery, University Hospital Zürich, Zurich, Switzerland
| | - Maksim Sorokin
- OmicsWay Corp., Walnut, CA, United States.,I.M. Sechenov First Moscow State Medical University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Anton Buzdin
- OmicsWay Corp., Walnut, CA, United States.,I.M. Sechenov First Moscow State Medical University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Oncobox Ltd., Moscow, Russia
| | - Ekaterina Kachaylo
- Laboratory of the Swiss Hepato-Pancreato-Biliary (HPB) and Transplantation Center, Department of Surgery, University Hospital Zürich, Zurich, Switzerland
| | - Rolf Graf
- Laboratory of the Swiss Hepato-Pancreato-Biliary (HPB) and Transplantation Center, Department of Surgery, University Hospital Zürich, Zurich, Switzerland
| | - Bostjan Humar
- Laboratory of the Swiss Hepato-Pancreato-Biliary (HPB) and Transplantation Center, Department of Surgery, University Hospital Zürich, Zurich, Switzerland
| | - Pierre-Alain Clavien
- Laboratory of the Swiss Hepato-Pancreato-Biliary (HPB) and Transplantation Center, Department of Surgery, University Hospital Zürich, Zurich, Switzerland
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4
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Claus EB, Cornish AJ, Broderick P, Schildkraut JM, Dobbins SE, Holroyd A, Calvocoressi L, Lu L, Hansen HM, Smirnov I, Walsh KM, Schramm J, Hoffmann P, Nöthen MM, Jöckel KH, Swerdlow A, Larsen SB, Johansen C, Simon M, Bondy M, Wrensch M, Houlston RS, Wiemels JL. Genome-wide association analysis identifies a meningioma risk locus at 11p15.5. Neuro Oncol 2019; 20:1485-1493. [PMID: 29762745 PMCID: PMC6176799 DOI: 10.1093/neuonc/noy077] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background Meningiomas are adult brain tumors originating in the meningeal coverings of the brain and spinal cord, with significant heritable basis. Genome-wide association studies (GWAS) have previously identified only a single risk locus for meningioma, at 10p12.31. Methods To identify a susceptibility locus for meningioma, we conducted a meta-analysis of 2 GWAS, imputed using a merged reference panel from the 1000 Genomes Project and UK10K data, with validation in 2 independent sample series totaling 2138 cases and 12081 controls. Results We identified a new susceptibility locus for meningioma at 11p15.5 (rs2686876, odds ratio = 1.44, P = 9.86 × 10–9). A number of genes localize to the region of linkage disequilibrium encompassing rs2686876, including RIC8A, which plays a central role in the development of neural crest-derived structures, such as the meninges. Conclusions This finding advances our understanding of the genetic basis of meningioma development and provides additional support for a polygenic model of meningioma.
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Affiliation(s)
- Elizabeth B Claus
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Sara E Dobbins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amy Holroyd
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Lisa Calvocoressi
- School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Lingeng Lu
- School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Helen M Hansen
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Ivan Smirnov
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Kyle M Walsh
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Johannes Schramm
- School of Public Health, Yale University, New Haven, Connecticut, USA.,University of Bonn Medical School, Bonn, Germany
| | - Per Hoffmann
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Karl-Heinz Jöckel
- School of Public Health, Yale University, New Haven, Connecticut, USA.,Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.,Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Signe Benzon Larsen
- Unit of Survivorship, The Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Christoffer Johansen
- Unit of Survivorship, The Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matthias Simon
- University of Bonn Medical School, Bonn, Germany.,Department of Neurosurgery, Bethel Clinic, Bielefeld, Germany
| | - Melissa Bondy
- Section of Epidemiology and Population Sciences, Department of Medicine and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Margaret Wrensch
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Joseph L Wiemels
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
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5
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Gao J, Lin L, Chen Z, Cai Y, Xiao C, Zhou F, Sun B, Zhao M. In Vitro Digestion and Fermentation of Three Polysaccharide Fractions from Laminaria japonica and Their Impact on Lipid Metabolism-Associated Human Gut Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:7496-7505. [PMID: 31124365 DOI: 10.1021/acs.jafc.9b00970] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Our previous study has proved that the three polysaccharide fractions from L. japonica (LP-A4, LP-A6, and LP-A8) had significantly different structure characterization. Herein, we conducted in vitro simulated digestion and fermentation to study the digestive mechanism of LP-As. The results of gastrointestinal digestion indicated that LP-A6 and LP-A8 would be easier to trap the enzyme molecules for their denser interconnected macromolecule network compared with LP-A4. Fermentation of LP-As by human gut microbiota, especially for LP-A8, generated a large amount of short-chain fatty acids (SCFAs), which could upregulate the abundance of Firmicutes ( Lachnoclostridium and Eubacterium). The high content of sulfate and highly branched sugar residue of LP-A8 might help it be easily used by Firmicutes in gut microbiota of hyperlipidemic patients. Functional analysis revealed that the increased metabolic activities of glycerophospholipid metabolism, ether lipid metabolism, and fatty acid metabolism induced by LP-A8 treatment were closely associated with metabolic syndromes and hyperlipidemia.
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Affiliation(s)
- Jie Gao
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center , Guangzhou 510640 , China
| | - Lianzhu Lin
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center , Guangzhou 510640 , China
| | - Zijie Chen
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center , Guangzhou 510640 , China
| | - Yongjian Cai
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center , Guangzhou 510640 , China
| | - Chuqiao Xiao
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center , Guangzhou 510640 , China
| | - Feibai Zhou
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center , Guangzhou 510640 , China
| | - Baoguo Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health , Beijing Technology & Business University , Beijing 100048 , China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health , Beijing Technology & Business University , Beijing 100048 , China
| | - Mouming Zhao
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health , Beijing Technology & Business University , Beijing 100048 , China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center , Guangzhou 510640 , China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health , Beijing Technology & Business University , Beijing 100048 , China
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6
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Law PJ, Timofeeva M, Fernandez-Rozadilla C, Broderick P, Studd J, Fernandez-Tajes J, Farrington S, Svinti V, Palles C, Orlando G, Sud A, Holroyd A, Penegar S, Theodoratou E, Vaughan-Shaw P, Campbell H, Zgaga L, Hayward C, Campbell A, Harris S, Deary IJ, Starr J, Gatcombe L, Pinna M, Briggs S, Martin L, Jaeger E, Sharma-Oates A, East J, Leedham S, Arnold R, Johnstone E, Wang H, Kerr D, Kerr R, Maughan T, Kaplan R, Al-Tassan N, Palin K, Hänninen UA, Cajuso T, Tanskanen T, Kondelin J, Kaasinen E, Sarin AP, Eriksson JG, Rissanen H, Knekt P, Pukkala E, Jousilahti P, Salomaa V, Ripatti S, Palotie A, Renkonen-Sinisalo L, Lepistö A, Böhm J, Mecklin JP, Buchanan DD, Win AK, Hopper J, Jenkins ME, Lindor NM, Newcomb PA, Gallinger S, Duggan D, Casey G, Hoffmann P, Nöthen MM, Jöckel KH, Easton DF, Pharoah PDP, Peto J, Canzian F, Swerdlow A, Eeles RA, Kote-Jarai Z, Muir K, Pashayan N, Harkin A, Allan K, McQueen J, Paul J, Iveson T, Saunders M, Butterbach K, Chang-Claude J, Hoffmeister M, Brenner H, Kirac I, Matošević P, Hofer P, Brezina S, Gsur A, Cheadle JP, Aaltonen LA, Tomlinson I, Houlston RS, Dunlop MG. Association analyses identify 31 new risk loci for colorectal cancer susceptibility. Nat Commun 2019; 10:2154. [PMID: 31089142 PMCID: PMC6517433 DOI: 10.1038/s41467-019-09775-w] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/29/2019] [Indexed: 02/02/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related death worldwide, and has a strong heritable basis. We report a genome-wide association analysis of 34,627 CRC cases and 71,379 controls of European ancestry that identifies SNPs at 31 new CRC risk loci. We also identify eight independent risk SNPs at the new and previously reported European CRC loci, and a further nine CRC SNPs at loci previously only identified in Asian populations. We use in situ promoter capture Hi-C (CHi-C), gene expression, and in silico annotation methods to identify likely target genes of CRC SNPs. Whilst these new SNP associations implicate target genes that are enriched for known CRC pathways such as Wnt and BMP, they also highlight novel pathways with no prior links to colorectal tumourigenesis. These findings provide further insight into CRC susceptibility and enhance the prospects of applying genetic risk scores to personalised screening and prevention.
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Affiliation(s)
- Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ceres Fernandez-Rozadilla
- Grupo de Medicina Xenómica, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación de Santiago, Santiago de Compostela, 15706, Spain
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - James Studd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Juan Fernandez-Tajes
- Wellcome Centre for Human Genetics, McCarthy Group, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Susan Farrington
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Steven Penegar
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Evropi Theodoratou
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Peter Vaughan-Shaw
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Harry Campbell
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Lina Zgaga
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Department of Public Health and Primary Care, Institute of Population Health, Trinity College Dublin, University of Dublin, Dublin, D02 PN40, Ireland
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Archie Campbell
- Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah Harris
- Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Ian J Deary
- Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - John Starr
- Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Medical Genetics Section, Centre for Genomics and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Laura Gatcombe
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Maria Pinna
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Sarah Briggs
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Lynn Martin
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Emma Jaeger
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Archana Sharma-Oates
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - James East
- Translational Gastroenterology Unit, Nuffield Department. of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Simon Leedham
- Wellcome Centre for Human Genetics, McCarthy Group, Roosevelt Drive, Oxford, OX3 7BN, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Roland Arnold
- Cancer Bioinfomatics Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Elaine Johnstone
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7LE, UK
| | - Haitao Wang
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7LE, UK
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7LE, UK
| | - Tim Maughan
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7LE, UK
| | - Richard Kaplan
- Medical Research Council Clinical Trials Unit, Aviation House, 125 Kingsway, London, WC2B 6NH, UK
| | - Nada Al-Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Ulrika A Hänninen
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Tatiana Cajuso
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Tomas Tanskanen
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Eevi Kaasinen
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00014, Finland
| | - Johan G Eriksson
- Folkhälsan Research Centre, 00250, Helsinki, Finland
- Unit of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, 00014, Finland
| | - Harri Rissanen
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Paul Knekt
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland, and Faculty of Social Sciences, University of Tampere, Tampere, 33014, Finland
- Faculty of Social Sciences, University of Tampere, Tampere, 33014, Finland
| | - Pekka Jousilahti
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00014, Finland
- Department of Public Health, University of Helsinki, Helsinki, 00014, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00014, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki, 00029, Finland
| | - Anna Lepistö
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki, 00029, Finland
| | - Jan Böhm
- Department of Pathology, Central Finland Central Hospital, Jyväskylä, 40620, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, Jyväskylä, 40620, Finland
- Department of Health Sciences, Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne, Centre for Cancer Research, Parkville, Victoria, 3010, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
| | - Aung-Ko Win
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - John Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Mark E Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, 85259, USA
| | - Polly A Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Steven Gallinger
- Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - David Duggan
- Translational Genomics Research Institute (TGen), An Affiliate of City of Hope, Phoenix, AZ, 85004, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Virginia, VA, 22903, USA
| | - Per Hoffmann
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, 4031, Switzerland
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, 53127, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, 45147, Germany
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Andrea Harkin
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Karen Allan
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - John McQueen
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - James Paul
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Timothy Iveson
- University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Mark Saunders
- The Christie NHS Foundation Trust, Manchester, M20 4BX, UK
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, Deutsches Krebsforschungszentrum, 69120, Heidelberg, Germany
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
- University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, 20251, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, Deutsches Krebsforschungszentrum, 69120, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, Deutsches Krebsforschungszentrum, 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, 69120, Germany
| | - Iva Kirac
- Department of Surgical Oncology, University Hospital for Tumours, Sestre milosrdnice University Hospital Centre, Zagreb, 10000, Croatia
| | - Petar Matošević
- Department of Surgery, University Hospital Center Zagreb, 10000, Zagreb, Croatia
| | - Philipp Hofer
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
| | - Stefanie Brezina
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
| | - Andrea Gsur
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
| | - Jeremy P Cheadle
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Ian Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
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7
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CBX6 is negatively regulated by EZH2 and plays a potential tumor suppressor role in breast cancer. Sci Rep 2019; 9:197. [PMID: 30655550 PMCID: PMC6336801 DOI: 10.1038/s41598-018-36560-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/22/2018] [Indexed: 12/21/2022] Open
Abstract
Chromobox 6 (CBX6) is a subunit of Polycomb Repressive Complex 1 (PRC1) that mediates epigenetic gene repression and acts as an oncogene or tumor suppressor in a cancer type-dependent manner. The specific function of CBX6 in breast cancer is currently undefined. In this study, a comprehensive analysis of The Cancer Genome Atlas (TCGA) dataset led to the identification of CBX6 as a consistently downregulated gene in breast cancer. We provided evidence showing enhancer of zeste homolog 2 (EZH2) negatively regulated CBX6 expression in a Polycomb Repressive Complex 2 (PRC2)-dependent manner. Exogenous overexpression of CBX6 inhibited cell proliferation and colony formation, and induced cell cycle arrest along with suppression of migration and invasion of breast cancer cells in vitro. Microarray analyses revealed that CBX6 governs a complex gene expression program. Moreover, CBX6 induced significant downregulation of bone marrow stromal cell antigen-2 (BST2), a potential therapeutic target, via interactions with its promoter region. Our collective findings support a tumor suppressor role of CBX6 in breast cancer.
