1
|
Corradi C, Lencioni G, Felici A, Rizzato C, Gentiluomo M, Ermini S, Archibugi L, Mickevicius A, Lucchesi M, Malecka-Wojciesko E, Basso D, Arcidiacono PG, Petrone MC, Carrara S, Götz M, Bunduc S, Holleczek B, Aoki MN, Uzunoglu FG, Zanette DL, Mambrini A, Jamroziak K, Oliverius M, Lovecek M, Cavestro GM, Milanetto AC, Peduzzi G, Duchonova BM, Izbicki JR, Zalinkevicius R, Hlavac V, van Eijck CHJ, Brenner H, Vanella G, Vokacova K, Soucek P, Tavano F, Perri F, Capurso G, Hussein T, Kiudelis M, Kupcinskas J, Busch OR, Morelli L, Theodoropoulos GE, Testoni SGG, Adamonis K, Neoptolemos JP, Gazouli M, Pasquali C, Kormos Z, Skalicky P, Pezzilli R, Sperti C, Kauffmann E, Büchler MW, Schöttker B, Hegyi P, Capretti G, Lawlor RT, Canzian F, Campa D. Potential association between PSCA rs2976395 functional variant and pancreatic cancer risk. Int J Cancer 2024; 155:1432-1442. [PMID: 38924078 DOI: 10.1002/ijc.35046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 06/28/2024]
Abstract
Correlated regions of systemic interindividual variation (CoRSIV) represent a small proportion of the human genome showing DNA methylation patterns that are the same in all human tissues, are different among individuals, and are partially regulated by genetic variants in cis. In this study we aimed at investigating single-nucleotide polymorphisms (SNPs) within CoRSIVs and their involvement with pancreatic ductal adenocarcinoma (PDAC) risk. We analyzed 29,099 CoRSIV-SNPs and 133,615 CoRSIV-mQTLs in 14,394 cases and 247,022 controls of European and Asian descent. We observed that the A allele of the rs2976395 SNP was associated with increased PDAC risk in Europeans (p = 2.81 × 10-5). This SNP lies in the prostate stem cell antigen gene and is in perfect linkage disequilibrium with a variant (rs2294008) that has been reported to be associated with risk of many other cancer types. The A allele is associated with the DNA methylation level of the gene according to the PanCan-meQTL database and with overexpression according to QTLbase. The expression of the gene has been observed to be deregulated in many tumors of the gastrointestinal tract including pancreatic cancer; however, functional studies are needed to elucidate the function relevance of the association.
Collapse
Affiliation(s)
| | | | | | | | | | - Stefano Ermini
- Blood Transfusion Service, Azienda Ospedaliera-Universitaria Meyer, Children's Hospital, Florence, Italy
| | - Livia Archibugi
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
- Digestive and Liver Disease Unit, Sant'Andrea Hospital, Rome, Italy
| | - Antanas Mickevicius
- Department of Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Maurizio Lucchesi
- Oncology of Massa Carrara, Oncological Department, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | | | - Daniela Basso
- Laboratory Medicine, Department DIMED, University of Padova, Padua, Italy
| | - Paolo Giorgio Arcidiacono
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - Maria Chiara Petrone
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Carrara
- Endoscoopic Unit, Gastroenterology Department, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Mara Götz
- Department of General, Visceral and Thoracic Surgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Stefania Bunduc
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | | | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, Parana, Brazil
| | - Faik G Uzunoglu
- Department of General, Visceral and Thoracic Surgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Dalila Lucíola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, Parana, Brazil
| | - Andrea Mambrini
- Oncology of Massa Carrara, Oncological Department, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Krzysztof Jamroziak
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Martin Oliverius
- Department of Surgery, University Hospital Kralovske Vinohrady, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | | | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Rimantas Zalinkevicius
- Clinics of Institute of Endocrinology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Viktor Hlavac
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Casper H J van Eijck
- Department of Surgery, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Giuseppe Vanella
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
- Digestive and Liver Disease Unit, Sant'Andrea Hospital, Rome, Italy
| | - Klara Vokacova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pavel Soucek
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Francesco Perri
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Gabriele Capurso
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
- Digestive and Liver Disease Unit, Sant'Andrea Hospital, Rome, Italy
| | - Tamás Hussein
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Mindaugas Kiudelis
- Department of Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Gastroenterology Department, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Olivier R Busch
- Department of Surgery, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Luca Morelli
- General Surgery, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - George E Theodoropoulos
- First Propaedeutic University Surgery Clinic, Hippocratio General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Sabrina Gloria Giulia Testoni
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - Kestutis Adamonis
- Gastroenterology Department, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Surgery, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - John P Neoptolemos
- First Propaedeutic University Surgery Clinic, Hippocratio General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Zita Kormos
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | | | | | - Cosimo Sperti
- Department of DiSCOG, University of Padova, Padua, Italy
| | - Emanuele Kauffmann
- Division of General and Transplant Surgery, Pisa University Hospital, Pisa, Italy
| | - Markus W Büchler
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Péter Hegyi
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- János Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Giovanni Capretti
- Pancreatic Surgery Department, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
- Humanitas University, Rozzano, Milan, Italy
| | - Rita T Lawlor
- ARC-NET Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| |
Collapse
|
2
|
Jacobs MF, Stoffel EM. Genetic and other risk factors for pancreatic ductal adenocarcinoma (PDAC). Fam Cancer 2024; 23:221-232. [PMID: 38573398 DOI: 10.1007/s10689-024-00372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at an advanced stage, resulting in poor prognosis and low 5-year survival rates. While early evidence suggests increased long-term survival in those with screen-detected resectable cancers, surveillance imaging is currently only recommended for individuals with a lifetime risk of PDAC ≥ 5%. Identification of risk factors for PDAC provides opportunities for early detection, risk reducing interventions, and targeted therapies, thus potentially improving patient outcomes. Here, we summarize modifiable and non-modifiable risk factors for PDAC. We review hereditary cancer syndromes associated with risk for PDAC and their implications for patients and their relatives. In addition, other biologically relevant pathways and environmental and lifestyle risk factors are discussed. Future work may focus on elucidating additional genetic, environmental, and lifestyle risk factors that may modify PDAC risk to continue to identify individuals at increased risk for PDAC who may benefit from surveillance and risk reducing interventions.
