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Ollila HM, Sinnott-Armstrong N, Kantojärvi K, Broberg M, Palviainen T, Jones S, Ripatti V, Pandit A, Rong R, Kristiansson K, Sandman N, Valli K, Hublin C, Ripatti S, Widen E, Kaprio J, Saxena R, Paunio T. Nightmares share genetic risk factors with sleep and psychiatric traits. Transl Psychiatry 2024; 14:123. [PMID: 38413574 PMCID: PMC10899618 DOI: 10.1038/s41398-023-02637-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/08/2023] [Accepted: 10/23/2023] [Indexed: 02/29/2024] Open
Abstract
Nightmares are vivid, extended, and emotionally negative or negative dreams that awaken the dreamer. While sporadic nightmares and bad dreams are common and generally harmless, frequent nightmares often reflect underlying pathologies of emotional regulation. Indeed, insomnia, depression, anxiety, or alcohol use have been associated with nightmares in epidemiological and clinical studies. However, the connection between nightmares and their comorbidities are poorly understood. Our goal was to examine the genetic risk factors for nightmares and estimate correlation or causality between nightmares and comorbidities. We performed a genome-wide association study (GWAS) in 45,255 individuals using a questionnaire-based assessment on the frequency of nightmares during the past month and genome-wide genotyping data. While the GWAS did not reveal individual risk variants, heritability was estimated at 5%. In addition, the genetic correlation analysis showed a robust correlation (rg > 0.4) of nightmares with anxiety (rg = 0.671, p = 7.507e-06), depressive (rg = 0.562, p = 1.282e-07) and posttraumatic stress disorders (rg = 0.4083, p = 0.0152), and personality trait neuroticism (rg = 0.667, p = 4.516e-07). Furthermore, Mendelian randomization suggested causality from insomnia to nightmares (beta = 0.027, p = 0.0002). Our findings suggest that nightmares share genetic background with psychiatric traits and that insomnia may increase an individual's liability to experience frequent nightmares. Given the significant correlations with psychiatric and psychological traits, it is essential to grow awareness of how nightmares affect health and disease and systematically collect information about nightmares, especially from clinical samples and larger cohorts.
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Affiliation(s)
- Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Katri Kantojärvi
- Population Health, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Martin Broberg
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Samuel Jones
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Vili Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Anita Pandit
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Robin Rong
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kati Kristiansson
- Population Health, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Nils Sandman
- Department of Psychology and Speech-Language Pathology, and Turku Brain and Mind Center, University of Turku, Turku, Finland
| | - Katja Valli
- Department of Psychology and Speech-Language Pathology, and Turku Brain and Mind Center, University of Turku, Turku, Finland
- Department of Cognitive Neuroscience and Philosophy, University of Skövde, Skövde, Sweden
| | | | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Richa Saxena
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Tiina Paunio
- Population Health, Finnish Institute for Health and Welfare, Helsinki, Finland.
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
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Shoham M, Yiu YY, Hansen PS, Subramaniam A, Broberg M, Gars E, Raveh T, FinnGen, Weissman IL, Sinnott-Armstrong N, Krishnan A, Ollila HM, Tal MC. SIRPα controls CD47-dependent platelet clearance in mice and humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.09.570874. [PMID: 38106070 PMCID: PMC10723388 DOI: 10.1101/2023.12.09.570874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Over the last decade, more data has revealed that increased surface expression of the "don't eat me" CD47 protein on cancer cells plays a role in immune evasion and tumor progression, with CD47 blockade emerging as a new therapy in immuno-oncology. CD47 is critical in regulating cell homeostasis and clearance, as binding of CD47 to the inhibitory receptor SIRPα can prevent phagocytosis and macrophage-mediated cell clearance. The purpose of this study was to examine the role of the CD47-SIRPα signal in platelet homeostasis and clearance. Therapeutic reagents targeting the CD47-SIRPα axis are very promising for treatment of hematologic malignancies and solid tumors, but lead to transient anemia or thrombocytopenia in a subset of patients. We found that platelet homeostatic clearance is regulated through the CD47-SIRPα axis and that therapeutic blockade to disrupt this interaction in mice and in humans has a significant impact on platelet levels. Furthermore, we identified genetic variations at the SIRPA locus that impact platelet levels in humans such that higher SIRPA gene expression is associated with higher platelet levels. SIRPA expression at either end of the normal range may affect clinical outcomes of treatment with anti-CD47 therapy.