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8
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Sud A, Thomsen H, Orlando G, Försti A, Law PJ, Broderick P, Cooke R, Hariri F, Pastinen T, Easton DF, Pharoah PDP, Dunning AM, Peto J, Canzian F, Eeles R, Kote-Jarai ZS, Muir K, Pashayan N, Campa D, Hoffmann P, Nöthen MM, Jöckel KH, von Strandmann EP, Swerdlow AJ, Engert A, Orr N, Hemminki K, Houlston RS. Genome-wide association study implicates immune dysfunction in the development of Hodgkin lymphoma. Blood 2018; 132:2040-2052. [PMID: 30194254 PMCID: PMC6236462 DOI: 10.1182/blood-2018-06-855296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/19/2018] [Indexed: 02/08/2023] Open
Abstract
To further our understanding of inherited susceptibility to Hodgkin lymphoma (HL), we performed a meta-analysis of 7 genome-wide association studies totaling 5325 HL cases and 22 423 control patients. We identify 5 new HL risk loci at 6p21.31 (rs649775; P = 2.11 × 10-10), 6q23.3 (rs1002658; P = 2.97 × 10-8), 11q23.1 (rs7111520; P = 1.44 × 10-11), 16p11.2 (rs6565176; P = 4.00 × 10-8), and 20q13.12 (rs2425752; P = 2.01 × 10-8). Integration of gene expression, histone modification, and in situ promoter capture Hi-C data at the 5 new and 13 known risk loci implicates dysfunction of the germinal center reaction, disrupted T-cell differentiation and function, and constitutive NF-κB activation as mechanisms of predisposition. These data provide further insights into the genetic susceptibility and biology of HL.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Fadi Hariri
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, and
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, and
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, and
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, United Kingdom
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- Department of Applied Health Research, University College London, London, United Kingdom
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Per Hoffmann
- Human Genomic Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics and
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics and
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | | | - Elke Pogge von Strandmann
- Experimental Tumor Research, Center for Tumor Biology and Immunology, Clinic for Hematology, Oncology and Immunology, Philipps University, Marburg, Germany
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom; and
| | - Andreas Engert
- Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Nick Orr
- Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom; and
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
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9
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Lowe EK, Cuomo C, Arnone MI. Omics approaches to study gene regulatory networks for development in echinoderms. Brief Funct Genomics 2018; 16:299-308. [PMID: 28957458 DOI: 10.1093/bfgp/elx012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gene regulatory networks (GRNs) describe the interactions for a developmental process at a given time and space. Historically, perturbation experiments represent one of the key methods for analyzing and reconstructing a GRN, and the GRN governing early development in the sea urchin embryo stands as one of the more deeply dissected so far. As technology progresses, so do the methods used to address different biological questions. Next-generation sequencing (NGS) has become a standard experimental technique for genome and transcriptome sequencing and studies of protein-DNA interactions and DNA accessibility. While several efforts have been made toward the integration of different omics approaches for the study of the regulatory genome in many animals, in a few cases, these are applied with the purpose of reconstructing and experimentally testing developmental GRNs. Here, we review emerging approaches integrating multiple NGS technologies for the prediction and validation of gene interactions within echinoderm GRNs. These approaches can be applied to both 'model' and 'non-model' organisms. Although a number of issues still need to be addressed, advances in NGS applications, such as assay for transposase-accessible chromatin sequencing, combined with the availability of embryos belonging to different species, all separated by various evolutionary distances and accessible to experimental regulatory biology, place echinoderms in an unprecedented position for the reconstruction and evolutionary comparison of developmental GRNs. We conclude that sequencing technologies and integrated omics approaches allow the examination of GRNs on a genome-wide scale only if biological perturbation and cis-regulatory analyses are experimentally accessible, as in the case of echinoderm embryos.
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10
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Vijayakrishnan J, Studd J, Broderick P, Kinnersley B, Holroyd A, Law PJ, Kumar R, Allan JM, Harrison CJ, Moorman AV, Vora A, Roman E, Rachakonda S, Kinsey SE, Sheridan E, Thompson PD, Irving JA, Koehler R, Hoffmann P, Nöthen MM, Heilmann-Heimbach S, Jöckel KH, Easton DF, Pharaoh PDP, Dunning AM, Peto J, Canzian F, Swerdlow A, Eeles RA, Kote-Jarai ZS, Muir K, Pashayan N, Greaves M, Zimmerman M, Bartram CR, Schrappe M, Stanulla M, Hemminki K, Houlston RS. Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia. Nat Commun 2018; 9:1340. [PMID: 29632299 PMCID: PMC5890276 DOI: 10.1038/s41467-018-03178-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/25/2018] [Indexed: 01/19/2023] Open
Abstract
Genome-wide association studies (GWAS) have advanced our understanding of susceptibility to B-cell precursor acute lymphoblastic leukemia (BCP-ALL); however, much of the heritable risk remains unidentified. Here, we perform a GWAS and conduct a meta-analysis with two existing GWAS, totaling 2442 cases and 14,609 controls. We identify risk loci for BCP-ALL at 8q24.21 (rs28665337, P = 3.86 × 10-9, odds ratio (OR) = 1.34) and for ETV6-RUNX1 fusion-positive BCP-ALL at 2q22.3 (rs17481869, P = 3.20 × 10-8, OR = 2.14). Our findings provide further insights into genetic susceptibility to ALL and its biology.
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Affiliation(s)
- Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - James Studd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, 69120, Heidelberg, Germany
| | - James M Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Christine J Harrison
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Anthony V Moorman
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Ajay Vora
- Department of Haematology, Great Ormond Street Hospital, London, WC1N 3JH, UK
| | - Eve Roman
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | | | - Sally E Kinsey
- Department of Paediatric and Adolescent Haematology and Oncology, Leeds General Infirmary, Leeds, LS1 3EX, UK
| | - Eamonn Sheridan
- Medical Genetics Research Group, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK
| | - Pamela D Thompson
- Paediatric and Familial Cancer Research Group, Institute of Cancer Sciences, St. Mary's Hospital, Manchester, M13 9WL, UK
| | - Julie A Irving
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Rolf Koehler
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Per Hoffmann
- Department of Genomics, Institute of Human Genetics, Life & Brain Centre, University of Bonn, D-53012, Bonn, Germany
- Department of Biomedicine, Human Genomics Research Group, University Hospital and University of Basel, 4031, Basel, Switzerland
| | - Markus M Nöthen
- Department of Genomics, Institute of Human Genetics, Life & Brain Centre, University of Bonn, D-53012, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- Department of Genomics, Institute of Human Genetics, Life & Brain Centre, University of Bonn, D-53012, Bonn, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Douglas F Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul D P Pharaoh
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Laboratory, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Frederico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Nora Pashayan
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Mel Greaves
- Centre for Evolution and Cancer, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Martin Zimmerman
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Claus R Bartram
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Martin Schrappe
- General Paediatrics, University Hospital Schleswig-Holstein, 24105, Kiel, Germany
| | - Martin Stanulla
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 221 00, Lund, Sweden
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK.
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11
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Loveday C, Litchfield K, Levy M, Holroyd A, Broderick P, Kote-Jarai Z, Dunning AM, Muir K, Peto J, Eeles R, Easton DF, Dudakia D, Orr N, Pashayan N, Reid A, Huddart RA, Houlston RS, Turnbull C. Validation of loci at 2q14.2 and 15q21.3 as risk factors for testicular cancer. Oncotarget 2018; 9:12630-12638. [PMID: 29560096 PMCID: PMC5849160 DOI: 10.18632/oncotarget.23117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/15/2017] [Indexed: 01/21/2023] Open
Abstract
Testicular germ cell tumor (TGCT), the most common cancer in men aged 18 to 45 years, has a strong heritable basis. Genome-wide association studies (GWAS) have proposed single nucleotide polymorphisms (SNPs) at a number of loci influencing TGCT risk. To further evaluate the association of recently proposed risk SNPs with TGCT at 2q14.2, 3q26.2, 7q36.3, 10q26.13 and 15q21.3, we analyzed genotype data on 3,206 cases and 7,422 controls. Our analysis provides independent replication of the associations for risk SNPs at 2q14.2 (rs2713206 at P = 3.03 × 10-2; P-meta = 3.92 × 10-8; nearest gene, TFCP2L1) and rs12912292 at 15q21.3 (P = 7.96 × 10-11; P-meta = 1.55 × 10-19; nearest gene PRTG). Case-only analyses did not reveal specific associations with TGCT histology. TFCP2L1 joins the growing list of genes located within TGCT risk loci with biologically plausible roles in developmental transcriptional regulation, further highlighting the importance of this phenomenon in TGCT oncogenesis.
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Affiliation(s)
- Chey Loveday
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Kevin Litchfield
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK
| | - Max Levy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Warwick, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Julian Peto
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Darshna Dudakia
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Nick Orr
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
| | - Alison Reid
- Academic Uro-oncology Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK
| | - Robert A Huddart
- Academic Radiotherapy Unit, Institute of Cancer Research, Sutton, Surrey, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- William Harvey Research Institute, Queen Mary University, London, UK
- Guys and St Thomas NHS Foundation Trust, London, UK
- National Cancer Registration and Analysis Service, Public Health England, London, UK
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12
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Alexandrova E, Nassa G, Corleone G, Buzdin A, Aliper AM, Terekhanova N, Shepelin D, Zhavoronkov A, Tamm M, Milanesi L, Miglino N, Weisz A, Borger P. Large-scale profiling of signalling pathways reveals an asthma specific signature in bronchial smooth muscle cells. Oncotarget 2018; 7:25150-61. [PMID: 26863634 PMCID: PMC5039037 DOI: 10.18632/oncotarget.7209] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/26/2016] [Indexed: 02/06/2023] Open
Abstract
Background Bronchial smooth muscle (BSM) cells from asthmatic patients maintain in vitro a distinct hyper-reactive (“primed”) phenotype, characterized by increased release of pro-inflammatory factors and mediators, as well as hyperplasia and/or hypertrophy. This “primed” phenotype helps to understand pathogenesis of asthma, as changes in BSM function are essential for manifestation of allergic and inflammatory responses and airway wall remodelling. Objective To identify signalling pathways in cultured primary BSMs of asthma patients and non-asthmatic subjects by genome wide profiling of differentially expressed mRNAs and activated intracellular signalling pathways (ISPs). Methods Transcriptome profiling by cap-analysis-of-gene-expression (CAGE), which permits selection of preferentially capped mRNAs most likely to be translated into proteins, was performed in human BSM cells from asthmatic (n=8) and non-asthmatic (n=6) subjects and OncoFinder tool were then exploited for identification of ISP deregulations. Results CAGE revealed >600 RNAs differentially expressed in asthma vs control cells (p≤0.005), with asthma samples showing a high degree of similarity among them. Comprehensive ISP activation analysis revealed that among 269 pathways analysed, 145 (p<0.05) or 103 (p<0.01) are differentially active in asthma, with profiles that clearly characterize BSM cells of asthmatic individuals. Notably, we identified 7 clusters of coherently acting pathways functionally related to the disease, with ISPs down-regulated in asthma mostly targeting cell death-promoting pathways and up-regulated ones affecting cell growth and proliferation, inflammatory response, control of smooth muscle contraction and hypoxia-related signalization. Conclusions These first-time results can now be exploited toward development of novel therapeutic strategies targeting ISP signatures linked to asthma pathophysiology.