Collapse
Affiliation(s)
- Michelle F Jacobs
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Elena M Stoffel
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| |
Collapse
|
3
|
Ünal P, Lu Y, Bueno-de-Mesquita B, van Eijck CHJ, Talar-Wojnarowska R, Szentesi A, Gazouli M, Kreivenaite E, Tavano F, Małecka-Wojciesko E, Erőss B, Oliverius M, Bunduc S, Nóbrega Aoki M, Vodickova L, Boggi U, Giaccherini M, Kondrackiene J, Chammas R, Palmieri O, Theodoropoulos GE, Bijlsma MF, Basso D, Mohelnikova-Duchonova B, Soucek P, Izbicki JR, Kiudelis V, Vanella G, Arcidiacono PG, Włodarczyk B, Hackert T, Schöttker B, Uzunoglu FG, Bambi F, Goetz M, Hlavac V, Brenner H, Perri F, Carrara S, Landi S, Hegyi P, Dijk F, Maiello E, Capretti G, Testoni SGG, Petrone MC, Stocker H, Ermini S, Archibugi L, Gentiluomo M, Cavestro GM, Pezzilli R, Di Franco G, Milanetto AC, Sperti C, Neoptolemos JP, Morelli L, Vokacova K, Pasquali C, Lawlor RT, Bazzocchi F, Kupcinskas J, Capurso G, Campa D, Canzian F. Polymorphisms in transcription factor binding sites and enhancer regions and pancreatic ductal adenocarcinoma risk. Hum Genomics 2024; 18:12. [PMID: 38308339 PMCID: PMC10837899 DOI: 10.1186/s40246-024-00576-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/23/2024] [Indexed: 02/04/2024] Open
Abstract
Genome-wide association studies (GWAS) are a powerful tool for detecting variants associated with complex traits and can help risk stratification and prevention strategies against pancreatic ductal adenocarcinoma (PDAC). However, the strict significance threshold commonly used makes it likely that many true risk loci are missed. Functional annotation of GWAS polymorphisms is a proven strategy to identify additional risk loci. We aimed to investigate single-nucleotide polymorphisms (SNP) in regulatory regions [transcription factor binding sites (TFBSs) and enhancers] that could change the expression profile of multiple genes they act upon and thereby modify PDAC risk. We analyzed a total of 12,636 PDAC cases and 43,443 controls from PanScan/PanC4 and the East Asian GWAS (discovery populations), and the PANDoRA consortium (replication population). We identified four associations that reached study-wide statistical significance in the overall meta-analysis: rs2472632(A) (enhancer variant, OR 1.10, 95%CI 1.06,1.13, p = 5.5 × 10-8), rs17358295(G) (enhancer variant, OR 1.16, 95%CI 1.10,1.22, p = 6.1 × 10-7), rs2232079(T) (TFBS variant, OR 0.88, 95%CI 0.83,0.93, p = 6.4 × 10-6) and rs10025845(A) (TFBS variant, OR 1.88, 95%CI 1.50,1.12, p = 1.32 × 10-5). The SNP with the most significant association, rs2472632, is located in an enhancer predicted to target the coiled-coil domain containing 34 oncogene. Our results provide new insights into genetic risk factors for PDAC by a focused analysis of polymorphisms in regulatory regions and demonstrating the usefulness of functional prioritization to identify loci associated with PDAC risk.
Collapse
Affiliation(s)
- Pelin Ünal
- Genomic Epidemiology Group, German Cancer Research Center, In Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ye Lu
- Genomic Epidemiology Group, German Cancer Research Center, In Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Casper H J van Eijck
- Department of Surgery, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | | | - Andrea Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Edita Kreivenaite
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, FG, Italy
| | | | - Bálint Erőss
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Martin Oliverius
- Department of Surgery, University Hospital Kralovske Vinohrady, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Stefania Bunduc
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Curitiba, PR, Brazil
| | - Ludmila Vodickova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Plzeň, Czech Republic
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, Institute of Physiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ugo Boggi
- Division of General and Transplant Surgery, Pisa University Hospital, Pisa, Italy
| | | | - Jurate Kondrackiene
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Roger Chammas
- Department of Radiology and Oncology, Institute of Cancer of São Paulo, São Paulo, Brazil
| | - Orazio Palmieri
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, FG, Italy
| | - George E Theodoropoulos
- First Propaedeutic University Surgery Clinic, Hippocratio General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center of Experimental Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Daniela Basso
- Department of Medicine, Laboratory Medicine, University of Padova, Padua, Italy
| | | | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Plzeň, Czech Republic
| | - Jakob R Izbicki
- Department of General Visceral and Thoracic Surgery, University of Hamburg Medical Institutions, Hamburg, Germany
| | - Vytautas Kiudelis
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Giuseppe Vanella
- PancreatoBiliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
- Digestive and Liver Disease Unit, S. Andrea Hospital, Rome, Italy
| | - Paolo Giorgio Arcidiacono
- PancreatoBiliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Włodarczyk
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Thilo Hackert
- Department of General, Visceral and Transplant Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Network Aging Research (NAR), Heidelberg University, Heidelberg, Germany
| | - Faik G Uzunoglu
- Department of General Visceral and Thoracic Surgery, University of Hamburg Medical Institutions, Hamburg, Germany
| | - Franco Bambi
- Blood Transfusion Service, Meyer Children's Hospital, Florence, Italy
| | - Mara Goetz
- Department of General Visceral and Thoracic Surgery, University of Hamburg Medical Institutions, Hamburg, Germany
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Plzeň, Czech Republic
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Network Aging Research (NAR), Heidelberg University, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | - Francesco Perri
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, FG, Italy
| | - Silvia Carrara
- Endoscopic Unit, Department of Gastroenterology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Péter Hegyi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- János Szentágothai Research Center, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Frederike Dijk
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Evaristo Maiello
- Department of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, FG, Italy
| | - Giovanni Capretti
- Pancreatic Unit, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Sabrina Gloria Giulia Testoni
- PancreatoBiliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Maria Chiara Petrone
- PancreatoBiliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Hannah Stocker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Network Aging Research (NAR), Heidelberg University, Heidelberg, Germany
| | - Stefano Ermini
- Blood Transfusion Service, Meyer Children's Hospital, Florence, Italy
| | - Livia Archibugi
- PancreatoBiliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
- Digestive and Liver Disease Unit, S. Andrea Hospital, Rome, Italy
| | | | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | | | - Gregorio Di Franco
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Cosimo Sperti
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - John P Neoptolemos
- Department of General, Visceral and Transplant Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Luca Morelli
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Klara Vokacova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, Institute of Physiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Claudio Pasquali
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Rita T Lawlor
- Department of Diagnostics and Public Health, ARC-Net Centre for Applied Research on Cancer, University of Verona, Verona, Italy
| | - Francesca Bazzocchi
- Department of Surgery, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, FG, Italy
| | - Juozas Kupcinskas
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Gabriele Capurso
- PancreatoBiliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
- Digestive and Liver Disease Unit, S. Andrea Hospital, Rome, Italy
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center, In Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| |
Collapse
|
4
|
Gholami M, Zoughi M, Hasanzad M, Larijani B, Amoli MM. Haplotypic variants of COVID-19 related genes are associated with blood pressure and metabolites levels. J Med Virol 2023; 95:e28355. [PMID: 36443248 PMCID: PMC9877746 DOI: 10.1002/jmv.28355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 07/27/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
The genetic association of coronavirus disease 2019 (COVID-19) with its complications has not been fully understood. This study aimed to identify variants and haplotypes of candidate genes implicated in COVID-19 related traits by combining the literature review and pathway analysis. To explore such genes, the protein-protein interactions and relevant pathways of COVID-19-associated genes were assessed. A number of variants on candidate genes were identified from Genome-wide association studies (GWASs) which were associated with COVID-19 related traits (p ˂ 10-6 ). Haplotypic blocks were assessed using haplotypic structures among the 1000 Genomes Project (r2 ≥ 0.8, D' ≥ 0.8). Further functional analyses were performed on the selected variants. The results demonstrated that a group of variants in ACE and AGT genes were significantly correlated with COVID-19 related traits. Three haplotypes were identified to be involved in the blood metabolites levels and the development of blood pressure. Functional analyses revealed that most GWAS index variants were expression quantitative trait loci and had transcription factor binding sites, exonic splicing enhancers or silencer activities. Furthermore, the proxy haplotype variants, rs4316, rs4353, rs4359, and three variants, namely rs2493133, rs2478543, and rs5051, were associated with blood metabolite and systolic blood pressure, respectively. These variants exerted more regulatory effects compared with other GWAS variants. The present study indicates that the genetic variants and candidate haplotypes of COVID-19 related genes are associated with blood pressure and blood metabolites. However, further observational studies are warranted to confirm these results.