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Affiliation(s)
- Maia Shoham
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Ying Ying Yiu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Paige S. Hansen
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aanya Subramaniam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin Broberg
- Institute for Molecular Medicine, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Eric Gars
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tal Raveh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Nasa Sinnott-Armstrong
- Department of Genetics, Stanford University, Stanford, CA, USA
- Metabolism Program and Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Anandi Krishnan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanna M. Ollila
- Institute for Molecular Medicine, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute for Harvard and MIT, Boston, MA, USA
- Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michal Caspi Tal
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Wang Z, Liu T, Li W, Yu G, Mi Z, Wang C, Liao X, Huai P, Chu T, Liu D, Sun L, Fu X, Sun Y, Wang H, Wang N, Liu J, Liu H, Zhang F. Genome-wide meta-analysis and fine-mapping prioritize potential causal variants and genes related to leprosy. MedComm (Beijing) 2023; 4:e415. [PMID: 38020709 PMCID: PMC10674079 DOI: 10.1002/mco2.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/05/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
To date, genome-wide association studies (GWASs) have discovered 35 susceptible loci of leprosy; however, the cumulative effects of these loci can only partially explain the overall risk of leprosy, and the causal variants and genes within these loci remain unknown. Here, we conducted out new GWASs in two independent cohorts of 5007 cases and 4579 controls and then a meta-analysis in these newly generated and multiple previously published (2277 cases and 3159 controls) datasets were performed. Three novel and 15 previously reported risk loci were identified from these datasets, increasing the known leprosy risk loci of explained genetic heritability from 23.0 to 38.5%. A comprehensive fine-mapping analysis was conducted, and 19 causal variants and 14 causal genes were identified. Specifically, manual checking of epigenomic information from the Epimap database revealed that the causal variants were mainly located within the immune-relevant or immune-specific regulatory elements. Furthermore, by using gene-set, tissue, and cell-type enrichment analyses, we highlighted the key roles of immune-related tissues and cells and implicated the PD-1 signaling pathways in the pathogenetic mechanism of leprosy. Collectively, our study identified candidate causal variants and elucidated the potential regulatory and coding mechanisms for genes associated with leprosy.
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Affiliation(s)
- Zhenzhen Wang
- Department of BiostatisticsSchool of Public HealthCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Tingting Liu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Wenchao Li
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Gongqi Yu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Zihao Mi
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Chuan Wang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Xiaojie Liao
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Pengcheng Huai
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Tongsheng Chu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Dianchang Liu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Lele Sun
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Xi'an Fu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Yonghu Sun
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Honglei Wang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Na Wang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Jianjun Liu
- Department of Human Genetics, Genome Institute of SingaporeSingaporeSingapore
| | - Hong Liu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Furen Zhang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
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Jiang Z, Chen Z, Chen X. Candidate gene-environment interactions in substance abuse: A systematic review. PLoS One 2023; 18:e0287446. [PMID: 37906564 PMCID: PMC10617739 DOI: 10.1371/journal.pone.0287446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 06/06/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND The abuse of psychogenic drugs can lead to multiple health-related problems. Genetic and environmental vulnerabilities are factors in the emergence of substance use disorders. Empirical evidence regarding the gene-environment interaction in substance use is mixed. Summaries of the latest findings from a candidate gene approach will be useful for revealing the significance of particular gene contributions. Thus, we aim to identify different gene-environment interactions in patterns of substance use and investigate whether any effects trend notably across different genders and races. METHODS We reviewed published studies, until March 1, 2022, on substance use for candidate gene-environment interaction. Basic demographics of the included studies, target genes, environmental factors, main findings, patterns of gene-environment interaction, and other relevant information were collected and summarized. RESULTS Among a total of 44 studies, 38 demonstrated at least one significant interaction effect. About 61.5% of studies on the 5-HTTLPR gene, 100% on the MAOA gene, 42.9% on the DRD2 gene, 50% on the DRD4 gene, 50% on the DAT gene, 80% on the CRHR1 gene, 100% on the OPRM1 gene, 100% on the GABRA1 gene, and 50% on the CHRNA gene had a significant gene-environment interaction effect. The diathesis-stress model represents a dominant interaction pattern (89.5%) in the studies with a significant interaction effect; the remaining significant effect on substance use is found in the differential susceptibility model. The social push and swing model were not reported in the included studies. CONCLUSION The gene-environment interaction research on substance use behavior is methodologically multidimensional, which causes difficulty in conducting pooled analysis, or stated differently-making it hard to identify single sources of significant influence over maladaptive patterns of drug taking. In decreasing the heterogeneity and facilitating future pooled analysis, researchers must (1) replicate the existing studies with consistent study designs and measures, (2) conduct power calculations to report gene-environment correlations, (3) control for covariates, and (4) generate theory-based hypotheses with factorial based experiments when designing future studies.