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Affiliation(s)
- Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi (SA), Italy.,Genomix4Life Srl, Campus of Medicine, University of Salerno, Baronissi (SA), Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi (SA), Italy
| | - Giacomo Corleone
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi (SA), Italy
| | - Anton Buzdin
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR
| | - Alexander M Aliper
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR
| | | | - Denis Shepelin
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,Group for Genomic Regulation of Cell Signalling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Michael Tamm
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Segregate (MI), Italy
| | - Nicola Miglino
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi (SA), Italy.,Molecular Pathology and Medical Genomics Unit, 'SS. Giovanni di Dio e Ruggi d'Aragona - Schola Medica Salernitana' University Hospital, Salerno (SA), Italy
| | - Pieter Borger
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
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13
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Sud A, Thomsen H, Law PJ, Försti A, Filho MIDS, Holroyd A, Broderick P, Orlando G, Lenive O, Wright L, Cooke R, Easton D, Pharoah P, Dunning A, Peto J, Canzian F, Eeles R, Kote-Jarai ZS, Muir K, Pashayan N, Hoffmann P, Nöthen MM, Jöckel KH, Strandmann EPV, Lightfoot T, Kane E, Roman E, Lake A, Montgomery D, Jarrett RF, Swerdlow AJ, Engert A, Orr N, Hemminki K, Houlston RS. Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility. Nat Commun 2017; 8:1892. [PMID: 29196614 PMCID: PMC5711884 DOI: 10.1038/s41467-017-00320-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/20/2017] [Indexed: 02/08/2023] Open
Abstract
Several susceptibility loci for classical Hodgkin lymphoma have been reported. However, much of the heritable risk is unknown. Here, we perform a meta-analysis of two existing genome-wide association studies, a new genome-wide association study, and replication totalling 5,314 cases and 16,749 controls. We identify risk loci for all classical Hodgkin lymphoma at 6q22.33 (rs9482849, P = 1.52 × 10-8) and for nodular sclerosis Hodgkin lymphoma at 3q28 (rs4459895, P = 9.43 × 10-17), 6q23.3 (rs6928977, P = 4.62 × 10-11), 10p14 (rs3781093, P = 9.49 × 10-13), 13q34 (rs112998813, P = 4.58 × 10-8) and 16p13.13 (rs34972832, P = 2.12 × 10-8). Additionally, independent loci within the HLA region are observed for nodular sclerosis Hodgkin lymphoma (rs9269081, HLA-DPB1*03:01, Val86 in HLA-DRB1) and mixed cellularity Hodgkin lymphoma (rs1633096, rs13196329, Val86 in HLA-DRB1). The new and established risk loci localise to areas of active chromatin and show an over-representation of transcription factor binding for determinants of B-cell development and immune response.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, 221 00, Sweden
| | | | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Oleg Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Lauren Wright
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alison Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SM2 5NG, UK
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M1 3BB, UK
- Division of Health Sciences, Warwick Medical School, Warwick University, Warwick, CV4 7AL, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Per Hoffmann
- Department of Biomedicine, Division of Medical Genetics, University of Basel, Basel, 4031, Switzerland
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | | | | | - Tracy Lightfoot
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Eve Roman
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Annette Lake
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Dorothy Montgomery
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Ruth F Jarrett
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Andreas Engert
- Department of Internal Medicine, University Hospital of Cologne, Cologne, 50937, Germany
| | - Nick Orr
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, 221 00, Sweden
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK.
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14
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Sowpati DT, Srivastava S, Dhawan J, Mishra RK. C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search. BMC Bioinformatics 2017; 18:392. [PMID: 28929968 PMCID: PMC5606219 DOI: 10.1186/s12859-017-1786-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge. Results We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge. Conclusions C-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1786-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Jyotsna Dhawan
- CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rakesh K Mishra
- CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India.
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15
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Goodstadt M, Marti‐Renom MA. Challenges for visualizing three-dimensional data in genomic browsers. FEBS Lett 2017; 591:2505-2519. [PMID: 28771695 PMCID: PMC5638070 DOI: 10.1002/1873-3468.12778] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 12/14/2022]
Abstract
Genomic interactions reveal the spatial organization of genomes and genomic domains, which is known to play key roles in cell function. Physical proximity can be represented as two-dimensional heat maps or matrices. From these, three-dimensional (3D) conformations of chromatin can be computed revealing coherent structures that highlight the importance of nonsequential relationships across genomic features. Mainstream genomic browsers have been classically developed to display compact, stacked tracks based on a linear, sequential, per-chromosome coordinate system. Genome-wide comparative analysis demands new approaches to data access and new layouts for analysis. The legibility can be compromised when displaying track-aligned second dimension matrices, which require greater screen space. Moreover, 3D representations of genomes defy vertical alignment in track-based genome browsers. Furthermore, investigation at previously unattainable levels of detail is revealing multiscale, multistate, time-dependent complexity. This article outlines how these challenges are currently handled in mainstream browsers as well as how novel techniques in visualization are being explored to address them. A set of requirements for coherent visualization of novel spatial genomic data is defined and the resulting potential for whole genome visualization is described.
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Affiliation(s)
- Mike Goodstadt
- Structural Genomics GroupCNAG‐CRGThe Barcelona Institute of Science and Technology (BIST)Spain
- Gene Regulation, Stem Cells and Cancer ProgramCentre for Genomic Regulation (CRG)The Barcelona Institute of Science and Technology (BIST)Spain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Marc A. Marti‐Renom
- Structural Genomics GroupCNAG‐CRGThe Barcelona Institute of Science and Technology (BIST)Spain
- Gene Regulation, Stem Cells and Cancer ProgramCentre for Genomic Regulation (CRG)The Barcelona Institute of Science and Technology (BIST)Spain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
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16
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Borisov N, Suntsova M, Sorokin M, Garazha A, Kovalchuk O, Aliper A, Ilnitskaya E, Lezhnina K, Korzinkin M, Tkachev V, Saenko V, Saenko Y, Sokov DG, Gaifullin NM, Kashintsev K, Shirokorad V, Shabalina I, Zhavoronkov A, Mishra B, Cantor CR, Buzdin A. Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data. Cell Cycle 2017; 16:1810-1823. [PMID: 28825872 DOI: 10.1080/15384101.2017.1361068] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
High throughput technologies opened a new era in biomedicine by enabling massive analysis of gene expression at both RNA and protein levels. Unfortunately, expression data obtained in different experiments are often poorly compatible, even for the same biologic samples. Here, using experimental and bioinformatic investigation of major experimental platforms, we show that aggregation of gene expression data at the level of molecular pathways helps to diminish cross- and intra-platform bias otherwise clearly seen at the level of individual genes. We created a mathematical model of cumulative suppression of data variation that predicts the ideal parameters and the optimal size of a molecular pathway. We compared the abilities to aggregate experimental molecular data for the 5 alternative methods, also evaluated by their capacity to retain meaningful features of biologic samples. The bioinformatic method OncoFinder showed optimal performance in both tests and should be very useful for future cross-platform data analyses.
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Affiliation(s)
- Nicolas Borisov
- a Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre "Kurchatov Institute" , Moscow , Russia.,b Department of R&D, First Oncology Research and Advisory Center , Moscow , Russia
| | - Maria Suntsova
- c Department of R&D, Center for Biogerontology and Regenerative Medicine , Moscow , Russia.,d Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Maxim Sorokin
- a Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre "Kurchatov Institute" , Moscow , Russia.,e Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia
| | - Andrew Garazha
- c Department of R&D, Center for Biogerontology and Regenerative Medicine , Moscow , Russia.,f Department of R&D, OmicsWay Corporation , Walnut , CA , USA
| | - Olga Kovalchuk
- g Department of Biological Sciences , University of Lethbridge , Lethbridge , AB , Canada
| | - Alexander Aliper
- d Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Elena Ilnitskaya
- c Department of R&D, Center for Biogerontology and Regenerative Medicine , Moscow , Russia
| | - Ksenia Lezhnina
- b Department of R&D, First Oncology Research and Advisory Center , Moscow , Russia
| | - Mikhail Korzinkin
- c Department of R&D, Center for Biogerontology and Regenerative Medicine , Moscow , Russia
| | - Victor Tkachev
- f Department of R&D, OmicsWay Corporation , Walnut , CA , USA
| | - Vyacheslav Saenko
- h Technological Research Institute S.P. Kapitsa , Ulyanovsk State University , Ulyanovsk , Russia
| | - Yury Saenko
- h Technological Research Institute S.P. Kapitsa , Ulyanovsk State University , Ulyanovsk , Russia
| | - Dmitry G Sokov
- i Chemotherapy Department, Moscow 1st Oncological Hospital , Moscow , Russia
| | - Nurshat M Gaifullin
- j Faculty of Fundamental Medicine , Lomonosov Moscow State University , Moscow , Russia.,k Department of Oncology, Russian Medical Postgraduate Academy , Moscow , Russia
| | - Kirill Kashintsev
- l Chemotherapy Department, Moscow Oncological Hospital 62 , Stepanovskoye , Russia
| | - Valery Shirokorad
- l Chemotherapy Department, Moscow Oncological Hospital 62 , Stepanovskoye , Russia
| | - Irina Shabalina
- m Faculty of Mathematics and Information Technologies , Petrozavodsk State University , Petrozavodsk , Russia
| | - Alex Zhavoronkov
- d Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | | | - Charles R Cantor
- o Department of Biomedical Engineering , Boston University , Boston , MA , USA
| | - Anton Buzdin
- a Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre "Kurchatov Institute" , Moscow , Russia.,b Department of R&D, First Oncology Research and Advisory Center , Moscow , Russia.,e Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia.,f Department of R&D, OmicsWay Corporation , Walnut , CA , USA
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17
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Duan LJ, Cao QF, Xu D, Liu HL, Qi J. Bioinformatic analysis of microRNA-mRNA expression profiles of bladder tissue induced by bladder outlet obstruction in a rat model. Mol Med Rep 2017; 16:4803-4810. [PMID: 28791388 DOI: 10.3892/mmr.2017.7188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 02/23/2017] [Indexed: 11/05/2022] Open
Abstract
Various microRNAs (miRNAs) have previously been demonstrated to exhibit an association with the process of bladder remodeling, induced by bladder outlet obstruction (BOO). However, little is known about miRNA and gene expression profiles and the molecular mechanism underlying bladder pathophysiological alterations. The present study used bioinformatic analysis technology to examine the altered miRNA and mRNA expression profiles of bladder tissue in a rat model of BOO and validate the involved signaling pathways. The gene expression profile data was downloaded from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were screened. Potential target genes of DEMs were predicted. The target genes and DEGs were used for further gene ontology (GO) analysis followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using the Database for Annotation, Visualization and Integrated Discovery. The present study additionally constructed a DEM‑DEG interaction network. A total of 9 DEMs (3 upregulated and 6 downregulated) were identified; 664 DEGs were screened. KEGG analysis revealed that the DEGs were involved in the regulation of the actin cytoske-leton, extracellular matrix (ECM) remodeling, cell adhesion and the cell cycle. Additionally, KEGG classification indicated that these genes were important in angiogenesis, and in the p53 and transforming growth factor‑β signaling pathways. Notably, rno‑miRNA (miR)‑26b and rno‑miR‑101b were the two larger nodes of the 7 obstruction‑associated DEMs and interacted with 32 and 27 DEGs, respectively. On removal of obstruction, few DEMs were present; however, 370 genes exhibited the opposite expression trend. The majority of pathways enriched for the DEGs were identified and were associated with ECM‑receptor interaction and focal adhesion. In the DEM‑DEG regulatory network, miR‑495, miR‑494 and their target genes were significantly differentially expressed. The present study demonstrated that miRNAs and genes may be potential biomarkers of bladder remodeling induced by BOO, and additionally provided novel insights into the molecular mechanisms underlying this disorder.