Collapse
Affiliation(s)
- Morteza Gholami
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical SciencesTehranIran,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Marziyeh Zoughi
- Metabolomics and genomics research center endocrinology and metabolism molecular‐cellular sciences instituteTehran University of medical sciencesTehranIran
| | - Mandana Hasanzad
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Mahsa M. Amoli
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical SciencesTehranIran
| |
Collapse
|
5
|
Afghani E, Klein AP. Pancreatic Adenocarcinoma: Trends in Epidemiology, Risk Factors, and Outcomes. Hematol Oncol Clin North Am 2022; 36:879-895. [PMID: 36154788 PMCID: PMC10548451 DOI: 10.1016/j.hoc.2022.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Pancreatic cancer is one of the most lethal cancers in the world; it is a silent disease in which symptoms do not present until advanced stages, thereby reducing the 5-year survival rate to 10%. The global burden of pancreatic cancer has doubled over the past 25 years despite advancements in medicine. This review aims to discuss the global trends and disparities in pancreatic cancer, as well as the up-to-date literature on the known risk factors. A better understanding of these risk factors will reduce mortality by providing opportunities to screen these patients as well as counseling on lifestyle modifications.
Collapse
Affiliation(s)
- Elham Afghani
- Johns Hopkins School of Medicine, 1830 E Monument Street, Room 436, Baltimore, MD 21205, USA
| | - Alison P Klein
- Johns Hopkins School of Medicine, 1830 E Monument Street, Room 436, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Bloomberg School of Public Health, 1550 Orleans Street, Baltimore, MD 21231, USA.
| |
Collapse
|
6
|
Tian J, Chen C, Rao M, Zhang M, Lu Z, Cai Y, Ying P, Li B, Wang H, Wang L, Li Y, Huang J, Fan L, Cai X, Ning C, Li Y, Zhang F, Wang W, Jiang Y, Liu Y, Wang M, Li H, Huang C, Yang Z, Chang J, Zhu Y, Yang X, Miao X. Aberrant RNA splicing is a primary link between genetic variation and pancreatic cancer risk. Cancer Res 2022; 82:2084-2096. [PMID: 35363263 DOI: 10.1158/0008-5472.can-21-4367] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/15/2022] [Accepted: 03/30/2022] [Indexed: 11/16/2022]
Abstract
Understanding the genetic variation underlying transcript splicing is essential for fully dissecting the molecular mechanisms of common diseases. The available evidence from splicing quantitative trait locus (sQTL) studies using pancreatic ductal adenocarcinoma (PDAC) tissues have been limited to small sample sizes. Here we present a genome-wide sQTL analysis to identify single nucleotide polymorphisms (SNPs) that control mRNA splicing in 176 PDAC samples from TCGA. From this analysis, 16,175 sQTLs were found to be significantly enriched in RNA binding protein (RBP) binding sites and chromatin regulatory elements and overlapped with known loci from PDAC genome-wide association studies (GWAS). sQTLs and expression QTLs (eQTL) showed mostly non-overlapping patterns, suggesting sQTLs provide additional insights into the etiology of disease. Target genes affected by sQTLs were closely related to cancer signaling pathways, high mutational burden, immune infiltration, and pharmaceutical targets, which will be helpful for clinical applications. Integration of a large-scale population consisting of 2,782 PDAC patients and 7,983 healthy controls identified an sQTL variant rs1785932-T allele that promotes alternative splicing of ELP2 exon 6 and leads to a lower level of the ELP2 full-length isoform (ELP2_V1) and a higher level of a truncated ELP2 isoform (ELP2_V2), resulting in decreased risk of PDAC (OR=0.83, 95%CI=0.77-0.89, P=1.16×10-6). The ELP2_V2 isoform functioned as a potential tumor suppressor gene, inhibiting PDAC cell proliferation by exhibiting stronger binding affinity to JAK1/STAT3 than ELP2_V1 and subsequently blocking the pathological activation of the p-STAT3 pathway. Collectively, these findings provide an informative sQTL resource and insights into the regulatory mechanisms linking splicing variants to PDAC risk.
Collapse
Affiliation(s)
| | | | | | - Ming Zhang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zequn Lu
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yimin Cai
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Pingting Ying
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Li
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haoxue Wang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lu Wang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Yao Li
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, China
| | - Jinyu Huang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Linyun Fan
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaomin Cai
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Caibo Ning
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yanmin Li
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fuwei Zhang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenzhuo Wang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | | | | | - Min Wang
- Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Heng Li
- Tongji Hospital, Wuhan, Hubei, China
| | | | | | - Jiang Chang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, China
| | | | | | | |
Collapse
|
7
|
Wu C, Huang ZH, Meng ZQ, Fan XT, Lu S, Tan YY, You LM, Huang JQ, Stalin A, Ye PZ, Wu ZS, Zhang JY, Liu XK, Zhou W, Zhang XM, Wu JR. A network pharmacology approach to reveal the pharmacological targets and biological mechanism of compound kushen injection for treating pancreatic cancer based on WGCNA and in vitro experiment validation. Chin Med 2021; 16:121. [PMID: 34809653 PMCID: PMC8607619 DOI: 10.1186/s13020-021-00534-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Compound kushen injection (CKI), a Chinese patent drug, is widely used in the treatment of various cancers, especially neoplasms of the digestive system. However, the underlying mechanism of CKI in pancreatic cancer (PC) treatment has not been totally elucidated. METHODS Here, to overcome the limitation of conventional network pharmacology methods with a weak combination with clinical information, this study proposes a network pharmacology approach of integrated bioinformatics that applies a weighted gene co-expression network analysis (WGCNA) to conventional network pharmacology, and then integrates molecular docking technology and biological experiments to verify the results of this network pharmacology analysis. RESULTS The WGCNA analysis revealed 2 gene modules closely associated with classification, staging and survival status of PC. Further CytoHubba analysis revealed 10 hub genes (NCAPG, BUB1, CDK1, TPX2, DLGAP5, INAVA, MST1R, TMPRSS4, TMEM92 and SFN) associated with the development of PC, and survival analysis found 5 genes (TSPOAP1, ADGRG6, GPR87, FAM111B and MMP28) associated with the prognosis and survival of PC. By integrating these results into the conventional network pharmacology study of CKI treating PC, we found that the mechanism of CKI for PC treatment was related to cell cycle, JAK-STAT, ErbB, PI3K-Akt and mTOR signalling pathways. Finally, we found that CDK1, JAK1, EGFR, MAPK1 and MAPK3 served as core genes regulated by CKI in PC treatment, and were further verified by molecular docking, cell proliferation assay, RT-qPCR and western blot analysis. CONCLUSIONS Overall, this study suggests that the optimized network pharmacology approach is suitable to explore the molecular mechanism of CKI in the treatment of PC, which provides a reference for further investigating biomarkers for diagnosis and prognosis of PC and even the clinical rational application of CKI.