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Affiliation(s)
- Zheng Jiang
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Zidong Chen
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Xi Chen
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
- Department of Sociology and Social Policy, Lingnan University, Tuen Mun, Hong Kong
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Munday RM, Haque R, Wojcik GL, Korpe P, Nayak U, Kirkpatrick BD, Petri WA, Duggal P. Genome-Wide Association Studies of Diarrhea Frequency and Duration in the First Year of Life in Bangladeshi Infants. J Infect Dis 2023; 228:979-989. [PMID: 36967705 PMCID: PMC11007397 DOI: 10.1093/infdis/jiad068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Diarrhea is the second leading cause of death in children under 5 years old worldwide. Known diarrhea risk factors include sanitation, water sources, and pathogens but do not fully explain the heterogeneity in frequency and duration of diarrhea in young children. We evaluated the role of host genetics in diarrhea. METHODS Using 3 well-characterized birth cohorts from an impoverished area of Dhaka, Bangladesh, we compared infants with no diarrhea in the first year of life to those with an abundance, measured by either frequency or duration. We performed a genome-wide association analysis for each cohort under an additive model and then meta-analyzed across the studies. RESULTS For diarrhea frequency, we identified 2 genome-wide significant loci associated with not having any diarrhea, on chromosome 21 within the noncoding RNA AP000959 (C allele odds ratio [OR] = 0.31, P = 4.01 × 10-8), and on chromosome 8 within SAMD12 (T allele OR = 0.35, P = 4.74 × 10-7). For duration of diarrhea, we identified 2 loci associated with no diarrhea, including the same locus on chromosome 21 (C allele OR = 0.31, P = 1.59 × 10-8) and another locus on chromosome 17 near WSCD1 (C allele OR = 0.35, P = 1.09 × 10-7). CONCLUSIONS These loci are in or near genes involved in enteric nervous system development and intestinal inflammation and may be potential targets for diarrhea therapeutics.
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Affiliation(s)
- Rebecca M Munday
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Poonum Korpe
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Uma Nayak
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Beth D Kirkpatrick
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - William A Petri
- Department of Medicine, Infectious Diseases, and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Kumaraguru M, L L, Priyadharsini VJ, I MA, S R. Identification of Pathogenic Missense Mutations in the CHRNA5 Gene: A Computational Approach. Cureus 2023; 15:e47519. [PMID: 38021533 PMCID: PMC10663970 DOI: 10.7759/cureus.47519] [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: 07/31/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Aim The CHRNA5/A3/B4 gene locus is closely related to nicotine dependence and other smoking-related disorders. Coupling genetic and clinical studies of nicotine dependence and smoking behaviors may open new avenues for medication development. The aim of this study is to investigate the functional missense mutations in the CHRNA5 gene. Methodology The Ensembl database was used to gather data on missense mutations of the human CHRNA5 gene. Computational tools viz. SIFT (Sorting Intolerant From Tolerant), PolyPhen (Polymorphism Phenotyping), PROVEAN (Protein Variation Effect Analyzer), I-Mutant, and MutPred were used to uncover the pathogenic mutations in the gene under investigation. Results Among 161 missense variants reported inthe CHRNA5 gene, 94 variants were found to be highly pathogenic. Moreover, 20 were pathogenic and 4 were not pathogenic. Conclusion The computational analysis disclosed harmful mutations in the CHRNA5 gene which could be potentially associated with smoking-related traits.