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Affiliation(s)
- Liu Jian Duan
- Department of Urology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Qi Feng Cao
- Department of Urology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Ding Xu
- Department of Urology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Hai Long Liu
- Department of Urology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Jun Qi
- Department of Urology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
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18
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Petrov I, Suntsova M, Ilnitskaya E, Roumiantsev S, Sorokin M, Garazha A, Spirin P, Lebedev T, Gaifullin N, Larin S, Kovalchuk O, Konovalov D, Prassolov V, Roumiantsev A, Buzdin A. Gene expression and molecular pathway activation signatures of MYCN-amplified neuroblastomas. Oncotarget 2017; 8:83768-83780. [PMID: 29137381 PMCID: PMC5663553 DOI: 10.18632/oncotarget.19662] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/05/2017] [Indexed: 12/30/2022] Open
Abstract
Neuroblastoma is a pediatric cancer arising from sympathetic nervous system. Remarkable heterogeneity in outcomes is one of its widely known features. One of the traits strongly associated with the unfavorable subtype is the amplification of oncogene MYCN. Here, we performed cross-platform biomarker detection by comparing gene expression and pathway activation patterns from the two literature reports and from our experimental dataset, combining profiles for the 761 neuroblastoma patients with known MYCN amplification status. We identified 109 / 25 gene expression / pathway activation biomarkers strongly linked with the MYCN amplification. The marker genes/pathways are involved in the processes of purine nucleotide biosynthesis, ATP-binding, tetrahydrofolate metabolism, building mitochondrial matrix, biosynthesis of amino acids, tRNA aminoacylation and NADP-linked oxidation-reduction processes, as well as in the tyrosine phosphatase activity, p53 signaling, cell cycle progression and the G1/S and G2/M checkpoints. To connect molecular functions of the genes involved in MYCN-amplified phenotype, we built a new molecular pathway using known intracellular protein interaction networks. The activation of this pathway was highly selective in discriminating MYCN-amplified neuroblastomas in all three datasets. Our data also suggest that the phosphoinositide 3-kinase (PI3K) inhibitors may provide new opportunities for the treatment of the MYCN-amplified neuroblastoma subtype.
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Affiliation(s)
- Ivan Petrov
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,First Oncology Research and Advisory Center, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia.,V.A. Trapeznikov Institute of Control Sciences, Russian Academy of Sciences, Moscow, Russia
| | - Maria Suntsova
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Sergey Roumiantsev
- Department of Oncology, Hematology and Radiology, N.I.Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maxim Sorokin
- National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia.,Pathway Pharmaceuticals, Hong Kong, China
| | - Andrew Garazha
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Centre for Biogerontology and Regenerative Medicine, IC Skolkovo, Moscow, Russia
| | - Pavel Spirin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Mosow, Russia
| | - Timofey Lebedev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Mosow, Russia
| | - Nurshat Gaifullin
- Moscow State University, Faculty of Fundamental Medicine, Moscow, Russia
| | - Sergey Larin
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Canada
| | - Dmitry Konovalov
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Federal State Budgetary Educational Institution of Further Professional Education "Russian Medical Academy of Continuous Professional Education" of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Mosow, Russia
| | - Alexander Roumiantsev
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anton Buzdin
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
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19
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Litchfield K, Levy M, Orlando G, Loveday C, Law P, Migliorini G, Holroyd A, Broderick P, Karlsson R, Haugen TB, Kristiansen W, Nsengimana J, Fenwick K, Assiotis I, Kote-Jarai ZS, Dunning AM, Muir K, Peto J, Eeles R, Easton DF, Dudakia D, Orr N, Pashayan N, Bishop DT, Reid A, Huddart RA, Shipley J, Grotmol T, Wiklund F, Houlston RS, Turnbull C. Identification of 19 new risk loci and potential regulatory mechanisms influencing susceptibility to testicular germ cell tumor. Nat Genet 2017; 49:1133-1140. [PMID: 28604728 PMCID: PMC6016736 DOI: 10.1038/ng.3896] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 05/16/2017] [Indexed: 12/29/2022]
Abstract
Genome-wide association studies (GWAS) have transformed understanding of susceptibility to testicular germ cell tumors (TGCTs), but much of the heritability remains unexplained. Here we report a new GWAS, a meta-analysis with previous GWAS and a replication series, totaling 7,319 TGCT cases and 23,082 controls. We identify 19 new TGCT risk loci, roughly doubling the number of known TGCT risk loci to 44. By performing in situ Hi-C in TGCT cells, we provide evidence for a network of physical interactions among all 44 TGCT risk SNPs and candidate causal genes. Our findings implicate widespread disruption of developmental transcriptional regulators as a basis of TGCT susceptibility, consistent with failed primordial germ cell differentiation as an initiating step in oncogenesis. Defective microtubule assembly and dysregulation of KIT-MAPK signaling also feature as recurrently disrupted pathways. Our findings support a polygenic model of risk and provide insight into the biological basis of TGCT.
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Affiliation(s)
- Kevin Litchfield
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Max Levy
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Giulia Orlando
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Chey Loveday
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Philip Law
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Gabriele Migliorini
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Amy Holroyd
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Peter Broderick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Trine B Haugen
- Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Wenche Kristiansen
- Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Jérémie Nsengimana
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, Leeds, LS9 7TF, UK
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ioannis Assiotis
- Tumour Profiling Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - ZSofia Kote-Jarai
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, CV4 7AL, UK
- Institute of Population Health, University of Manchester, M1 3BB, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Rosalind Eeles
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, SM2 5NG, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Darshna Dudakia
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nick Orr
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, WC1E 6BT, UK
| | | | | | - D. Timothy Bishop
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, Leeds, LS9 7TF, UK
| | - Alison Reid
- Academic Radiotherapy Unit, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Robert A Huddart
- Academic Radiotherapy Unit, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Janet Shipley
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Tom Grotmol
- Department of Research, Cancer Registry of Norway, Oslo, 0369, Norway
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Richard S Houlston
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Clare Turnbull
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
- William Harvey Research Institute, Queen Mary University, London, EC1M 6BQ, UK
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20
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Wirsching A, Melloul E, Lezhnina K, Buzdin AA, Ogunshola OO, Borger P, Clavien PA, Lesurtel M. Temporary portal vein embolization is as efficient as permanent portal vein embolization in mice. Surgery 2017; 162:68-81. [DOI: 10.1016/j.surg.2017.01.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 10/19/2016] [Accepted: 01/06/2017] [Indexed: 01/30/2023]
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21
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Melin BS, Barnholtz-Sloan JS, Wrensch MR, Johansen C, Il'yasova D, Kinnersley B, Ostrom QT, Labreche K, Chen Y, Armstrong G, Liu Y, Eckel-Passow JE, Decker PA, Labussière M, Idbaih A, Hoang-Xuan K, Di Stefano AL, Mokhtari K, Delattre JY, Broderick P, Galan P, Gousias K, Schramm J, Schoemaker MJ, Fleming SJ, Herms S, Heilmann S, Nöthen MM, Wichmann HE, Schreiber S, Swerdlow A, Lathrop M, Simon M, Sanson M, Andersson U, Rajaraman P, Chanock S, Linet M, Wang Z, Yeager M, Wiencke JK, Hansen H, McCoy L, Rice T, Kosel ML, Sicotte H, Amos CI, Bernstein JL, Davis F, Lachance D, Lau C, Merrell RT, Shildkraut J, Ali-Osman F, Sadetzki S, Scheurer M, Shete S, Lai RK, Claus EB, Olson SH, Jenkins RB, Houlston RS, Bondy ML. Genome-wide association study of glioma subtypes identifies specific differences in genetic susceptibility to glioblastoma and non-glioblastoma tumors. Nat Genet 2017; 49:789-794. [PMID: 28346443 PMCID: PMC5558246 DOI: 10.1038/ng.3823] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 03/01/2017] [Indexed: 01/07/2023]
Abstract
Genome-wide association studies (GWAS) have transformed our understanding of glioma susceptibility, but individual studies have had limited power to identify risk loci. We performed a meta-analysis of existing GWAS and two new GWAS, which totaled 12,496 cases and 18,190 controls. We identified five new loci for glioblastoma (GBM) at 1p31.3 (rs12752552; P = 2.04 × 10-9, odds ratio (OR) = 1.22), 11q14.1 (rs11233250; P = 9.95 × 10-10, OR = 1.24), 16p13.3 (rs2562152; P = 1.93 × 10-8, OR = 1.21), 16q12.1 (rs10852606; P = 1.29 × 10-11, OR = 1.18) and 22q13.1 (rs2235573; P = 1.76 × 10-10, OR = 1.15), as well as eight loci for non-GBM tumors at 1q32.1 (rs4252707; P = 3.34 × 10-9, OR = 1.19), 1q44 (rs12076373; P = 2.63 × 10-10, OR = 1.23), 2q33.3 (rs7572263; P = 2.18 × 10-10, OR = 1.20), 3p14.1 (rs11706832; P = 7.66 × 10-9, OR = 1.15), 10q24.33 (rs11598018; P = 3.39 × 10-8, OR = 1.14), 11q21 (rs7107785; P = 3.87 × 10-10, OR = 1.16), 14q12 (rs10131032; P = 5.07 × 10-11, OR = 1.33) and 16p13.3 (rs3751667; P = 2.61 × 10-9, OR = 1.18). These data substantiate that genetic susceptibility to GBM and non-GBM tumors are highly distinct, which likely reflects different etiology.
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Affiliation(s)
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Margaret R Wrensch
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, California, USA
- Institute of Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Christoffer Johansen
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark and Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Dora Il'yasova
- Department of Epidemiology and Biostatistics, School of Public Health, Georgia State University, Atlanta, Georgia, USA
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
- Cancer Control and Prevention Program, Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Quinn T Ostrom
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Karim Labreche
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, Paris, France
| | - Yanwen Chen
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Georgina Armstrong
- Department of Medicine, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yanhong Liu
- Department of Medicine, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jeanette E Eckel-Passow
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Paul A Decker
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Marianne Labussière
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, Paris, France
| | - Ahmed Idbaih
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de neurologie 2-Mazarin, Paris, France
| | - Khe Hoang-Xuan
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de neurologie 2-Mazarin, Paris, France
| | - Anna-Luisa Di Stefano
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de neurologie 2-Mazarin, Paris, France
| | - Karima Mokhtari
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de neurologie 2-Mazarin, Paris, France
| | - Jean-Yves Delattre
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de neurologie 2-Mazarin, Paris, France
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Pilar Galan
- Université Paris 13 Sorbonne Paris Cité, INSERM U557, INRA U1125, CNAM, Paris, France
| | | | - Johannes Schramm
- Department of Neurosurgery, University of Bonn Medical Center, Bonn, Germany
| | - Minouk J Schoemaker
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Sarah J Fleming
- Centre for Epidemiology and Biostatistics, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - Stefan Herms
- Centre for Epidemiology and Biostatistics, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Heinz-Erich Wichmann
- Helmholtz Center Munich, Institute of Epidemiology I, Munich, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | - Stefan Schreiber
- 1st Medical Department, University Clinic Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, Institute of Cancer Research, London, UK
| | - Mark Lathrop
- Génome Québec, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Matthias Simon
- Department of Neurosurgery, University of Bonn Medical Center, Bonn, Germany
| | - Marc Sanson
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de neurologie 2-Mazarin, Paris, France
| | | | - Preetha Rajaraman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Martha Linet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - John K Wiencke
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, California, USA
- Institute of Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Helen Hansen
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Lucie McCoy
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Terri Rice
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Matthew L Kosel
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Hugues Sicotte
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Faith Davis
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Dan Lachance
- Department of Neurology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota, USA
| | - Ching Lau
- Department of Pediatrics, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ryan T Merrell
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Joellen Shildkraut
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
- Cancer Control and Prevention Program, Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Francis Ali-Osman
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Siegal Sadetzki
- Cancer and Radiation Epidemiology Unit, Gertner Institute, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michael Scheurer
- Department of Pediatrics, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Sanjay Shete
- Department of Biostatistics, University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA
| | - Rose K Lai
- Departments of Neurology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Elizabeth B Claus
- School of Public Health, Yale University, New Haven, Connecticut, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Melissa L Bondy
- Department of Medicine, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
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22
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Genetic and regulatory mechanism of susceptibility to high-hyperdiploid acute lymphoblastic leukaemia at 10p21.2. Nat Commun 2017; 8:14616. [PMID: 28256501 PMCID: PMC5337971 DOI: 10.1038/ncomms14616] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 01/17/2017] [Indexed: 01/28/2023] Open
Abstract
Despite high-hyperdiploid acute lymphoblastic leukaemia (HD-ALL) being the most common subgroup of paediatric ALL, its aetiology remains unknown. Genome-wide association studies have demonstrated association at 10q21.2. Here, we sought to determine how this region influences HD-ALL risk. We impute genotypes across the locus, finding the single nucleotide polymorphism rs7090445 highly associated with HD-ALL (P=1.54 × 10−38), and residing in a predicted enhancer element. We show this region physically interacts with the transcription start site of ARID5B, that alleles of rs7090445 have differential enhancer activity and influence RUNX3 binding. RUNX3 knock-down reduces ARID5B expression and rs7090445 enhancer activity. Individuals carrying the rs7090445-C risk allele also have reduced ARID5B expression. Finally, the rs7090445-C risk allele is preferentially retained in HD-ALL blasts consistent with inherited genetic variation contributing to arrest of normal lymphocyte development, facilitating leukaemic clonal expansion. These data provide evidence for a biological mechanism underlying hereditary risk of HD-ALL at 10q21.2. Risk for the paediatric cancer high-hyperdiploid acute lymphoblastic leukaemia (HD-ALL) has been associated with genetic variants at 10q21.2. Here, the authors characterize this region, establishing a single risk variant and showing its role in dysregulated expression of ARID5B.