Collapse
Affiliation(s)
- Chao Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zhi-Hong Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zi-Qi Meng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Xiao-Tian Fan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Shan Lu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Ying-Ying Tan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Lei-Ming You
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jia-Qi Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Antony Stalin
- State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Pei-Zhi Ye
- National Cancer Center/National Clinical Research Center for Cancer/Chinese Medicine Department of the Caner Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhi-Shan Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jing-Yuan Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Xin-Kui Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Wei Zhou
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
- China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiao-Meng Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jia-Rui Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China.
| |
Collapse
|
8
|
Venkat S, Alahmari AA, Feigin ME. Drivers of Gene Expression Dysregulation in Pancreatic Cancer. Trends Cancer 2021; 7:594-605. [PMID: 33618999 PMCID: PMC8217125 DOI: 10.1016/j.trecan.2021.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease with a poor prognosis. The functional consequences of common genetic aberrations and their roles in treatment strategies have been extensively reviewed. In addition to these genomic aberrations, consideration of non-genetic drivers of altered oncogene expression is essential to account for the diversity in PDAC phenotypes. In this review we seek to assess our current understanding of mechanisms of gene expression dysregulation. We focus on four drivers of gene expression dysregulation, including mutations, transcription factors, epigenetic regulators, and RNA stability/isoform regulation, in the context of PDAC pathogenesis. Recent studies provide much-needed insight into the role of gene expression dysregulation in dissecting tumor heterogeneity and stratifying patients for the development of personalized treatment strategies.
Collapse
Affiliation(s)
- Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Abdulrahman A Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA; Department of Medical Laboratory Sciences, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Michael E Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
| |
Collapse
|
9
|
Pancreatic cancer epidemiology: understanding the role of lifestyle and inherited risk factors. Nat Rev Gastroenterol Hepatol 2021; 18:493-502. [PMID: 34002083 PMCID: PMC9265847 DOI: 10.1038/s41575-021-00457-x] [Citation(s) in RCA: 407] [Impact Index Per Article: 135.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/20/2021] [Indexed: 12/24/2022]
Abstract
Pancreatic cancer is a leading cause of cancer death worldwide and its global burden has more than doubled over the past 25 years. The highest incidence regions for pancreatic cancer include North America, Europe and Australia, and although much of this increase is due to ageing worldwide populations, there are key modifiable risk factors for pancreatic cancer such as cigarette smoking, obesity, diabetes and alcohol intake. The prevalence of these risk factors is increasing in many global regions, resulting in increasing age-adjusted incidence rates for pancreatic cancer, but the relative contribution from these risk factors varies globally due to variation in the underlying prevalence and prevention strategies. Inherited genetic factors, although not directly modifiable, are an important component of pancreatic cancer risk, and include pathogenic variants in hereditary cancer genes, genes associated with hereditary pancreatitis, as well as common variants identified in genome-wide association studies. Identification of the genetic changes that underlie pancreatic cancer not only provides insight into the aetiology of this cancer but also provides an opportunity to guide early detection strategies. The goal of this Review is to provide an up-to-date overview of the established modifiable and inherited risk factors for pancreatic cancer.
Collapse
|
10
|
Nelson SR, Roche S, Cotter M, Garcia PA, Reitmeier D, Zollbrecht E, O'Neill F, Clynes M, Doolan P, Mehta JP, Swan N, Larkin A, Walsh N. Genomic Profiling and Functional Analysis of let-7c miRNA-mRNA Interactions Identify SOX13 to Be Involved in Invasion and Progression of Pancreatic Cancer. JOURNAL OF ONCOLOGY 2020; 2020:2951921. [PMID: 33424970 PMCID: PMC7775161 DOI: 10.1155/2020/2951921] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Pancreatic cancer is a devastating disease; its lethality is related to rapid growth and tendency to invade adjacent organs and metastasize at an early stage. OBJECTIVE The aim of this study was to identify miRNAs and their gene targets involved in the invasive phenotype in pancreatic cancer to better understand the biological behaviour and the rapid progression of this disease. METHODS miRNA profiling was performed in isogenic matched high invasive and low-invasive subclones derived from the MiaPaCa-2 cell line and validated in a panel of pancreatic cancer cell lines, tumour, and normal pancreas. Online miRNA target prediction algorithms and gene expression arrays were used to predict the target genes of the differentially expressed miRNAs. miRNAs and potential target genes were subjected to overexpression and knockdown approaches and downstream functional assays to determine their pathological role in pancreatic cancer. RESULTS Differential expression analysis revealed 10 significantly dysregulated miRNAs associated with invasive capacity (Student's t-tests; P value <0.05; fold change = ±2). The expression of top upregulated miR-135b and downregulated let-7c miRNAs correlated with the invasive abilities of eight pancreatic cancer cell lines and displayed differential expression in pancreatic cancer and adjacent normal tissue specimens. Ectopic overexpression of let-7c decreased proliferation, invasion, and colony formation. Integrated analysis of miRNA-mRNA using in silico algorithms and experimental validation databases identified four putative gene targets of let-7c. One of these targets, SOX13, was found to be upregulated in PDAC tumour compared with normal tissue in TCGA and an independent data set by qPCR and immunohistochemistry. RNAi knockdown of SOX13 reduced the invasion and colony formation ability of pancreatic cancer cells. CONCLUSION The identification of key miRNA-mRNA gene interactions and networks provide potential diagnostic and therapeutic strategies for better treatment options for pancreatic cancer patients.
Collapse
Affiliation(s)
- Shannon R. Nelson
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Sandra Roche
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Maura Cotter
- Histopathology Department, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - Pablo Anton Garcia
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Daniela Reitmeier
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Elisabeth Zollbrecht
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Fiona O'Neill
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Padraig Doolan
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Jai P. Mehta
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Niall Swan
- Histopathology Department, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - AnneMarie Larkin
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Naomi Walsh
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland
| |
Collapse
|
11
|
Liu K, Zhao J, Chen C, Xu J, Bell RL, Hall FS, Koob GF, Volkow ND, Qing H, Lin Z. Epistatic evidence for gender-dependant slow neurotransmission signalling in substance use disorders: PPP1R12B versus PPP1R1B. EBioMedicine 2020; 61:103066. [PMID: 33096475 PMCID: PMC7581882 DOI: 10.1016/j.ebiom.2020.103066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Slow neurotransmission including DARPP-32 signalling is implicated in substance use disorders (SUDs) by experimental systems but not yet in the human aetiology. PPP1R12B, encoding another protein in the DARPP-32 family, hasn't been studied in the brain. METHODS Brain-regional gene activity was assessed in three different animal models of SUDs for mRNA level alterations. Genetic associations were assessed by meta-analysis of pre-existing dbGaP GWAS datasets for main effects and epistasis with known genetic risks, followed by cell type-specific pathway delineation. Parkinson's disease (PD) was included as a dopamine-related disease control for SUDs. FINDINGS In animal models of SUDs, environmentally-altered PPP1R12B expression sex-dependently involves motivation-related brain regions. In humans with polysubstance abuse, meta-analysis of pre-existing datasets revealed that PPP1R12B and PPP1R1B, although expressed in dopamine vs. dopamine-recipient neurons, exerted similar interactions with known genetic risks such as ACTR1B and DRD2 in men but with ADH1B, HGFAC and DRD3 in women. These interactions reached genome-wide significances (Pmeta<10-20) for SUDs but not for PD (disease selectivity: P = 4.8 × 10-142, OR = 6.7 for PPP1R12B; P = 8.0 × 10-8, OR = 2.1 for PPP1R1B). CADM2 was the common risk in the molecular signalling regardless of gender and cell type. INTERPRETATION Gender-dependant slow neurotransmission may convey both genetic and environmental vulnerabilities selectively to SUDs. FUNDING Grants from National Institute on Drug Abuse (NIDA) and National Institute on Alcohol Abuse and Alcoholism (NIAAA) of U.S.A. and National Natural Science Foundation of China (NSFC).
