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Yang T, Mills LJ, Hubbard AK, Cao R, Raduski A, Machiela MJ, Spector LG. Genetic analyses identify evidence for a causal relationship between Ewing sarcoma and hernias. HGG ADVANCES 2024; 5:100254. [PMID: 37919896 PMCID: PMC10692953 DOI: 10.1016/j.xhgg.2023.100254] [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: 08/01/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023] Open
Abstract
Knowledge of Ewing sarcoma (EWS) risk factors is exceedingly limited; however, multiple small, independent studies have suggested a possible connection between hernia and EWS. By leveraging hernia summary statistics from the UK Biobank and a recently published genome-wide association study of EWS (733 EWS cases and 1,346 controls), we conducted a genetic investigation of the relationship of 5 hernia types (diaphragmatic, inguinal, umbilical, femoral, and ventral) and EWS. We discovered a positive causal relationship between inguinal hernia and EWS (OR 1.27, 95% confidence interval [CI] 1.01-1.59, and p = 0.041) through Mendelian randomization analysis. Further analyses suggested shared pathways through three genes: HMGA2, LOX, and FBXW7. Diaphragmatic hernia showed a stronger causal relationship with EWS among all of the hernia types (OR 2.26, 95% CI 1.30-3.95, p = 0.004), but no statistically significant local correlation pattern was observed. No evidence of a causal or genetic relationship was observed between EWS and the other three hernia types, including umbilical hernia, despite a previous report indicating an OR as high as 3.3. The finding of our genetic analysis provided additional support to the hypothesis that EWS and hernias may share a common origin.
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Affiliation(s)
- Tianzhong Yang
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, MN, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lauren J Mills
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aubrey K Hubbard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Rui Cao
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Andrew Raduski
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Logan G Spector
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA.
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Monte AA, Vest A, Reisz JA, Berninzoni D, Hart C, Dylla L, D'Alessandro A, Heard KJ, Wood C, Pattee J. A Multi-Omic Mosaic Model of Acetaminophen Induced Alanine Aminotransferase Elevation. J Med Toxicol 2023; 19:255-261. [PMID: 37231244 PMCID: PMC10212224 DOI: 10.1007/s13181-023-00951-5] [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: 03/23/2023] [Revised: 05/13/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Acetaminophen (APAP) is the most common cause liver injury following alcohol in US patients. Predicting liver injury and subsequent hepatic regeneration in patients taking therapeutic doses of APAP may be possible using new 'omic methods such as metabolomics and genomics. Multi'omic techniques increase our ability to find new mechanisms of injury and regeneration. METHODS We used metabolomic and genomic data from a randomized controlled trial of patients administered 4 g of APAP per day for 14 days or longer with blood samples obtained at 0 (baseline), 4, 7, 10, 13 and 16 days. We used the highest ALT as the clinical outcome to be predicted in our integrated analysis. We used penalized regression to model the relationship between genetic variants and day 0 metabolite level, and then performed a metabolite-wide colocalization scan to associate the genetically regulated component of metabolite expression with ALT elevation. Genome-wide association study (GWAS) analyses were conducted for ALT elevation and metabolite level using linear regression, with age, sex, and the first five principal components included as covariates. Colocalization was tested via a weighted sum test. RESULTS Out of the 164 metabolites modeled, 120 met the criteria for predictive accuracy and were retained for genetic analyses. After genomic examination, eight metabolites were found to be under genetic control and predictive of ALT elevation due to therapeutic acetaminophen. The metabolites were: 3-oxalomalate, allantoate, diphosphate, L-carnitine, L-proline, maltose, and ornithine. These genes are important in the tricarboxylic acid cycle (TCA), urea breakdown pathway, glutathione production, mitochondrial energy production, and maltose metabolism. CONCLUSIONS This multi'omic approach can be used to integrate metabolomic and genomic data allowing identification of genes that control downstream metabolites. These findings confirm prior work that have identified mitochondrial energy production as critical to APAP induced liver injury and have confirmed our prior work that demonstrate the importance of the urea cycle in therapeutic APAP liver injury.
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Affiliation(s)
- Andrew A Monte
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA.
- Center for Bioinformatics & Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA.
- Skaggs School of Pharmacy, University of Colorado, Aurora, CO, USA.