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23
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Vijayakrishnan J, Kumar R, Henrion MYR, Moorman AV, Rachakonda PS, Hosen I, da Silva Filho MI, Holroyd A, Dobbins SE, Koehler R, Thomsen H, Irving JA, Allan JM, Lightfoot T, Roman E, Kinsey SE, Sheridan E, Thompson PD, Hoffmann P, Nöthen MM, Heilmann-Heimbach S, Jöckel KH, Greaves M, Harrison CJ, Bartram CR, Schrappe M, Stanulla M, Hemminki K, Houlston RS. A genome-wide association study identifies risk loci for childhood acute lymphoblastic leukemia at 10q26.13 and 12q23.1. Leukemia 2017; 31:573-579. [PMID: 27694927 PMCID: PMC5336191 DOI: 10.1038/leu.2016.271] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/26/2016] [Accepted: 09/06/2016] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies (GWASs) have shown that common genetic variation contributes to the heritable risk of childhood acute lymphoblastic leukemia (ALL). To identify new susceptibility loci for the largest subtype of ALL, B-cell precursor ALL (BCP-ALL), we conducted a meta-analysis of two GWASs with imputation using 1000 Genomes and UK10K Project data as reference (totaling 1658 cases and 7224 controls). After genotyping an additional 2525 cases and 3575 controls, we identify new susceptibility loci for BCP-ALL mapping to 10q26.13 (rs35837782, LHPP, P=1.38 × 10-11) and 12q23.1 (rs4762284, ELK3, P=8.41 × 10-9). We also provide confirmatory evidence for the existence of independent risk loci at 9p21.3, but show that the association marked by rs77728904 can be accounted for by linkage disequilibrium with the rare high-impact CDKN2A p.Ala148Thr variant rs3731249. Our data provide further insights into genetic susceptibility to ALL and its biology.
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Affiliation(s)
- J Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - R Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - M Y R Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - A V Moorman
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - P S Rachakonda
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - I Hosen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - M I da Silva Filho
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - A Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - S E Dobbins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - R Koehler
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - H Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - J A Irving
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - J M Allan
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - T Lightfoot
- Department of Health Sciences, Epidemiology and Cancer Statistics Group, University of York, York, UK
| | - E Roman
- Department of Health Sciences, Epidemiology and Cancer Statistics Group, University of York, York, UK
| | - S E Kinsey
- Department of Paediatric and Adolescent Haematology and Oncology, Leeds General Infirmary, Leeds, UK
| | - E Sheridan
- Medical Genetics Research Group, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - P D Thompson
- Paediatric and Familial Cancer Research Group, Institute of Cancer Sciences, University of Manchester, St Mary's Hospital, Manchester, UK
| | - P Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Biomedicine, Human Genomics Research Group, University Hospital Basel, Basel, Switzerland
| | - M M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - K H Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - M Greaves
- Haemato-Oncology Research Unit, Division of Molecular Pathology, Institute of Cancer Research, Sutton, UK
| | - C J Harrison
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - C R Bartram
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - M Schrappe
- General Paediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - M Stanulla
- Department of Paediatric Haematology and Oncology, Hannover Medical School, Hannover, Germany
| | - K Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - R S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
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24
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Law PJ, Berndt SI, Speedy HE, Camp NJ, Sava GP, Skibola CF, Holroyd A, Joseph V, Sunter NJ, Nieters A, Bea S, Monnereau A, Martin-Garcia D, Goldin LR, Clot G, Teras LR, Quintela I, Birmann BM, Jayne S, Cozen W, Majid A, Smedby KE, Lan Q, Dearden C, Brooks-Wilson AR, Hall AG, Purdue MP, Mainou-Fowler T, Vajdic CM, Jackson GH, Cocco P, Marr H, Zhang Y, Zheng T, Giles GG, Lawrence C, Call TG, Liebow M, Melbye M, Glimelius B, Mansouri L, Glenn M, Curtin K, Diver WR, Link BK, Conde L, Bracci PM, Holly EA, Jackson RD, Tinker LF, Benavente Y, Boffetta P, Brennan P, Maynadie M, McKay J, Albanes D, Weinstein S, Wang Z, Caporaso NE, Morton LM, Severson RK, Riboli E, Vineis P, Vermeulen RCH, Southey MC, Milne RL, Clavel J, Topka S, Spinelli JJ, Kraft P, Ennas MG, Summerfield G, Ferri GM, Harris RJ, Miligi L, Pettitt AR, North KE, Allsup DJ, Fraumeni JF, Bailey JR, Offit K, Pratt G, Hjalgrim H, Pepper C, Chanock SJ, Fegan C, Rosenquist R, de Sanjose S, Carracedo A, Dyer MJS, Catovsky D, Campo E, Cerhan JR, Allan JM, Rothman N, Houlston R, Slager S. Genome-wide association analysis implicates dysregulation of immunity genes in chronic lymphocytic leukaemia. Nat Commun 2017; 8:14175. [PMID: 28165464 PMCID: PMC5303820 DOI: 10.1038/ncomms14175] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/06/2016] [Indexed: 02/07/2023] Open
Abstract
Several chronic lymphocytic leukaemia (CLL) susceptibility loci have been reported; however, much of the heritable risk remains unidentified. Here we perform a meta-analysis of six genome-wide association studies, imputed using a merged reference panel of 1,000 Genomes and UK10K data, totalling 6,200 cases and 17,598 controls after replication. We identify nine risk loci at 1p36.11 (rs34676223, P=5.04 × 10-13), 1q42.13 (rs41271473, P=1.06 × 10-10), 4q24 (rs71597109, P=1.37 × 10-10), 4q35.1 (rs57214277, P=3.69 × 10-8), 6p21.31 (rs3800461, P=1.97 × 10-8), 11q23.2 (rs61904987, P=2.64 × 10-11), 18q21.1 (rs1036935, P=3.27 × 10-8), 19p13.3 (rs7254272, P=4.67 × 10-8) and 22q13.33 (rs140522, P=2.70 × 10-9). These new and established risk loci map to areas of active chromatin and show an over-representation of transcription factor binding for the key determinants of B-cell development and immune response.
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Affiliation(s)
- Philip J. Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Helen E. Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Nicola J. Camp
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Georgina P. Sava
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Christine F. Skibola
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35233, USA
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Vijai Joseph
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Nicola J. Sunter
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alexandra Nieters
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Baden-Württemberg 79108, Germany
| | - Silvia Bea
- Institut d'Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Hospital Clínic, Barcelona 08036, Spain
| | - Alain Monnereau
- Registre des hémopathies malignes de la Gironde, Institut Bergonié, Inserm U1219 EPICENE, 33076 Bordeaux, France
- Epidemiology of Childhood and Adolescent Cancers Group, Inserm, Center of Research in Epidemiology and Statistics Sorbonne Paris Cité, Paris, F-94807, France
- Université Paris Descartes, Paris 75270, France
| | - David Martin-Garcia
- Institut d'Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Hospital Clínic, Barcelona 08036, Spain
| | - Lynn R. Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Hospital Clínic, Barcelona 08036, Spain
| | - Lauren R. Teras
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Inés Quintela
- Grupo de Medicina Xenomica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado (CeGen-PRB2-ISCIII), CIBERER, 15782 Santiago de Compostela, Spain
| | - Brenda M. Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sandrine Jayne
- Ernest and Helen Scott Haematological Research Institute, University of Leicester, Leicester LE2 7LX, UK
| | - Wendy Cozen
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
- Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Aneela Majid
- Ernest and Helen Scott Haematological Research Institute, University of Leicester, Leicester LE2 7LX, UK
| | - Karin E. Smedby
- Unit of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Hematology Center, Karolinsak University Hospital, Stockholm 17176, Sweden
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Claire Dearden
- The Royal Marsden NHS Foundation Trust, London SM2 5PT, UK
| | - Angela R. Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada V5Z1L3
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Andrew G. Hall
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Mark P. Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Tryfonia Mainou-Fowler
- Haematological Sciences, Medical School, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Claire M. Vajdic
- Centre for Big Data Research in Health, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Graham H. Jackson
- Department of Haematology, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - Pierluigi Cocco
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Helen Marr
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut 06520, USA
| | - Tongzhang Zheng
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut 06520, USA
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | | | - Timothy G. Call
- Division of Hematology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Mark Liebow
- Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Mads Melbye
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, 2300 Copenhagen, Denmark
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - Martha Glenn
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Karen Curtin
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Brian K. Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Lucia Conde
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35233, USA
| | - Paige M. Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94118, USA
| | - Elizabeth A. Holly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94118, USA
| | - Rebecca D. Jackson
- Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, Ohio 43210, USA
| | - Lesley F. Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98117, USA
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona 08036, Spain
| | - Paolo Boffetta
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon 69372, France
| | - Marc Maynadie
- Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon 21070, France
| | - James McKay
- International Agency for Research on Cancer, Lyon 69372, France
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Zhaoming Wang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Lindsay M. Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Richard K. Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, Michigan 48201, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London W2 1PG, UK
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
- Human Genetics Foundation, 10126 Turin, Italy
| | - Roel C. H. Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3508 TD, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jacqueline Clavel
- Epidemiology of Childhood and Adolescent Cancers Group, Inserm, Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), Paris F-94807, France
- Université Paris Descartes, 75270 Paris, France
| | - Sabine Topka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - John J. Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada V5Z1L3
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada V6T1Z3
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Maria Grazia Ennas
- Department of Biomedical Science, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | | | - Giovanni M. Ferri
- Interdisciplinary Department of Medicine, University of Bari, Bari 70124, Italy
| | - Robert J. Harris
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Lucia Miligi
- Environmental and Occupational Epidemiology Unit, Cancer Prevention and Research Institute (ISPO), Florence 50139, Italy
| | - Andrew R. Pettitt
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Kari E. North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - David J. Allsup
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, Cottingham HU16 5JQ, UK
| | - Joseph F. Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - James R. Bailey
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, Cottingham HU16 5JQ, UK
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Guy Pratt
- Department of Haematology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, 2300 Copenhagen, Denmark
| | - Chris Pepper
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Chris Fegan
- Cardiff and Vale National Health Service Trust, Heath Park, Cardiff CF14 4XW, UK
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - Silvia de Sanjose
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- International Agency for Research on Cancer, Lyon 69372, France
| | - Angel Carracedo
- Grupo de Medicina Xenomica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado (CeGen-PRB2-ISCIII), CIBERER, 15782 Santiago de Compostela, Spain
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, KSA
| | - Martin J. S. Dyer
- Ernest and Helen Scott Haematological Research Institute, University of Leicester, Leicester LE2 7LX, UK
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Hospital Clínic, Barcelona 08036, Spain
- Unitat de Hematología, Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona 08036, Spain
| | - James R. Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - James M. Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Nathanial Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Susan Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
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25
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Law PJ, Sud A, Mitchell JS, Henrion M, Orlando G, Lenive O, Broderick P, Speedy HE, Johnson DC, Kaiser M, Weinhold N, Cooke R, Sunter NJ, Jackson GH, Summerfield G, Harris RJ, Pettitt AR, Allsup DJ, Carmichael J, Bailey JR, Pratt G, Rahman T, Pepper C, Fegan C, von Strandmann EP, Engert A, Försti A, Chen B, Filho MIDS, Thomsen H, Hoffmann P, Noethen MM, Eisele L, Jöckel KH, Allan JM, Swerdlow AJ, Goldschmidt H, Catovsky D, Morgan GJ, Hemminki K, Houlston RS. Genome-wide association analysis of chronic lymphocytic leukaemia, Hodgkin lymphoma and multiple myeloma identifies pleiotropic risk loci. Sci Rep 2017; 7:41071. [PMID: 28112199 PMCID: PMC5253627 DOI: 10.1038/srep41071] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/14/2016] [Indexed: 02/08/2023] Open
Abstract
B-cell malignancies (BCM) originate from the same cell of origin, but at different maturation stages and have distinct clinical phenotypes. Although genetic risk variants for individual BCMs have been identified, an agnostic, genome-wide search for shared genetic susceptibility has not been performed. We explored genome-wide association studies of chronic lymphocytic leukaemia (CLL, N = 1,842), Hodgkin lymphoma (HL, N = 1,465) and multiple myeloma (MM, N = 3,790). We identified a novel pleiotropic risk locus at 3q22.2 (NCK1, rs11715604, P = 1.60 × 10-9) with opposing effects between CLL (P = 1.97 × 10-8) and HL (P = 3.31 × 10-3). Eight established non-HLA risk loci showed pleiotropic associations. Within the HLA region, Ser37 + Phe37 in HLA-DRB1 (P = 1.84 × 10-12) was associated with increased CLL and HL risk (P = 4.68 × 10-12), and reduced MM risk (P = 1.12 × 10-2), and Gly70 in HLA-DQB1 (P = 3.15 × 10-10) showed opposing effects between CLL (P = 3.52 × 10-3) and HL (P = 3.41 × 10-9). By integrating eQTL, Hi-C and ChIP-seq data, we show that the pleiotropic risk loci are enriched for B-cell regulatory elements, as well as an over-representation of binding of key B-cell transcription factors. These data identify shared biological pathways influencing the development of CLL, HL and MM. The identification of these risk loci furthers our understanding of the aetiological basis of BCMs.