Collapse
Affiliation(s)
- Kefu Liu
- School of Life Science, Beijing Institute of Technology, 100081 Beijing, China; Laboratory of Psychiatric Neurogenomics, McLean Hospital, Belmont, MA 02478, United States of America
| | - Juan Zhao
- School of Life Science, Beijing Institute of Technology, 100081 Beijing, China; Laboratory of Psychiatric Neurogenomics, McLean Hospital, Belmont, MA 02478, United States of America
| | - Chunnuan Chen
- Laboratory of Psychiatric Neurogenomics, McLean Hospital, Belmont, MA 02478, United States of America; Department of Neurology, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, P. R. China
| | - Jie Xu
- Department of Computer Information Systems, Bentley University, Waltham, MA, 02452, United States of America
| | - Richard L Bell
- Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States of America
| | - Frank S Hall
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, Ohio 43614, United States of America
| | - George F Koob
- National Institute on Drug Abuse and National Institute of Alcohol Abuse and Alcoholism, Bethesda, Maryland, 20892 United States of America
| | - Nora D Volkow
- National Institute on Drug Abuse and National Institute of Alcohol Abuse and Alcoholism, Bethesda, Maryland, 20892 United States of America
| | - Hong Qing
- School of Life Science, Beijing Institute of Technology, 100081 Beijing, China.
| | - Zhicheng Lin
- Laboratory of Psychiatric Neurogenomics, McLean Hospital, Belmont, MA 02478, United States of America.
| |
Collapse
|
12
|
Purdue MP, Song L, Scélo G, Houlston RS, Wu X, Sakoda LC, Thai K, Graff RE, Rothman N, Brennan P, Chanock SJ, Yu K. Pathway Analysis of Renal Cell Carcinoma Genome-Wide Association Studies Identifies Novel Associations. Cancer Epidemiol Biomarkers Prev 2020; 29:2065-2069. [PMID: 32732251 PMCID: PMC9438507 DOI: 10.1158/1055-9965.epi-20-0472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/23/2020] [Accepted: 07/23/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Much of the heritable risk of renal cell carcinoma (RCC) associated with common genetic variation is unexplained. New analytic approaches have been developed to increase the discovery of risk variants in genome-wide association studies (GWAS), including multi-locus testing through pathway analysis. METHODS We conducted a pathway analysis using GWAS summary data from six previous scans (10,784 cases and 20,406 controls) and evaluated 3,678 pathways and gene sets drawn from the Molecular Signatures Database. To replicate findings, we analyzed GWAS summary data from the UK Biobank (903 cases and 451,361 controls) and the Genetic Epidemiology Research on Adult Health and Aging cohort (317 cases and 50,511 controls). RESULTS We identified 14 pathways/gene sets associated with RCC in both the discovery (P < 1.36 × 10-5, the Bonferroni correction threshold) and replication (P < 0.05) sets, 10 of which include components of the PI3K/AKT pathway. In tests across 2,035 genes in these pathways, associations (Bonferroni corrected P < 2.46 × 10-5 in discovery and replication sets combined) were observed for CASP9, TIPIN, and CDKN2C. The strongest SNP signal was for rs12124078 (P Discovery = 2.6 × 10-5; P Replication = 1.5 × 10-4; P Combined = 6.9 × 10-8), a CASP9 expression quantitative trait locus. CONCLUSIONS Our pathway analysis implicates genetic variation within the PI3K/AKT pathway as a source of RCC heritability and identifies several promising novel susceptibility genes, including CASP9, which warrant further investigation. IMPACT Our findings illustrate the value of pathway analysis as a complementary approach to analyzing GWAS data.
Collapse
Affiliation(s)
- Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland.
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Ghislaine Scélo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, London, United Kingdom
| | - Xifeng Wu
- Department of Big Data in Health Science, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Khanh Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| |
Collapse
|
13
|
Zhong J, Jermusyk A, Wu L, Hoskins JW, Collins I, Mocci E, Zhang M, Song L, Chung CC, Zhang T, Xiao W, Albanes D, Andreotti G, Arslan AA, Babic A, Bamlet WR, Beane-Freeman L, Berndt S, Borgida A, Bracci PM, Brais L, Brennan P, Bueno-de-Mesquita B, Buring J, Canzian F, Childs EJ, Cotterchio M, Du M, Duell EJ, Fuchs C, Gallinger S, Gaziano JM, Giles GG, Giovannucci E, Goggins M, Goodman GE, Goodman PJ, Haiman C, Hartge P, Hasan M, Helzlsouer KJ, Holly EA, Klein EA, Kogevinas M, Kurtz RJ, LeMarchand L, Malats N, Männistö S, Milne R, Neale RE, Ng K, Obazee O, Oberg AL, Orlow I, Patel AV, Peters U, Porta M, Rothman N, Scelo G, Sesso HD, Severi G, Sieri S, Silverman D, Sund M, Tjønneland A, Thornquist MD, Tobias GS, Trichopoulou A, Van Den Eeden SK, Visvanathan K, Wactawski-Wende J, Wentzensen N, White E, Yu H, Yuan C, Zeleniuch-Jacquotte A, Hoover R, Brown K, Kooperberg C, Risch HA, Jacobs EJ, Li D, Yu K, Shu XO, Chanock SJ, Wolpin BM, Stolzenberg-Solomon RZ, Chatterjee N, Klein AP, Smith JP, Kraft P, Shi J, Petersen GM, Zheng W, Amundadottir LT. A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer. J Natl Cancer Inst 2020; 112:1003-1012. [PMID: 31917448 PMCID: PMC7566474 DOI: 10.1093/jnci/djz246] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/12/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Although 20 pancreatic cancer susceptibility loci have been identified through genome-wide association studies in individuals of European ancestry, much of its heritability remains unexplained and the genes responsible largely unknown. METHODS To discover novel pancreatic cancer risk loci and possible causal genes, we performed a pancreatic cancer transcriptome-wide association study in Europeans using three approaches: FUSION, MetaXcan, and Summary-MulTiXcan. We integrated genome-wide association studies summary statistics from 9040 pancreatic cancer cases and 12 496 controls, with gene expression prediction models built using transcriptome data from histologically normal pancreatic tissue samples (NCI Laboratory of Translational Genomics [n = 95] and Genotype-Tissue Expression v7 [n = 174] datasets) and data from 48 different tissues (Genotype-Tissue Expression v7, n = 74-421 samples). RESULTS We identified 25 genes whose genetically predicted expression was statistically significantly associated with pancreatic cancer risk (false discovery rate < .05), including 14 candidate genes at 11 novel loci (1p36.12: CELA3B; 9q31.1: SMC2, SMC2-AS1; 10q23.31: RP11-80H5.9; 12q13.13: SMUG1; 14q32.33: BTBD6; 15q23: HEXA; 15q26.1: RCCD1; 17q12: PNMT, CDK12, PGAP3; 17q22: SUPT4H1; 18q11.22: RP11-888D10.3; and 19p13.11: PGPEP1) and 11 at six known risk loci (5p15.33: TERT, CLPTM1L, ZDHHC11B; 7p14.1: INHBA; 9q34.2: ABO; 13q12.2: PDX1; 13q22.1: KLF5; and 16q23.1: WDR59, CFDP1, BCAR1, TMEM170A). The association for 12 of these genes (CELA3B, SMC2, and PNMT at novel risk loci and TERT, CLPTM1L, INHBA, ABO, PDX1, KLF5, WDR59, CFDP1, and BCAR1 at known loci) remained statistically significant after Bonferroni correction. CONCLUSIONS By integrating gene expression and genotype data, we identified novel pancreatic cancer risk loci and candidate functional genes that warrant further investigation.