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Affiliation(s)
- Mahalakshmi Kumaraguru
- Public Health Dentistry, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Leelavathi L
- Public Health Dentistry, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Vijayashree J Priyadharsini
- Clinical Genetics, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Meignana Arumugham I
- Public Health Dentistry, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Rajeshkumar S
- Pharmacology, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
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Bierut L, Biroli P, Galama TJ, Thom K. Challenges in studying the interplay of genes and environment. A study of childhood financial distress moderating genetic predisposition for peak smoking. JOURNAL OF ECONOMIC PSYCHOLOGY 2023; 98:102636. [PMID: 37484514 PMCID: PMC10358858 DOI: 10.1016/j.joep.2023.102636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Smoking is one of the leading causes of preventable disease and death in the U.S., and it is strongly influenced both by genetic predisposition and childhood adversity. Using polygenic indices (PGIs) of predisposition to smoking, we evaluate whether childhood financial distress (CFD; a composite measure of financial adversity) moderates genetic risk in explaining peak-cigarette consumption in adulthood. Using the Health and Retirement Study (HRS), we find a substantial reduction in the relationship between genetic risk and peak smoking for those who did not suffer financial adversity in childhood. Among adult smokers who grew up in high-CFD households, a one standard deviation higher PGI is associated with 2.9 more cigarettes smoked per day at peak. By contrast, among smokers who grew up in low-CFD households, this gradient is reduced by 37 percent (or 1.1 fewer). These results are robust to controlling for a host of prime confounders. By contrast, we find no evidence of interactions between the PGI and typical measures of childhood SES such as parental education - a null result that we replicate in the Wisconsin Longitudinal Study (WLS) and the English Longitudinal Study of Aging (ELSA). This suggests the role of childhood financial distress in the relationship with peak smoking is distinct from that of low childhood SES, with high CFD potentially reflecting more acute distress than do measures of low childhood SES. Our evidence also suggests low childhood SES is a weaker proxy for acute distress, providing an alternative explanation for the childhood SES null result.
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Affiliation(s)
- Laura Bierut
- Washington University School of Medicine, St. Louis, MO, USA
| | - Pietro Biroli
- Department of Economics, University of Bologna, Italy
| | - Titus J Galama
- Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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McLaren PJ, Porreca I, Iaconis G, Mok HP, Mukhopadhyay S, Karakoc E, Cristinelli S, Pomilla C, Bartha I, Thorball CW, Tough RH, Angelino P, Kiar CS, Carstensen T, Fatumo S, Porter T, Jarvis I, Skarnes WC, Bassett A, DeGorter MK, Sathya Moorthy MP, Tuff JF, Kim EY, Walter M, Simons LM, Bashirova A, Buchbinder S, Carrington M, Cossarizza A, De Luca A, Goedert JJ, Goldstein DB, Haas DW, Herbeck JT, Johnson EO, Kaleebu P, Kilembe W, Kirk GD, Kootstra NA, Kral AH, Lambotte O, Luo M, Mallal S, Martinez-Picado J, Meyer L, Miro JM, Moodley P, Motala AA, Mullins JI, Nam K, Obel N, Pirie F, Plummer FA, Poli G, Price MA, Rauch A, Theodorou I, Trkola A, Walker BD, Winkler CA, Zagury JF, Montgomery SB, Ciuffi A, Hultquist JF, Wolinsky SM, Dougan G, Lever AML, Gurdasani D, Groom H, Sandhu MS, Fellay J. Africa-specific human genetic variation near CHD1L associates with HIV-1 load. Nature 2023; 620:1025-1030. [PMID: 37532928 PMCID: PMC10848312 DOI: 10.1038/s41586-023-06370-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/26/2023] [Indexed: 08/04/2023]
Abstract
HIV-1 remains a global health crisis1, highlighting the need to identify new targets for therapies. Here, given the disproportionate HIV-1 burden and marked human genome diversity in Africa2, we assessed the genetic determinants of control of set-point viral load in 3,879 people of African ancestries living with HIV-1 participating in the international collaboration for the genomics of HIV3. We identify a previously undescribed association signal on chromosome 1 where the peak variant associates with an approximately 0.3 log10-transformed copies per ml lower set-point viral load per minor allele copy and is specific to populations of African descent. The top associated variant is intergenic and lies between a long intergenic non-coding RNA (LINC00624) and the coding gene CHD1L, which encodes a helicase that is involved in DNA repair4. Infection assays in iPS cell-derived macrophages and other immortalized cell lines showed increased HIV-1 replication in CHD1L-knockdown and CHD1L-knockout cells. We provide evidence from population genetic studies that Africa-specific genetic variation near CHD1L associates with HIV replication in vivo. Although experimental studies suggest that CHD1L is able to limit HIV infection in some cell types in vitro, further investigation is required to understand the mechanisms underlying our observations, including any potential indirect effects of CHD1L on HIV spread in vivo that our cell-based assays cannot recapitulate.