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Affiliation(s)
- Philip J. Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Jonathan S. Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Oleg Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Helen E. Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - David C. Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Nicola J. Sunter
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Graham H. Jackson
- Department of Haematology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Geoffrey Summerfield
- Department of Haematology, Queen Elizabeth Hospital, Gateshead, Newcastle upon Tyne, UK
| | - Robert J. Harris
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Andrew R. Pettitt
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - David J. Allsup
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - Jonathan Carmichael
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - James R. Bailey
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - Guy Pratt
- Department of Haematology, Birmingham Heartlands Hospital, Birmingham, UK
| | - Thahira Rahman
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Chris Pepper
- Department of Haematology, School of Medicine, Cardiff University, Cardiff, UK
| | - Chris Fegan
- Cardiff and Vale National Health Service Trust, Heath Park, Cardiff, UK
| | | | - Andreas Engert
- Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Bowang Chen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | | | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, Switzerland
| | - Markus M. Noethen
- Institute of Human Genetics, University of Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Germany
| | | | | | - James M. Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Anthony J. Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center of Tumor Diseases, Heidelberg, Germany
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Gareth J. Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
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26
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Petrov I, Suntsova M, Mutorova O, Sorokin M, Garazha A, Ilnitskaya E, Spirin P, Larin S, Zhavoronkov A, Kovalchuk O, Prassolov V, Roumiantsev A, Buzdin A. Molecular pathway activation features of pediatric acute myeloid leukemia (AML) and acute lymphoblast leukemia (ALL) cells. Aging (Albany NY) 2016; 8:2936-2947. [PMID: 27870639 PMCID: PMC5182073 DOI: 10.18632/aging.101102] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 11/04/2016] [Indexed: 12/11/2022]
Abstract
Acute lymphoblast leukemia (ALL) is characterized by overproduction of immature white blood cells in the bone marrow. ALL is most common in the childhood and has high (>80%) cure rate. In contrast, acute myeloid leukemia (AML) has far greater mortality rate than the ALL and is most commonly affecting older adults. However, AML is a leading cause of childhood cancer mortality. In this study, we compare gene expression and molecular pathway activation patterns in three normal blood, seven pediatric ALL and seven pediatric AML bone marrow samples. We identified 172/94 and 148/31 characteristic gene expression/pathway activation signatures, clearly distinguishing pediatric ALL and AML cells, respectively, from the normal blood. The pediatric AML and ALL cells differed by 139/34 gene expression/pathway activation biomarkers. For the adult 30 AML and 17 normal blood samples, we found 132/33 gene expression/pathway AML-specific features, of which only 7/2 were common for the adult and pediatric AML and, therefore, age-independent. At the pathway level, we found more differences than similarities between the adult and pediatric forms. These findings suggest that the adult and pediatric AMLs may require different treatment strategies.
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MESH Headings
- Adolescent
- Adult
- Age Factors
- Biomarkers, Tumor
- Bone Marrow
- Case-Control Studies
- Child
- Child, Preschool
- Female
- Gene Expression
- Gene Expression Profiling
- Humans
- Infant
- Leukemia, Myeloid, Acute/blood
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Male
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/blood
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/mortality
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
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Affiliation(s)
- Ivan Petrov
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
- First Oncology Research and Advisory Center, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, 141700, Russia
| | - Maria Suntsova
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Olga Mutorova
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
- Morozov Pediatric Clinical Hospital, Moscow, 101000, Russia
| | - Maxim Sorokin
- National Research Centre “Kurchatov Institute”, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, 123182, Russia
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR
| | - Andrew Garazha
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, 141700, Russia
| | - Elena Ilnitskaya
- First Oncology Research and Advisory Center, Moscow, 117997, Russia
| | - Pavel Spirin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Mosow, Russia,119991
| | - Sergey Larin
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
| | - Alex Zhavoronkov
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
- First Oncology Research and Advisory Center, Moscow, 117997, Russia
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Mosow, Russia,119991
| | - Alexander Roumiantsev
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
| | - Anton Buzdin
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- National Research Centre “Kurchatov Institute”, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, 123182, Russia
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27
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Rodina A, Wang T, Yan P, Gomes ED, Dunphy MPS, Pillarsetty N, Koren J, Gerecitano JF, Taldone T, Zong H, Caldas-Lopes E, Alpaugh M, Corben A, Riolo M, Beattie B, Pressl C, Peter RI, Xu C, Trondl R, Patel HJ, Shimizu F, Bolaender A, Yang C, Panchal P, Farooq MF, Kishinevsky S, Modi S, Lin O, Chu F, Patil S, Erdjument-Bromage H, Zanzonico P, Hudis C, Studer L, Roboz GJ, Cesarman E, Cerchietti L, Levine R, Melnick A, Larson SM, Lewis JS, Guzman ML, Chiosis G. The epichaperome is an integrated chaperome network that facilitates tumour survival. Nature 2016; 538:397-401. [PMID: 27706135 DOI: 10.1038/nature19807] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 09/02/2016] [Indexed: 01/01/2023]
Abstract
Transient, multi-protein complexes are important facilitators of cellular functions. This includes the chaperome, an abundant protein family comprising chaperones, co-chaperones, adaptors, and folding enzymes-dynamic complexes of which regulate cellular homeostasis together with the protein degradation machinery. Numerous studies have addressed the role of chaperome members in isolation, yet little is known about their relationships regarding how they interact and function together in malignancy. As function is probably highly dependent on endogenous conditions found in native tumours, chaperomes have resisted investigation, mainly due to the limitations of methods needed to disrupt or engineer the cellular environment to facilitate analysis. Such limitations have led to a bottleneck in our understanding of chaperome-related disease biology and in the development of chaperome-targeted cancer treatment. Here we examined the chaperome complexes in a large set of tumour specimens. The methods used maintained the endogenous native state of tumours and we exploited this to investigate the molecular characteristics and composition of the chaperome in cancer, the molecular factors that drive chaperome networks to crosstalk in tumours, the distinguishing factors of the chaperome in tumours sensitive to pharmacologic inhibition, and the characteristics of tumours that may benefit from chaperome therapy. We find that under conditions of stress, such as malignant transformation fuelled by MYC, the chaperome becomes biochemically 'rewired' to form a network of stable, survival-facilitating, high-molecular-weight complexes. The chaperones heat shock protein 90 (HSP90) and heat shock cognate protein 70 (HSC70) are nucleating sites for these physically and functionally integrated complexes. The results indicate that these tightly integrated chaperome units, here termed the epichaperome, can function as a network to enhance cellular survival, irrespective of tissue of origin or genetic background. The epichaperome, present in over half of all cancers tested, has implications for diagnostics and also provides potential vulnerability as a target for drug intervention.
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Affiliation(s)
- Anna Rodina
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Tai Wang
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Pengrong Yan
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Erica DaGama Gomes
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Mark P S Dunphy
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | - John Koren
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - John F Gerecitano
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tony Taldone
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Hongliang Zong
- Haematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Eloisi Caldas-Lopes
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Mary Alpaugh
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Adriana Corben
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Matthew Riolo
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Brad Beattie
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christina Pressl
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Radu I Peter
- Department of Mathematics, Technical University of Cluj-Napoca, Cluj-Napoca 400114, Romania
| | - Chao Xu
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Robert Trondl
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Hardik J Patel
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Fumiko Shimizu
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Alexander Bolaender
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Chenghua Yang
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Palak Panchal
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Mohammad F Farooq
- Molecular, Cellular &Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Sarah Kishinevsky
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA
| | - Shanu Modi
- Breast Cancer Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Oscar Lin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Feixia Chu
- Molecular, Cellular &Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Sujata Patil
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Hediye Erdjument-Bromage
- Microchemistry and Proteomics Core, Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Pat Zanzonico
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Clifford Hudis
- Breast Cancer Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Lorenz Studer
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Gail J Roboz
- Haematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Ethel Cesarman
- Haematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Leandro Cerchietti
- Haematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Ari Melnick
- Haematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Steven M Larson
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jason S Lewis
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Monica L Guzman
- Haematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Gabriela Chiosis
- Program in Chemical Biology, Sloan Kettering Institute, New York, New York 10065, USA.,Breast Cancer Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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28
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Kandaswamy R, Sava GP, Speedy HE, Beà S, Martín-Subero JI, Studd JB, Migliorini G, Law PJ, Puente XS, Martín-García D, Salaverria I, Gutiérrez-Abril J, López-Otín C, Catovsky D, Allan JM, Campo E, Houlston RS. Genetic Predisposition to Chronic Lymphocytic Leukemia Is Mediated by a BMF Super-Enhancer Polymorphism. Cell Rep 2016; 16:2061-2067. [PMID: 27524613 PMCID: PMC4999417 DOI: 10.1016/j.celrep.2016.07.053] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/14/2016] [Accepted: 07/20/2016] [Indexed: 12/26/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is an adult B cell malignancy. Genome-wide association studies show that variation at 15q15.1 influences CLL risk. We deciphered the causal variant at 15q15.1 and the mechanism by which it influences tumorigenesis. We imputed all possible genotypes across the locus and then mapped highly associated SNPs to areas of chromatin accessibility, evolutionary conservation, and transcription factor binding. SNP rs539846 C>A, the most highly associated variant (p = 1.42 × 10(-13), odds ratio = 1.35), localizes to a super-enhancer defined by extensive histone H3 lysine 27 acetylation in intron 3 of B cell lymphoma 2 (BCL2)-modifying factor (BMF). The rs539846-A risk allele alters a conserved RELA-binding motif, disrupts RELA binding, and is associated with decreased BMF expression in CLL. These findings are consistent with rs539846 influencing CLL susceptibility through differential RELA binding, with direct modulation of BMF expression impacting on anti-apoptotic BCL2, a hallmark of oncogenic dependency in CLL.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Alleles
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Binding Sites
- Cell Line, Tumor
- Chromatin/chemistry
- Chromatin/metabolism
- Chromosome Mapping
- Chromosomes, Human, Pair 15
- Enhancer Elements, Genetic
- Genetic Loci
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Histones/genetics
- Histones/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Odds Ratio
- Polymorphism, Single Nucleotide
- Protein Binding
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Risk
- Transcription Factor RelA/genetics
- Transcription Factor RelA/metabolism
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Affiliation(s)
- Radhika Kandaswamy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Georgina P Sava
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Helen E Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Departament d'Anatomía Patològica, Microbiología i Farmacología, Universitat de Barcelona, 08036 Barcelona, Spain
| | - James B Studd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Gabriele Migliorini
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Xose S Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - David Martín-García
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Itziar Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Jesús Gutiérrez-Abril
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, UK
| | - James M Allan
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Elías Campo
- Unitat de Hematología, Hospital Clínic, IDIBAPS, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK; Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, UK.