Collapse
Affiliation(s)
- Jun Zhong
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ashley Jermusyk
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jason W Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Evelina Mocci
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- US Food and Drug Administration, Silver Spring, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wenming Xiao
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
- Division of Molecular Genetics and Pathology, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY, USA
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Ana Babic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Laura Beane-Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sonja Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, CA, USA
| | - Lauren Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases, National Institute for Public Health and the Environment, BA, Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Julie Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Erica J Childs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michelle Cotterchio
- Cancer Care Ontario, University of Toronto, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute, Catalan Institute of Oncology, Barcelona, Spain
| | | | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - J Michael Gaziano
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Aging, Brigham and Women’s Hospital, Boston, MA, USA
- Boston VA Healthcare System, Boston, MA, USA
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Edward Giovannucci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gary E Goodman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Manal Hasan
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathy J Helzlsouer
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Barcelona, Spain
- Hospital del Mar Institute of Medical Research, Universitat Autònoma de Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Robert J Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Loic LeMarchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center, Madrid, Spain
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Roger Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
| | - Rachel E Neale
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ofure Obazee
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alpa V Patel
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Miquel Porta
- CIBER Epidemiología y Salud Pública, Barcelona, Spain
- Hospital del Mar Institute of Medical Research, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer, Lyon, France
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Howard D Sesso
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gianluca Severi
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Facultés de Medicine, Université Paris-Saclay, UPS, UVSQ, Gustave Roussy, Villejuif, France
| | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Debra Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Malin Sund
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Hellenic Health Foundation, Athens, Greece
| | - Mark D Thornquist
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Geoffrey S Tobias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kevin Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Eric J Jacobs
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rachael Z Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jill P Smith
- Department of Medicine, Georgetown University, Washington, DC, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laufey T Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
14
|
Yuan F, Hung RJ, Walsh N, Zhang H, Platz EA, Wheeler W, Song L, Arslan AA, Beane Freeman LE, Bracci P, Canzian F, Du M, Gallinger S, Giles GG, Goodman PJ, Kooperberg C, Le Marchand L, Neale RE, Rosendahl J, Scelo G, Shu XO, Visvanathan K, White E, Zheng W, Albanes D, Amiano P, Andreotti G, Babic A, Bamlet WR, Berndt SI, Brennan P, Bueno-de-Mesquita B, Buring JE, Campbell PT, Chanock SJ, Fuchs CS, Gaziano JM, Goggins MG, Hackert T, Hartge P, Hassan MM, Holly EA, Hoover RN, Katzke V, Kirsten H, Kurtz RC, Lee IM, Malats N, Milne RL, Murphy N, Ng K, Oberg AL, Porta M, Rabe KG, Real FX, Rothman N, Sesso HD, Silverman DT, Thompson IM, Wactawski-Wende J, Wang X, Wentzensen N, Wilkens LR, Yu H, Zeleniuch-Jacquotte A, Shi J, Duell EJ, Amundadottir LT, Li D, Petersen GM, Wolpin BM, Risch HA, Yu K, Klein AP, Stolzenberg-Solomon R. Genome-Wide Association Study Data Reveal Genetic Susceptibility to Chronic Inflammatory Intestinal Diseases and Pancreatic Ductal Adenocarcinoma Risk. Cancer Res 2020; 80:4004-4013. [PMID: 32641412 PMCID: PMC7861352 DOI: 10.1158/0008-5472.can-20-0447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/27/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022]
Abstract
Registry-based epidemiologic studies suggest associations between chronic inflammatory intestinal diseases and pancreatic ductal adenocarcinoma (PDAC). As genetic susceptibility contributes to a large proportion of chronic inflammatory intestinal diseases, we hypothesize that the genomic regions surrounding established genome-wide associated variants for these chronic inflammatory diseases are associated with PDAC. We examined the association between PDAC and genomic regions (±500 kb) surrounding established common susceptibility variants for ulcerative colitis, Crohn's disease, inflammatory bowel disease, celiac disease, chronic pancreatitis, and primary sclerosing cholangitis. We analyzed summary statistics from genome-wide association studies data for 8,384 cases and 11,955 controls of European descent from two large consortium studies using the summary data-based adaptive rank truncated product method to examine the overall association of combined genomic regions for each inflammatory disease group. Combined genomic susceptibility regions for ulcerative colitis, Crohn disease, inflammatory bowel disease, and chronic pancreatitis were associated with PDAC at P values < 0.05 (0.0040, 0.0057, 0.011, and 3.4 × 10-6, respectively). After excluding the 20 PDAC susceptibility regions (±500 kb) previously identified by GWAS, the genomic regions for ulcerative colitis, Crohn disease, and inflammatory bowel disease remained associated with PDAC (P = 0.0029, 0.0057, and 0.0098, respectively). Genomic regions for celiac disease (P = 0.22) and primary sclerosing cholangitis (P = 0.078) were not associated with PDAC. Our results support the hypothesis that genomic regions surrounding variants associated with inflammatory intestinal diseases, particularly, ulcerative colitis, Crohn disease, inflammatory bowel disease, and chronic pancreatitis are associated with PDAC. SIGNIFICANCE: The joint effects of common variants in genomic regions containing susceptibility loci for inflammatory bowel disease and chronic pancreatitis are associated with PDAC and may provide insights to understanding pancreatic cancer etiology.