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Affiliation(s)
- Paul J McLaren
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.
| | | | - Gennaro Iaconis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hoi Ping Mok
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Subhankar Mukhopadhyay
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - István Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian W Thorball
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Riley H Tough
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Paolo Angelino
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Cher S Kiar
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Tommy Carstensen
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Department of Non-Communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Isobel Jarvis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marianne K DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mohana Prasad Sathya Moorthy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey F Tuff
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Eun-Young Kim
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Miriam Walter
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lacy M Simons
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea De Luca
- University Division of Infectious Diseases, Siena University Hospital, Siena, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - James J Goedert
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Eric O Johnson
- GenOmics and Translational Research Center and Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex H Kral
- Community Health Research Division, RTI International, Berkeley, CA, USA
| | - Olivier Lambotte
- Université Paris Saclay, Inserm UMR1184, CEA, Le Kremlin-Bicêtre, France
- APHP, Department of Clinical Immunology, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Vaccine and Therapeutics Laboratory, Medical and Scientific Affairs, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Simon Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Javier Martinez-Picado
- University of Vic-Central University of Catalonia, Vic, Spain
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Laurence Meyer
- INSERM U1018, Université Paris-Saclay, Le Kremlin Bicêtre, France
- AP-HP, Hôpital de Bicêtre, Département d'Épidémiologie, Le Kremlin Bicêtre, France
| | - José M Miro
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases Service, Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Pravi Moodley
- National Health Laboratory Service, South Africa and University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha A Motala
- Department of Diabetes and Endocrinology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kireem Nam
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Niels Obel
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Guido Poli
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Matthew A Price
- International AIDS Vaccine Initiative, New York, NY, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ioannis Theodorou
- Laboratoire d'Immunologie, Hôpital Robert Debré Paris, Paris, France
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Frederick National Laboratory for Cancer Research and Cancer Innovative Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Judd F Hultquist
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Deepti Gurdasani
- Queen Mary University of London, London, UK
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Harriet Groom
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Manjinder S Sandhu
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK.
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.
- Omnigen Biodata, Cambridge, UK.
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland.
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9
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Chen Z, Liu XA, Kenny PJ. Central and peripheral actions of nicotine that influence blood glucose homeostasis and the development of diabetes. Pharmacol Res 2023; 194:106860. [PMID: 37482325 DOI: 10.1016/j.phrs.2023.106860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/06/2023] [Accepted: 07/18/2023] [Indexed: 07/25/2023]
Abstract
Cigarette smoking has long been recognized as a risk factor for type 2 diabetes (T2D), although the precise causal mechanisms underlying this relationship remain poorly understood. Recent evidence suggests that nicotine, the primary reinforcing component in tobacco, may play a pivotal role in connecting cigarette smoking and T2D. Extensive research conducted in both humans and animals has demonstrated that nicotine can elevate blood glucose levels, disrupt glucose homeostasis, and induce insulin resistance. The review aims to elucidate the genetic variants of nicotinic acetylcholine receptors associated with diabetes risk and provide a comprehensive overview of the available data on the mechanisms through which nicotine influences blood glucose homeostasis and the development of diabetes. Here we emphasize the central and peripheral actions of nicotine on the release of glucoregulatory hormones, as well as its effects on glucose tolerance and insulin sensitivity. Notably, the central actions of nicotine within the brain, which encompass both insulin-dependent and independent mechanisms, are highlighted as potential targets for intervention strategies in diabetes management.
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Affiliation(s)
- Zuxin Chen
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; University of Chinese Academy of Sciences, Beijing, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | - Xin-An Liu
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; University of Chinese Academy of Sciences, Beijing, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China.
| | - Paul J Kenny
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA.