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29
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Mitchell JS, Li N, Weinhold N, Försti A, Ali M, van Duin M, Thorleifsson G, Johnson DC, Chen B, Halvarsson BM, Gudbjartsson DF, Kuiper R, Stephens OW, Bertsch U, Broderick P, Campo C, Einsele H, Gregory WA, Gullberg U, Henrion M, Hillengass J, Hoffmann P, Jackson GH, Johnsson E, Jöud M, Kristinsson SY, Lenhoff S, Lenive O, Mellqvist UH, Migliorini G, Nahi H, Nelander S, Nickel J, Nöthen MM, Rafnar T, Ross FM, da Silva Filho MI, Swaminathan B, Thomsen H, Turesson I, Vangsted A, Vogel U, Waage A, Walker BA, Wihlborg AK, Broyl A, Davies FE, Thorsteinsdottir U, Langer C, Hansson M, Kaiser M, Sonneveld P, Stefansson K, Morgan GJ, Goldschmidt H, Hemminki K, Nilsson B, Houlston RS. Genome-wide association study identifies multiple susceptibility loci for multiple myeloma. Nat Commun 2016; 7:12050. [PMID: 27363682 PMCID: PMC4932178 DOI: 10.1038/ncomms12050] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/24/2016] [Indexed: 02/08/2023] Open
Abstract
Multiple myeloma (MM) is a plasma cell malignancy with a significant heritable basis. Genome-wide association studies have transformed our understanding of MM predisposition, but individual studies have had limited power to discover risk loci. Here we perform a meta-analysis of these GWAS, add a new GWAS and perform replication analyses resulting in 9,866 cases and 239,188 controls. We confirm all nine known risk loci and discover eight new loci at 6p22.3 (rs34229995, P=1.31 × 10(-8)), 6q21 (rs9372120, P=9.09 × 10(-15)), 7q36.1 (rs7781265, P=9.71 × 10(-9)), 8q24.21 (rs1948915, P=4.20 × 10(-11)), 9p21.3 (rs2811710, P=1.72 × 10(-13)), 10p12.1 (rs2790457, P=1.77 × 10(-8)), 16q23.1 (rs7193541, P=5.00 × 10(-12)) and 20q13.13 (rs6066835, P=1.36 × 10(-13)), which localize in or near to JARID2, ATG5, SMARCD3, CCAT1, CDKN2A, WAC, RFWD3 and PREX1. These findings provide additional support for a polygenic model of MM and insight into the biological basis of tumour development.
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Affiliation(s)
- Jonathan S. Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Ni Li
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
- Department of Internal Medicine V, University of Heidelberg, 69117 Heidelberg, Germany
| | - Asta Försti
- German Cancer Research Center, 69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02 Malmo, Sweden
| | - Mina Ali
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Mark van Duin
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA Rotterdam, The Netherlands
| | | | - David C. Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, Surrey SM2 5NG, UK
| | - Bowang Chen
- German Cancer Research Center, 69120 Heidelberg, Germany
| | - Britt-Marie Halvarsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Daniel F. Gudbjartsson
- deCODE Genetics, Sturlugata 8, IS-101 Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, IS-101 Reykjavik, Iceland
| | - Rowan Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA Rotterdam, The Netherlands
| | - Owen W. Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Uta Bertsch
- Department of Internal Medicine V, University of Heidelberg, 69117 Heidelberg, Germany
- National Centre of Tumor Diseases, 69120 Heidelberg, Germany
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Chiara Campo
- German Cancer Research Center, 69120 Heidelberg, Germany
| | | | - Walter A. Gregory
- Clinical Trials Research Unit, University of Leeds, Leeds LS2 9PH, UK
| | - Urban Gullberg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Jens Hillengass
- Department of Internal Medicine V, University of Heidelberg, 69117 Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127 Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003 Basel, Switzerland
| | | | - Ellinor Johnsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Magnus Jöud
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
- Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office of Medical Services, SE-221 85 Lund, Sweden
| | - Sigurður Y. Kristinsson
- Department of Hematology, Landspitali, National University Hospital of Iceland, IS-101 Reykjavik, Iceland
| | - Stig Lenhoff
- Hematology Clinic, Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Oleg Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Ulf-Henrik Mellqvist
- Section of Hematology, Sahlgrenska University Hospital, Gothenburg 413 45, Sweden
| | - Gabriele Migliorini
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Hareth Nahi
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Sven Nelander
- Rudbeck Laboratory, Department of Immunology, Pathology and Genetics, Uppsala University, SE-751 05 Uppsala, Sweden
| | - Jolanta Nickel
- Department of Internal Medicine V, University of Heidelberg, 69117 Heidelberg, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, D-53127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, D-53127 Bonn, Germany
| | - Thorunn Rafnar
- deCODE Genetics, Sturlugata 8, IS-101 Reykjavik, Iceland
| | - Fiona M. Ross
- Wessex Regional Genetics Laboratory, University of Southampton, Salisbury SP2 8BJ, UK
| | | | - Bhairavi Swaminathan
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Hauke Thomsen
- German Cancer Research Center, 69120 Heidelberg, Germany
| | - Ingemar Turesson
- Hematology Clinic, Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Annette Vangsted
- Department of Haematology, University Hospital of Copenhagen at Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, DK-2100 Copenhagen, Denmark
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Box 8905, N-7491 Trondheim, Norway
| | - Brian A. Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Anna-Karin Wihlborg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
| | - Annemiek Broyl
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA Rotterdam, The Netherlands
| | - Faith E. Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Sturlugata 8, IS-101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101 Reykjavik, Iceland
| | - Christian Langer
- Department of Internal Medicine III, University of Ulm, D-89081 Ulm, Germany
| | - Markus Hansson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
- Hematology Clinic, Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, Surrey SM2 5NG, UK
| | - Pieter Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA Rotterdam, The Netherlands
| | | | - Gareth J. Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117 Heidelberg, Germany
- National Centre of Tumor Diseases, 69120 Heidelberg, Germany
| | - Kari Hemminki
- German Cancer Research Center, 69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02 Malmo, Sweden
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund, Sweden
- Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office of Medical Services, SE-221 85 Lund, Sweden
- Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
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30
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Orlando G, Law PJ, Palin K, Tuupanen S, Gylfe A, Hänninen UA, Cajuso T, Tanskanen T, Kondelin J, Kaasinen E, Sarin AP, Kaprio J, Eriksson JG, Rissanen H, Knekt P, Pukkala E, Jousilahti P, Salomaa V, Ripatti S, Palotie A, Järvinen H, Renkonen-Sinisalo L, Lepistö A, Böhm J, Mecklin JP, Al-Tassan NA, Palles C, Martin L, Barclay E, Tenesa A, Farrington S, Timofeeva MN, Meyer BF, Wakil SM, Campbell H, Smith CG, Idziaszczyk S, Maughan TS, Kaplan R, Kerr R, Kerr D, Buchanan DD, Win AK, Hopper J, Jenkins M, Lindor NM, Newcomb PA, Gallinger S, Conti D, Schumacher F, Casey G, Taipale J, Cheadle JP, Dunlop MG, Tomlinson IP, Aaltonen LA, Houlston RS. Variation at 2q35 (PNKD and TMBIM1) influences colorectal cancer risk and identifies a pleiotropic effect with inflammatory bowel disease. Hum Mol Genet 2016; 25:2349-2359. [PMID: 27005424 PMCID: PMC5081051 DOI: 10.1093/hmg/ddw087] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/05/2016] [Accepted: 03/14/2016] [Indexed: 01/07/2023] Open
Abstract
To identify new risk loci for colorectal cancer (CRC), we conducted a meta-analysis of seven genome-wide association studies (GWAS) with independent replication, totalling 13 656 CRC cases and 21 667 controls of European ancestry. The combined analysis identified a new risk association for CRC at 2q35 marked by rs992157 (P = 3.15 × 10-8, odds ratio = 1.10, 95% confidence interval = 1.06-1.13), which is intronic to PNKD (paroxysmal non-kinesigenic dyskinesia) and TMBIM1 (transmembrane BAX inhibitor motif containing 1). Intriguingly this susceptibility single-nucleotide polymorphism (SNP) is in strong linkage disequilibrium (r2 = 0.90, D' = 0.96) with the previously discovered GWAS SNP rs2382817 for inflammatory bowel disease (IBD). Following on from this observation we examined for pleiotropy, or shared genetic susceptibility, between CRC and the 200 established IBD risk loci, identifying an additional 11 significant associations (false discovery rate [FDR]) < 0.05). Our findings provide further insight into the biological basis of inherited genetic susceptibility to CRC, and identify risk factors that may influence the development of both CRC and IBD.
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Affiliation(s)
- Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Kimmo Palin
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Sari Tuupanen
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Alexandra Gylfe
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Ulrika A Hänninen
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Tatiana Cajuso
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Tomas Tanskanen
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Johanna Kondelin
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Eevi Kaasinen
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Johan G Eriksson
- Folkhälsan Research Centre, Helsinki 00250, Finland Unit of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Harri Rissanen
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Paul Knekt
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki 00130, Finland School of Health Sciences, University of Tampere, Tampere 33014, Finland
| | - Pekka Jousilahti
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Heikki Järvinen
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki 00029, Finland
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki 00029, Finland
| | - Anna Lepistö
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki 00029, Finland
| | - Jan Böhm
- Department of Pathology, Central Finland Central Hospital, Jyväskylä 40620, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, University of Eastern Finland, Jyväskylä 40620, Finland
| | - Nada A Al-Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford OX3 7BN, UK
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford OX3 7BN, UK
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford OX3 7BN, UK
| | - Albert Tenesa
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK The Roslin Institute, University of Edinburgh, Easter Bush, Roslin EH25 9RG, UK
| | - Susan Farrington
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Maria N Timofeeva
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia
| | - Salma M Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Christopher G Smith
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Shelley Idziaszczyk
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Timothy S Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Richard Kaplan
- MRC Clinical Trials Unit, Aviation House, London WC2B 6NH, UK
| | - Rachel Kerr
- Department of Oncology, Oxford Cancer Centre, Churchill Hospital
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 7LE, UK
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Vic. 3010, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Vic. 3010, Australia
| | - John Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Vic. 3010, Australia
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Vic. 3010, Australia
| | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Polly A Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Steve Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - David Conti
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Fred Schumacher
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jussi Taipale
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum Department of Biosciences and Nutrition, SciLife Center, Karolinska Institute, Stockholm, SE 141 83, Sweden
| | - Jeremy P Cheadle
- Genome-Scale Biology Research Program, Research Programs Unit Genome-Scale Biology Research Program, Research Programs Unit
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Ian P Tomlinson
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford OX3 7BN, UK
| | - Lauri A Aaltonen
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
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31
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Harmston N, Ing-Simmons E, Perry M, Barešić A, Lenhard B. GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data. BMC Genomics 2015; 16:963. [PMID: 26576536 PMCID: PMC4650858 DOI: 10.1186/s12864-015-2140-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/23/2015] [Indexed: 12/31/2022] Open
Abstract
Background Precise quantitative and spatiotemporal control of gene expression is necessary to ensure proper cellular differentiation and the maintenance of homeostasis. The relationship between gene expression and the spatial organisation of chromatin is highly complex, interdependent and not completely understood. The development of experimental techniques to interrogate both the higher-order structure of chromatin and the interactions between regulatory elements has recently lead to important insights on how gene expression is controlled. The ability to gain these and future insights is critically dependent on computational tools for the analysis and visualisation of data produced by these techniques. Results and conclusion We have developed GenomicInteractions, a freely available R/Bioconductor package designed for processing, analysis and visualisation of data generated from various types of chromosome conformation capture experiments. The package allows the easy annotation and summarisation of large genome-wide datasets at both the level of individual interactions and sets of genomic features, and provides several different methods for interrogating and visualising this type of data. We demonstrate this package’s utility by showing example analyses performed on interaction datasets generated using Hi-C and ChIA-PET. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2140-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nathan Harmston
- Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK. .,Program in Cardiovascular and Metabolic Disease, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Elizabeth Ing-Simmons
- Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
| | - Malcolm Perry
- Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
| | - Anja Barešić
- Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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32
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Litchfield K, Holroyd A, Lloyd A, Broderick P, Nsengimana J, Eeles R, Easton DF, Dudakia D, Bishop DT, Reid A, Huddart RA, Grotmol T, Wiklund F, Shipley J, Houlston RS, Turnbull C. Identification of four new susceptibility loci for testicular germ cell tumour. Nat Commun 2015; 6:8690. [PMID: 26503584 PMCID: PMC4846317 DOI: 10.1038/ncomms9690] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/17/2015] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple risk loci for testicular germ cell tumour (TGCT), revealing a polygenic model of disease susceptibility strongly influenced by common variation. To identify additional single-nucleotide polymorphisms (SNPs) associated with TGCT, we conducted a multistage GWAS with a combined data set of >25,000 individuals (6,059 cases and 19,094 controls). We identified new risk loci for TGCT at 3q23 (rs11705932, TFDP2, P=1.5 × 10(-9)), 11q14.1 (rs7107174, GAB2, P=9.7 × 10(-11)), 16p13.13 (rs4561483, GSPT1, P=1.6 × 10(-8)) and 16q24.2 (rs55637647, ZFPM1, P=3.4 × 10(-9)). We additionally present detailed functional analysis of these loci, identifying a statistically significant relationship between rs4561483 risk genotype and increased GSPT1 expression in TGCT patient samples. These findings provide additional support for a polygenic model of TGCT risk and further insight into the biological basis of disease development.