Collapse
Affiliation(s)
- Fangcheng Yuan
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, Ontario, Canada
| | - Naomi Walsh
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - William Wheeler
- Information Management Services, Inc., Silver Spring, Maryland
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, New York, USA
- Department of Population Health, New York University School of Medicine, New York, New York
- Department of Environmental Medicine, New York University School of Medicine, New York, New York
- Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | | | - Paige Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, Ontario, Canada
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Loic Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Rachel E Neale
- Department of Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jonas Rosendahl
- Department of Internal Medicine I, Martin Luther University, Halle, Germany
| | | | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Emily White
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Pilar Amiano
- Public Health Division of Gipuzkoa, Ministry of Health of the Basque Government, Donostia-San Sebastian, Spain
- Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | | | - Ana Babic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, the Netherlands
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
- Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Julie E Buring
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Charles S Fuchs
- Yale Cancer Center, New Haven, Connecticut
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut
- Smilow Cancer Hospital, New Haven, Connecticut
| | - J Michael Gaziano
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Boston Veteran Affairs Healthcare System, Boston, Massachusetts
| | - Michael G Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Manal M Hassan
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Verena Katzke
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE-Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Robert C Kurtz
- Gastroenterology, Hepatology, and Nutrition Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - I-Min Lee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Nuria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Neil Murphy
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Miquel Porta
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Hospital del Mar Institute of Medical Research (IMIM), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Kari G Rabe
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Francisco X Real
- CIBERONC, Madrid, Spain
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre, Madrid, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Howard D Sesso
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Debra T Silverman
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Ian M Thompson
- CHRISTUS Santa Rosa Hospital - Medical Center, San Antonio, Texas
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, New York
| | - Xiaoliang Wang
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, New York
- Department of Environmental Medicine, New York University School of Medicine, New York, New York
- Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), Barcelona, Spain
| | | | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Alison P Klein
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | |
Collapse
|
15
|
Genome-Wide Association Study and Pathway Analysis for Heterophil/Lymphocyte (H/L) Ratio in Chicken. Genes (Basel) 2020; 11:genes11091005. [PMID: 32867375 PMCID: PMC7563235 DOI: 10.3390/genes11091005] [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: 07/12/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 12/27/2022] Open
Abstract
Disease control and prevention have been critical factors in the dramatic growth of the poultry industry. Disease resistance in chickens can be improved through genetic selection for immunocompetence. The heterophil/lymphocyte ratio (H/L) in the blood reflects the immune system status of chickens. Our objective was to conduct a genome-wide association study (GWAS) and pathway analysis to identify possible biological mechanisms involved in H/L traits. In this study, GWAS for H/L was performed in 1317 Cobb broilers to identify significant single-nucleotide polymorphisms (SNPs) associated with H/L. Eight SNPs (p < 1/8068) reached a significant level of association. The significant SNP on GGA 19 (chicken chromosome 19) was in the gene for complement C1q binding protein (C1QBP). The wild-type and mutant individuals showed significant differences in H/L at five identified SNPs (p < 0.05). According to the results of pathway analysis, nine associated pathways (p < 0.05) were identified. By combining GWAS with pathway analysis, we found that all SNPs after QC explained 12.4% of the phenotypic variation in H/L, and 52 SNPs associated with H/L explained as much as 9.7% of the phenotypic variation in H/L. Our findings contribute to understanding of the genetic regulation of H/L and provide theoretical support.
Collapse
|
16
|
Ni J, Deng B, Zhu M, Wang Y, Yan C, Wang T, Liu Y, Li G, Ding Y, Jin G. Integration of GWAS and eQTL Analysis to Identify Risk Loci and Susceptibility Genes for Gastric Cancer. Front Genet 2020; 11:679. [PMID: 32754194 PMCID: PMC7366424 DOI: 10.3389/fgene.2020.00679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/03/2020] [Indexed: 02/05/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified several susceptibility loci for gastric cancer (GC), but the majority of identified single-nucleotide polymorphisms (SNPs) fall within the non-coding region and are likely to exert their biological function by modulating gene expression. To systematically estimate expression-associated SNPs (eSNPs) that confer genetic predisposition to GC, we evaluated the associations of 314,203 stomach tissue-specific eSNPs with GC risk in three GWAS datasets (2,631 cases and 4,373 controls). Subsequently, we conducted a gene-based analysis to calculate the cumulative effect of eSNPs through sequence kernel association combined test and Sherlock integrative analysis. At the SNP-level, we identified two novel variants (rs836545 at 7p22.1 and rs1892252 at 6p22.2) associated with GC risk. The risk allele carriers of rs836545-T and rs1892252-G exhibited higher expression levels of DAGLB (P = 3.70 × 10–18) and BTN3A2 (P = 3.20 × 10–5), respectively. Gene-based analyses identified DAGLB and FBXO43 as novel susceptibility genes for GC. DAGLB and FBXO43 were significantly overexpressed in GC tissues than in their adjacent tissues (P = 5.59 × 10–7 and P = 3.90 × 10–6, respectively), and high expression level of these two genes was associated with an unfavorable prognosis of GC patients (P = 1.30 × 10–7 and P = 7.60 × 10–3, respectively). Co-expression genes with these two novel genes in normal stomach tissues were significantly enriched in several cancer-related pathways, including P53, MAPK and TGF-beta pathways. In summary, our findings confirm the importance of eSNPs in dissecting the genetic basis of GC, and the identified eSNPs and relevant genes will provide new insight into the genetic and biological basis for the mechanism of GC development.
Collapse
Affiliation(s)
- Jing Ni
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Bin Deng
- Department of Gastroenterology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yuzhuo Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Caiwang Yan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Tianpei Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yaqian Liu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Gang Li
- Department of General Surgery, Jiangsu Institute of Cancer Research, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yanbing Ding
- Department of Gastroenterology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| |
Collapse
|
17
|
Zhao LL, Liu HL, Luo S, Walsh KM, Li W, Wei Q. Associations of novel variants in PIK3C3, INSR and MAP3K4 of the ATM pathway genes with pancreatic cancer risk. Am J Cancer Res 2020; 10:2128-2144. [PMID: 32775006 PMCID: PMC7407350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023] Open
Abstract
The ATM serine/threonine kinase (ATM) pathway plays important roles in pancreatic cancer (PanC) development and progression, but the roles of genetic variants of the genes in this pathway in the etiology of PanC are unknown. In the present study, we assessed associations between 31,499 single nucleotide polymorphisms (SNPs) in 198 ATM pathway-related genes and PanC risk using genotyping data from two previously published PanC genome-wide association studies (GWASs) of 15,423 subjects of European ancestry. In multivariable logistic regression analysis, we identified three novel independent SNPs to be significantly associated with PanC risk [PIK3C3 rs76692125 G>A: odds ratio (OR)=1.26, 95% confidence interval (CI)=1.12-1.43 and P=2.07×10-4, INSR rs11668724 G>A: OR=0.89, 95% CI=0.84-0.94 and P=4.21×10-5 and MAP3K4 rs13207108 C>T: OR=0.83, 95% CI=0.75-0.92, P=2.26×10-4]. The combined analysis of these three SNPs exhibited an increased PanC risk in a dose-response manner as the number of unfavorable genotypes increased (P trend<0.0001). The risk-associated rs76692125 A allele was correlated with decreased PIK3C3 mRNA expression levels, while the protective-associated rs11668724 A allele was correlated with increased INSR mRNA expression levels, but additional mechanistic studies of these SNPs are warranted. Once validated, these SNPs may serve as biomarkers for PanC risk in populations of European ancestry.