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10
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Carrette LLG, Kimbrough A, Davoudian PA, Kwan AC, Collazo A, George O. Hyperconnectivity of Two Separate Long-Range Cholinergic Systems Contributes to the Reorganization of the Brain Functional Connectivity during Nicotine Withdrawal in Male Mice. eNeuro 2023; 10:ENEURO.0019-23.2023. [PMID: 37295945 PMCID: PMC10306126 DOI: 10.1523/eneuro.0019-23.2023] [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: 12/19/2022] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 06/12/2023] Open
Abstract
Chronic nicotine results in dependence with withdrawal symptoms on discontinuation of use, through desensitization of nicotinic acetylcholine receptors and altered cholinergic neurotransmission. Nicotine withdrawal is associated with increased whole-brain functional connectivity and decreased network modularity; however, the role of cholinergic neurons in those changes is unknown. To identify the contribution of nicotinic receptors and cholinergic regions to changes in the functional network, we analyzed the contribution of the main cholinergic regions to brain-wide activation of the immediate early-gene Fos during withdrawal in male mice and correlated these changes with the expression of nicotinic receptor mRNA throughout the brain. We show that the main functional connectivity modules included the main long-range cholinergic regions, which were highly synchronized with the rest of the brain. However, despite this hyperconnectivity, they were organized into two anticorrelated networks that were separated into basal forebrain-projecting and brainstem-thalamic-projecting cholinergic regions, validating a long-standing hypothesis of the organization of the brain cholinergic systems. Moreover, baseline (without nicotine) expression of Chrna2, Chrna3, Chrna10, and Chrnd mRNA of each brain region correlated with withdrawal-induced changes in Fos expression. Finally, by mining the Allen Brain mRNA expression database, we were able to identify 1755 gene candidates and three pathways (Sox2-Oct4-Nanog, JAK-STAT, and MeCP2-GABA) that may contribute to nicotine withdrawal-induced Fos expression. These results identify the dual contribution of the basal forebrain and brainstem-thalamic cholinergic systems to whole-brain functional connectivity during withdrawal; and identify nicotinic receptors and novel cellular pathways that may be critical for the transition to nicotine dependence.
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Affiliation(s)
| | - Adam Kimbrough
- Department of Psychiatry, UC San Diego, California 92093
| | - Pasha A Davoudian
- Medical Scientist Training Program, Yale University School of Medicine, New Haven, Connecticut 06511
- Interdepartmental Neuroscience Program, Yale University School of Medicine, New Haven, Connecticut 06511
| | - Alex C Kwan
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853
| | - Andres Collazo
- Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Olivier George
- Department of Psychiatry, UC San Diego, California 92093
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11
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Ollila HM, Sharon E, Lin L, Sinnott-Armstrong N, Ambati A, Yogeshwar SM, Hillary RP, Jolanki O, Faraco J, Einen M, Luo G, Zhang J, Han F, Yan H, Dong XS, Li J, Zhang J, Hong SC, Kim TW, Dauvilliers Y, Barateau L, Lammers GJ, Fronczek R, Mayer G, Santamaria J, Arnulf I, Knudsen-Heier S, Bredahl MKL, Thorsby PM, Plazzi G, Pizza F, Moresco M, Crowe C, Van den Eeden SK, Lecendreux M, Bourgin P, Kanbayashi T, Martínez-Orozco FJ, Peraita-Adrados R, Benetó A, Montplaisir J, Desautels A, Huang YS, Jennum P, Nevsimalova S, Kemlink D, Iranzo A, Overeem S, Wierzbicka A, Geisler P, Sonka K, Honda M, Högl B, Stefani A, Coelho FM, Mantovani V, Feketeova E, Wadelius M, Eriksson N, Smedje H, Hallberg P, Hesla PE, Rye D, Pelin Z, Ferini-Strambi L, Bassetti CL, Mathis J, Khatami R, Aran A, Nampoothiri S, Olsson T, Kockum I, Partinen M, Perola M, Kornum BR, Rueger S, Winkelmann J, Miyagawa T, Toyoda H, Khor SS, Shimada M, Tokunaga K, Rivas M, Pritchard JK, Risch N, Kutalik Z, O'Hara R, Hallmayer J, Ye CJ, Mignot EJ. Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy. Nat Commun 2023; 14:2709. [PMID: 37188663 DOI: 10.1038/s41467-023-36120-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/17/2023] [Indexed: 05/17/2023] Open
Abstract
Narcolepsy type 1 (NT1) is caused by a loss of hypocretin/orexin transmission. Risk factors include pandemic 2009 H1N1 influenza A infection and immunization with Pandemrix®. Here, we dissect disease mechanisms and interactions with environmental triggers in a multi-ethnic sample of 6,073 cases and 84,856 controls. We fine-mapped GWAS signals within HLA (DQ0602, DQB1*03:01 and DPB1*04:02) and discovered seven novel associations (CD207, NAB1, IKZF4-ERBB3, CTSC, DENND1B, SIRPG, PRF1). Significant signals at TRA and DQB1*06:02 loci were found in 245 vaccination-related cases, who also shared polygenic risk. T cell receptor associations in NT1 modulated TRAJ*24, TRAJ*28 and TRBV*4-2 chain-usage. Partitioned heritability and immune cell enrichment analyses found genetic signals to be driven by dendritic and helper T cells. Lastly comorbidity analysis using data from FinnGen, suggests shared effects between NT1 and other autoimmune diseases. NT1 genetic variants shape autoimmunity and response to environmental triggers, including influenza A infection and immunization with Pandemrix®.