- Denver Health and Hospital Authority, Rocky Mountain Poison & Drug Center, Denver, CO, USA.
| | - Alexis Vest
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Julie A Reisz
- Metabolomics Core, Department of Biochemistry and Molecular Genetics, University of Colorado-Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Danielle Berninzoni
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Claire Hart
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Layne Dylla
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA
- Center for Bioinformatics & Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Angelo D'Alessandro
- Metabolomics Core, Department of Biochemistry and Molecular Genetics, University of Colorado-Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Kennon J Heard
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA
- Denver Health and Hospital Authority, Rocky Mountain Poison & Drug Center, Denver, CO, USA
| | - Cheyret Wood
- Department of Biostatistics & Informatics, Colorado School of Public Health, University of Colorado-Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Jack Pattee
- Department of Biostatistics & Informatics, Colorado School of Public Health, University of Colorado-Denver Anschutz Medical Campus, Aurora, CO, USA
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Watts EL, Perez-Cornago A, Fensom GK, Smith-Byrne K, Noor U, Andrews CD, Gunter MJ, Holmes MV, Martin RM, Tsilidis KK, Albanes D, Barricarte A, Bueno-de-Mesquita HB, Cohn BA, Deschasaux-Tanguy M, Dimou NL, Ferrucci L, Flicker L, Freedman ND, Giles GG, Giovannucci EL, Haiman CA, Hankey GJ, Holly JMP, Huang J, Huang WY, Hurwitz LM, Kaaks R, Kubo T, Le Marchand L, MacInnis RJ, Männistö S, Metter EJ, Mikami K, Mucci LA, Olsen AW, Ozasa K, Palli D, Penney KL, Platz EA, Pollak MN, Roobol MJ, Schaefer CA, Schenk JM, Stattin P, Tamakoshi A, Thysell E, Tsai CJ, Touvier M, Van Den Eeden SK, Weiderpass E, Weinstein SJ, Wilkens LR, Yeap BB. Circulating insulin-like growth factors and risks of overall, aggressive and early-onset prostate cancer: a collaborative analysis of 20 prospective studies and Mendelian randomization analysis. Int J Epidemiol 2023; 52:71-86. [PMID: 35726641 PMCID: PMC9908067 DOI: 10.1093/ije/dyac124] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Previous studies had limited power to assess the associations of circulating insulin-like growth factors (IGFs) and IGF-binding proteins (IGFBPs) with clinically relevant prostate cancer as a primary endpoint, and the association of genetically predicted IGF-I with aggressive prostate cancer is not known. We aimed to investigate the associations of IGF-I, IGF-II, IGFBP-1, IGFBP-2 and IGFBP-3 concentrations with overall, aggressive and early-onset prostate cancer. METHODS Prospective analysis of biomarkers using the Endogenous Hormones, Nutritional Biomarkers and Prostate Cancer Collaborative Group dataset (up to 20 studies, 17 009 prostate cancer cases, including 2332 aggressive cases). Odds ratios (OR) and 95% confidence intervals (CI) for prostate cancer were estimated using conditional logistic regression. For IGF-I, two-sample Mendelian randomization (MR) analysis was undertaken using instruments identified using UK Biobank (158 444 men) and outcome data from PRACTICAL (up to 85 554 cases, including 15 167 aggressive cases). Additionally, we used colocalization to rule out confounding by linkage disequilibrium. RESULTS In observational analyses, IGF-I was positively associated with risks of overall (OR per 1 SD = 1.09: 95% CI 1.07, 1.11), aggressive (1.09: 1.03, 1.16) and possibly early-onset disease (1.11: 1.00, 1.24); associations were similar in MR analyses (OR per 1 SD = 1.07: 1.00, 1.15; 1.10: 1.01, 1.20; and 1.13; 0.98, 1.30, respectively). Colocalization also indicated a shared signal for IGF-I and prostate cancer (PP4: 99%). Men with higher IGF-II (1.06: 1.02, 1.11) and IGFBP-3 (1.08: 1.04, 1.11) had higher risks of overall prostate cancer, whereas higher IGFBP-1 was associated with a lower risk (0.95: 0.91, 0.99); these associations were attenuated following adjustment for IGF-I. CONCLUSIONS These findings support the role of IGF-I in the development of prostate cancer, including for aggressive disease.