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Affiliation(s)
- Kevin Litchfield
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Amy Lloyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, Leeds LS9 7TF, UK
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Douglas F Easton
- Cancer Research UK, Genetic Epidemiology Unit, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Darshna Dudakia
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, Leeds LS9 7TF, UK
| | - Alison Reid
- Academic Radiotherapy Unit, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Robert A. Huddart
- Academic Radiotherapy Unit, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Tom Grotmol
- Department of Research, Cancer Registry of Norway, 0369 Oslo, Norway
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
- William Harvey Research Institute, Queen Mary University, London EC1M 6BQ, UK
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33
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Vijayakrishnan J, Henrion M, Moorman AV, Fiege B, Kumar R, Inacio da Silva Filho M, Holroyd A, Koehler R, Thomsen H, Irving JA, Allan JM, Lightfoot T, Roman E, Kinsey SE, Sheridan E, Thompson PD, Hoffmann P, Nöthen MM, Mühleisen TW, Eisele L, Bartram CR, Schrappe M, Greaves M, Hemminki K, Harrison CJ, Stanulla M, Houlston RS. The 9p21.3 risk of childhood acute lymphoblastic leukaemia is explained by a rare high-impact variant in CDKN2A. Sci Rep 2015; 5:15065. [PMID: 26463672 PMCID: PMC4604478 DOI: 10.1038/srep15065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/12/2015] [Indexed: 02/08/2023] Open
Abstract
Genome-wide association studies (GWAS) have provided strong evidence for inherited predisposition to childhood acute lymphoblastic leukaemia (ALL) identifying a number of risk loci. We have previously shown common SNPs at 9p21.3 influence ALL risk. These SNP associations are generally not themselves candidates for causality, but simply act as markers for functional variants. By means of imputation of GWAS data and subsequent validation SNP genotyping totalling 2,177 ALL cases and 8,240 controls, we have shown that the 9p21.3 association can be ascribed to the rare high-impact CDKN2A p.Ala148Thr variant (rs3731249; Odds ratio = 2.42, P = 3.45 × 10(-19)). The association between rs3731249 genotype and risk was not specific to particular subtype of B-cell ALL. The rs3731249 variant is associated with predominant nuclear localisation of the CDKN2A transcript suggesting the functional effect of p.Ala148Thr on ALL risk may be through compromised ability to inhibit cyclin D within the cytoplasm.
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Affiliation(s)
- Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Anthony V. Moorman
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bettina Fiege
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | | | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Rolf Koehler
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Julie A. Irving
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James M. Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tracy Lightfoot
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Eve Roman
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Sally E. Kinsey
- Department of Paediatric and Adolescent Haematology and Oncology, Leeds General Infirmary, Leeds, United Kingdom
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Eamonn Sheridan
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Pamela D. Thompson
- Paediatric and Familial Cancer, Institute of Cancer Sciences, Manchester, United Kingdom
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Genomic Imaging Group, Institute of Neuroscience and Medicine (INM-1), Research Centre Juelich, Juelich, Germany
| | | | - Lewin Eisele
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg–Essen, Essen, Germany
| | - Claus R. Bartram
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Martin Schrappe
- General Paediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Mel Greaves
- Haemato-Oncology Research Unit, Division of Molecular Pathology, Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Christine J. Harrison
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Stanulla
- General Paediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
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34
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Kinnersley B, Labussière M, Holroyd A, Di Stefano AL, Broderick P, Vijayakrishnan J, Mokhtari K, Delattre JY, Gousias K, Schramm J, Schoemaker MJ, Fleming SJ, Herms S, Heilmann S, Schreiber S, Wichmann HE, Nöthen MM, Swerdlow A, Lathrop M, Simon M, Bondy M, Sanson M, Houlston RS. Genome-wide association study identifies multiple susceptibility loci for glioma. Nat Commun 2015; 6:8559. [PMID: 26424050 PMCID: PMC4600760 DOI: 10.1038/ncomms9559] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/04/2015] [Indexed: 12/25/2022] Open
Abstract
Previous genome-wide association studies (GWASs) have shown that common genetic variation contributes to the heritable risk of glioma. To identify new glioma susceptibility loci, we conducted a meta-analysis of four GWAS (totalling 4,147 cases and 7,435 controls), with imputation using 1000 Genomes and UK10K Project data as reference. After genotyping an additional 1,490 cases and 1,723 controls we identify new risk loci for glioblastoma (GBM) at 12q23.33 (rs3851634, near POLR3B, P=3.02 × 10(-9)) and non-GBM at 10q25.2 (rs11196067, near VTI1A, P=4.32 × 10(-8)), 11q23.2 (rs648044, near ZBTB16, P=6.26 × 10(-11)), 12q21.2 (rs12230172, P=7.53 × 10(-11)) and 15q24.2 (rs1801591, near ETFA, P=5.71 × 10(-9)). Our findings provide further insights into the genetic basis of the different glioma subtypes.
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Affiliation(s)
- Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Marianne Labussière
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013 Paris, France
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Anna-Luisa Di Stefano
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013 Paris, France
- Onconeurotek, F-75013 Paris, France
- AP-HP, GH Pitié-Salpêtrière, Service de Neurologie 2, F-75013 Paris, France
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Karima Mokhtari
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013 Paris, France
- Onconeurotek, F-75013 Paris, France
- AP-HP, GH Pitié-Salpêtrière, Laboratoire de neuropathologie R Escourolle, F-75013 Paris, France
| | - Jean-Yves Delattre
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013 Paris, France
- Onconeurotek, F-75013 Paris, France
- AP-HP, GH Pitié-Salpêtrière, Service de Neurologie 2, F-75013 Paris, France
| | - Konstantinos Gousias
- Department of Neurosurgery, University of Bonn Medical Center, Sigmund-Freud-Straße 25, 53105 Bonn, Germany
| | - Johannes Schramm
- Department of Neurosurgery, University of Bonn Medical Center, Sigmund-Freud-Straße 25, 53105 Bonn, Germany
| | - Minouk J. Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Sarah J. Fleming
- Centre for Epidemiology and Biostatistics, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK
| | - Stefan Herms
- Department of Biomedicine, Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
| | - Stefanie Heilmann
- Department of Biomedicine, Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Stefan Schreiber
- 1st Medical Department, University Clinic Schleswig-Holstein, Campus Kiel, House 6, Arnold-Heller-Straße 3, Kiel 24105, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Arnold-Heller-Straße 3, Kiel 24105, Germany
| | - Heinz-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Markus M. Nöthen
- Department of Biomedicine, Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Mark Lathrop
- AP-HP, GH Pitié-Salpêtrière, Laboratoire de neuropathologie R Escourolle, F-75013 Paris, France
- Foundation Jean Dausset-CEPH, 27 Rue Juliette Dodu, 75010 Paris, France
- Génome Québec, Department of Human Genetics, McGill University, Montreal, Quebec, Canada H3A 0G1
| | - Matthias Simon
- Department of Neurosurgery, University of Bonn Medical Center, Sigmund-Freud-Straße 25, 53105 Bonn, Germany
| | - Melissa Bondy
- Division of Hematology-Oncology, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marc Sanson
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013 Paris, France
- Onconeurotek, F-75013 Paris, France
- AP-HP, GH Pitié-Salpêtrière, Service de Neurologie 2, F-75013 Paris, France
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
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35
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Henrion MYR, Purdue MP, Scelo G, Broderick P, Frampton M, Ritchie A, Meade A, Li P, McKay J, Johansson M, Lathrop M, Larkin J, Rothman N, Wang Z, Chow WH, Stevens VL, Diver WR, Albanes D, Virtamo J, Brennan P, Eisen T, Chanock S, Houlston RS. Common variation at 1q24.1 (ALDH9A1) is a potential risk factor for renal cancer. PLoS One 2015; 10:e0122589. [PMID: 25826619 PMCID: PMC4380462 DOI: 10.1371/journal.pone.0122589] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/11/2015] [Indexed: 01/08/2023] Open
Abstract
So far six susceptibility loci for renal cell carcinoma (RCC) have been discovered by genome-wide association studies (GWAS). To identify additional RCC common risk loci, we performed a meta-analysis of published GWAS (totalling 2,215 cases and 8,566 controls of Western-European background) with imputation using 1000 Genomes Project and UK10K Project data as reference panels and followed up the most significant association signals [22 single nucleotide polymorphisms (SNPs) and 3 indels in eight genomic regions] in 383 cases and 2,189 controls from The Cancer Genome Atlas (TCGA). A combined analysis identified a promising susceptibility locus mapping to 1q24.1 marked by the imputed SNP rs3845536 (Pcombined =2.30x10-8). Specifically, the signal maps to intron 4 of the ALDH9A1 gene (aldehyde dehydrogenase 9 family, member A1). We further evaluated this potential signal in 2,461 cases and 5,081 controls from the International Agency for Research on Cancer (IARC) GWAS of RCC cases and controls from multiple European regions. In contrast to earlier findings no association was shown in the IARC series (P=0.94; Pcombined =2.73x10-5). While variation at 1q24.1 represents a potential risk locus for RCC, future replication analyses are required to substantiate our observation.
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Affiliation(s)
- Marc Y. R. Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Mark P. Purdue
- Division of Cancer Epidemiology and Genetics, Department Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Matthew Frampton
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Alastair Ritchie
- MRC Clinical Trials Unit at University College London, Aviation House, London, United Kingdom
| | - Angela Meade
- MRC Clinical Trials Unit at University College London, Aviation House, London, United Kingdom
| | - Peng Li
- International Agency for Research on Cancer, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | | | - Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - James Larkin
- Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, Department Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, Department Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, Maryland, United States of America
| | - Wong-Ho Chow
- Division of Cancer Epidemiology and Genetics, Department Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Victoria L. Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, United States of America
| | - W. Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, United States of America
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, Department Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Timothy Eisen
- Cambridge University Health Partners, Cambridge, United Kingdom
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, Department Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
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36
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Jäger R, Migliorini G, Henrion M, Kandaswamy R, Speedy HE, Heindl A, Whiffin N, Carnicer MJ, Broome L, Dryden N, Nagano T, Schoenfelder S, Enge M, Yuan Y, Taipale J, Fraser P, Fletcher O, Houlston RS. Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat Commun 2015; 6:6178. [PMID: 25695508 PMCID: PMC4346635 DOI: 10.1038/ncomms7178] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 12/30/2014] [Indexed: 12/25/2022] Open
Abstract
Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.
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Affiliation(s)
- Roland Jäger
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Gabriele Migliorini
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Radhika Kandaswamy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Helen E. Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Andreas Heindl
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Maria J. Carnicer
- Division of Molecular Pathology, Haemato-Oncology Research Unit, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Laura Broome
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Nicola Dryden
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Takashi Nagano
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Martin Enge
- Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, 14 183, Huddinge, Sweden
| | - Yinyin Yuan
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Jussi Taipale
- Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, 14 183, Huddinge, Sweden
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
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