Collapse
Affiliation(s)
- Ling-Ling Zhao
- Cancer Center, The First Hospital of Jilin UniversityChangchun, China
- Duke Cancer Institute, Duke University Medical CenteDurham, NC, USA
- Department of Medicine, Duke University School of MedicineDurham, NC, USA
| | - Hong-Liang Liu
- Duke Cancer Institute, Duke University Medical CenteDurham, NC, USA
- Department of Medicine, Duke University School of MedicineDurham, NC, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of MedicineDurham, NC, USA
| | - Kyle M Walsh
- Duke Cancer Institute, Duke University Medical CenteDurham, NC, USA
- Department of Neurosurgery, Duke University School of MedicineDurham, NC, USA
| | - Wei Li
- Cancer Center, The First Hospital of Jilin UniversityChangchun, China
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical CenteDurham, NC, USA
- Department of Medicine, Duke University School of MedicineDurham, NC, USA
- Department of Population Health Sciences, Duke University School of MedicineDurham, NC, USA
| |
Collapse
|
18
|
Nelson SR, Walsh N. Genetic Alterations Featuring Biological Models to Tailor Clinical Management of Pancreatic Cancer Patients. Cancers (Basel) 2020; 12:E1233. [PMID: 32423157 PMCID: PMC7281628 DOI: 10.3390/cancers12051233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related death worldwide. This high mortality rate is due to the disease's lack of symptoms, resulting in a late diagnosis. Biomarkers and treatment options for pancreatic cancer are also limited. In order to overcome this, new research models and novel approaches to discovering PDAC biomarkers are required. In this review, we outline the hereditary and somatic causes of PDAC and provide an overview of the recent genome wide association studies (GWAS) and pathway analysis studies. We also provide a summary of some of the systems used to study PDAC, including established and primary cell lines, patient-derived xenografts (PDX), and newer models such as organoids and organ-on-chip. These ex vitro laboratory systems allow for critical research into the development and progression of PDAC.
Collapse
Affiliation(s)
| | - Naomi Walsh
- National Institute for Cellular Biotechnology, School of Biotechnology, Dublin City University, Dublin 9, Ireland;
| |
Collapse
|
19
|
Gong R, Jiang Y. Non-coding RNAs in Pancreatic Ductal Adenocarcinoma. Front Oncol 2020; 10:309. [PMID: 32257946 PMCID: PMC7089935 DOI: 10.3389/fonc.2020.00309] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/20/2020] [Indexed: 12/15/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are reported to be expressed in human cancers, including pancreatic ductal adenocarcinoma (PDAC). These ncRNAs affect the growth, migration and invasion of tumor cells by regulating cell cycle and apoptosis, as well as playing important roles in epigenetic processes, transcription and post-transcriptional regulation. It is still unclear whether alterations in ncRNAs influence PDAC development and progression. Because of this, analysis based on existing data on ncRNAs, which are crucial for modulating pancreatic tumorigenesis, will be important for future research on PDAC. Here, we summarize ncRNAs with tumor-promoting functions: HOTAIR, HOTTIP, MALAT1, lncRNA H19, lncRNA PVT1, circ-RNA ciRS-7, circ-0030235, circ-RNA_100782, circ-LDLRAD3, circ-0007534, circRHOT1, circZMYM2, circ-IARS, circ-RNA PDE8A, miR-21, miR-155, miR-221/222, miR-196b, miR-10a. While others including GAS5, MEG3, and lncRNA ENST00000480739, has_circ_0001649, miR-34a, miR-100, miR-217, miR-143 inhibit the proliferation and invasion of PDAC. Hence, we summarize the functions of ncRNAs in the occurrence, development and metastasis of PDAC, with the goal to provide guidance in the clinical diagnosis and treatment of PDAC.
Collapse
Affiliation(s)
- Ruining Gong
- Department of Gastroenterology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yueping Jiang
- Department of Gastroenterology, Affiliated Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
20
|
Xu Q, Wu N, Li X, Guo C, Li C, Jiang B, Wang H, Shi D. Inhibition of PTP1B blocks pancreatic cancer progression by targeting the PKM2/AMPK/mTOC1 pathway. Cell Death Dis 2019; 10:874. [PMID: 31745071 PMCID: PMC6864061 DOI: 10.1038/s41419-019-2073-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/27/2019] [Accepted: 09/03/2019] [Indexed: 02/08/2023]
Abstract
Pancreatic cancer is a highly malignant cancer and lacks effective therapeutic targets. Protein-tyrosine phosphatase 1B (PTP1B), a validated therapeutic target for diabetes and obesity, also plays a critical positive or negative role in tumorigenesis. However, the role of PTP1B in pancreatic cancer remains elusive. Here, we initially demonstrated that PTP1B was highly expressed in pancreatic tumors, and was positively correlated with distant metastasis and tumor staging, and indicated poor survival. Then, inhibition of PTP1B either by shRNA or by a specific small-molecule inhibitor significantly suppressed pancreatic cancer cell growth, migration and colony formation with cell cycle arrest in vitro and inhibited pancreatic cancer progression in vivo. Mechanism studies revealed that PTP1B targeted the PKM2/AMPK/mTOC1 signaling pathway to regulate cell growth. PTP1B inhibition directly increased PKM2 Tyr-105 phosphorylation to further result in significant activation of AMPK, which decreased mTOC1 activity and led to inhibition of p70S6K. Meanwhile, the decreased phosphorylation of PRAS40 caused by decreased PKM2 activity also helped to inhibit mTOC1. Collectively, these findings support the notion of PTP1B as an oncogene and a promising therapeutic target for PDAC.
Collapse
MESH Headings
- AMP-Activated Protein Kinases/antagonists & inhibitors
- AMP-Activated Protein Kinases/metabolism
- Animals
- Carcinoma, Pancreatic Ductal/metabolism
- Carcinoma, Pancreatic Ductal/pathology
- Carcinoma, Pancreatic Ductal/therapy
- Carrier Proteins/antagonists & inhibitors
- Carrier Proteins/metabolism
- Cell Line, Tumor
- Disease Progression
- Female
- Humans
- Male
- Mechanistic Target of Rapamycin Complex 1/antagonists & inhibitors
- Mechanistic Target of Rapamycin Complex 1/metabolism
- Membrane Proteins/antagonists & inhibitors
- Membrane Proteins/metabolism
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/pathology
- Pancreatic Neoplasms/therapy
- Protein Tyrosine Phosphatase, Non-Receptor Type 1/antagonists & inhibitors
- Protein Tyrosine Phosphatase, Non-Receptor Type 1/biosynthesis
- Protein Tyrosine Phosphatase, Non-Receptor Type 1/genetics
- Protein Tyrosine Phosphatase, Non-Receptor Type 1/metabolism
- RNA, Small Interfering/administration & dosage
- RNA, Small Interfering/genetics
- Random Allocation
- Signal Transduction/drug effects
- Small Molecule Libraries/pharmacology
- Thyroid Hormones/metabolism
- Xenograft Model Antitumor Assays
- Thyroid Hormone-Binding Proteins
Collapse
Affiliation(s)
- Qi Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- The University of Chinese Academy of Sciences, Beijing, China
| | - Ning Wu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiangqian Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, Shandong, China
- The University of Chinese Academy of Sciences, Beijing, China
| | - Chuanlong Guo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- The University of Chinese Academy of Sciences, Beijing, China
| | - Chao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- The University of Chinese Academy of Sciences, Beijing, China
| | - Bo Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Huaizhi Wang
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China.
| | - Dayong Shi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, Shandong, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- The University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|