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Affiliation(s)
- Eleanor L Watts
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Aurora Perez-Cornago
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Georgina K Fensom
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Karl Smith-Byrne
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Urwah Noor
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Colm D Andrews
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Michael V Holmes
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Richard M Martin
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and Weston NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Konstantinos K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Aurelio Barricarte
- Group of Epidemiology of Cancer and Other Chronic Diseases, Navarra Public Health Institute, Pamplona, Spain
- Group of Epidemiology of Cancer and Other Chronic Diseases, Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- CIBER Epidemiology and Public Health CIBERESP, Madrid, Spain
| | - H Bas Bueno-de-Mesquita
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment (RIVM), Utrecht, The Netherlands
| | - Barbara A Cohn
- Child Health and Development Studies, Public Health Institute, Berkeley, CA, USA
| | - Melanie Deschasaux-Tanguy
- Sorbonne Paris Nord University, Nutritional Epidemiology Research Team, Epidemiology and Statistics Research Center, University of Paris, Bobigny, France
| | - Niki L Dimou
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | | | - Leon Flicker
- WA Centre for Health & Ageing, Medical School, University of Western Australia, Perth, WA, Australia
- Western Australian Centre for Health and Ageing, University of Western Australia, Perth, WA, Australia
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Graham J Hankey
- WA Centre for Health & Ageing, Medical School, University of Western Australia, Perth, WA, Australia
| | - Jeffrey M P Holly
- IGFs & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jiaqi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lauren M Hurwitz
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tatsuhiko Kubo
- Department of Public Health and Health Policy, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | | | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
| | - Satu Männistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - E Jeffrey Metter
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kazuya Mikami
- Departmemt of Urology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anja W Olsen
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Cancer Society, Research Center, Copenhagen, Denmark
| | - Kotaro Ozasa
- Departmemt of Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Domenico Palli
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network, Florence, Italy
| | - Kathryn L Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Michael N Pollak
- Departments of Medicine and Oncology, McGill University, Montreal, QC, Canada
| | - Monique J Roobol
- Department of Urology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Jeannette M Schenk
- Cancer Prevention Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Pär Stattin
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Akiko Tamakoshi
- Department of Public Health, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Elin Thysell
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Chiaojung Jillian Tsai
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mathilde Touvier
- Sorbonne Paris Nord University, Nutritional Epidemiology Research Team, Epidemiology and Statistics Research Center, University of Paris, Bobigny, France
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
- Department of Urology, University of CaliforniaSan Francisco, San Francisco, CA, USA
| | - Elisabete Weiderpass
- Director’s Office, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Bu B Yeap
- WA Centre for Health & Ageing, Medical School, University of Western Australia, Perth, WA, Australia
- Department of Endocrinology and Diabetes, Fiona Stanley Hospital, Perth, WA, Australia
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Adam Y, Samtal C, Brandenburg JT, Falola O, Adebiyi E. Performing post-genome-wide association study analysis: overview, challenges and recommendations. F1000Res 2021; 10:1002. [PMID: 35222990 PMCID: PMC8847724 DOI: 10.12688/f1000research.53962.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies (GWAS) provide huge information on statistically significant single-nucleotide polymorphisms (SNPs) associated with various human complex traits and diseases. By performing GWAS studies, scientists have successfully identified the association of hundreds of thousands to millions of SNPs to a single phenotype. Moreover, the association of some SNPs with rare diseases has been intensively tested. However, classic GWAS studies have not yet provided solid, knowledgeable insight into functional and biological mechanisms underlying phenotypes or mechanisms of diseases. Therefore, several post-GWAS (pGWAS) methods have been recommended. Currently, there is no simple scientific document to provide a quick guide for performing pGWAS analysis. pGWAS is a crucial step for a better understanding of the biological machinery beyond the SNPs. Here, we provide an overview to performing pGWAS analysis and demonstrate the challenges behind each method. Furthermore, we direct readers to key articles for each pGWAS method and present the overall issues in pGWAS analysis. Finally, we include a custom pGWAS pipeline to guide new users when performing their research.
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Affiliation(s)
- Yagoub Adam
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun, 112233, Nigeria
| | - Chaimae Samtal
- Laboratory of Biotechnology, Environment, Agri-food and Health, Sidi Mohammed Ben Abdellah University, Fez, Fez-Meknes, 30000, Morocco
| | - Jean-tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa
| | - Oluwadamilare Falola
- Laboratory of Biotechnology, Environment, Agri-food and Health, Sidi Mohammed Ben Abdellah University, Fez, Fez-Meknes, 30000, Morocco
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun, 112233, Nigeria
- Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence, Covenant University, Ota, Ogun, 112233, Nigeria
- Applied Bioinformatics Division, German Cancer Center DKFZ - Heidelberg University, Heidelberg, Baden-Württemberg, 69120, Germany
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