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Affiliation(s)
- Hanna M Ollila
- Stanford University, Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, 94304, USA
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
- Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eilon Sharon
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Ling Lin
- Stanford University, Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, 94304, USA
| | - Nasa Sinnott-Armstrong
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Aditya Ambati
- Stanford University, Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, 94304, USA
| | - Selina M Yogeshwar
- Stanford University, Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, 94304, USA
- Department of Neurology, Charité-Universitätsmedizin, 10117, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Einstein Center for Neurosciences Berlin, 10117, Berlin, Germany
| | - Ryan P Hillary
- Stanford University, Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, 94304, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Juliette Faraco
- Stanford University, Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, 94304, USA
| | - Mali Einen
- Stanford University, Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, 94304, USA
| | - Guo Luo
- Stanford University, Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, 94304, USA
| | - Jing Zhang
- Stanford University, Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, 94304, USA
| | - Fang Han
- Division of Sleep Medicine, The Peking University People's Hospital, Beijing, China
| | - Han Yan
- Division of Sleep Medicine, The Peking University People's Hospital, Beijing, China
| | - Xiao Song Dong
- Division of Sleep Medicine, The Peking University People's Hospital, Beijing, China
| | - Jing Li
- Division of Sleep Medicine, The Peking University People's Hospital, Beijing, China
| | - Jun Zhang
- Department of Neurology, The Peking University People's Hospital, Beijing, China
| | - Seung-Chul Hong
- Department of Psychiatry, St. Vincent's Hospital, The Catholic University of Korea, Suwon, Korea
| | - Tae Won Kim
- Department of Psychiatry, St. Vincent's Hospital, The Catholic University of Korea, Suwon, Korea
| | - Yves Dauvilliers
- Sleep-Wake Disorders Center, National Reference Network for Narcolepsy, Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier; Institute for Neurosciences of Montpellier (INM), INSERM, Université Montpellier 1, Montpellier, France
| | - Lucie Barateau
- Sleep-Wake Disorders Center, National Reference Network for Narcolepsy, Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier; Institute for Neurosciences of Montpellier (INM), INSERM, Université Montpellier 1, Montpellier, France
| | - Gert Jan Lammers
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Sleep-Wake Centre, Heemstede, The Netherlands
| | - Rolf Fronczek
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Sleep-Wake Centre, Heemstede, The Netherlands
| | - Geert Mayer
- Hephata Klinik, Schimmelpfengstr. 6, 34613, Schwalmstadt, Germany
- Philipps Universität Marburg, Baldinger Str., 35043, Marburg, Germany
| | - Joan Santamaria
- Neurology Service, Institut de Neurociències Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Isabelle Arnulf
- Sleep Disorder Unit, Pitié-Salpêtrière Hospital, Assistance Publique-Hopitaux de Paris, 75013, Paris, France
| | - Stine Knudsen-Heier
- Norwegian Centre of Expertise for Neurodevelopment Disorders and Hypersomnias (NevSom), Department of Rare Disorders, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - May Kristin Lyamouri Bredahl
- Norwegian Centre of Expertise for Neurodevelopment Disorders and Hypersomnias (NevSom), Department of Rare Disorders, Oslo University Hospital and University of Oslo, Oslo, Norway
- Hormone Laboratory, Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Per Medbøe Thorsby
- Hormone Laboratory, Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Giuseppe Plazzi
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Via Ugo Foscolo 7, 40123, Bologna, Italy
- IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Fabio Pizza
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Via Ugo Foscolo 7, 40123, Bologna, Italy
- IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Monica Moresco
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Via Ugo Foscolo 7, 40123, Bologna, Italy
- IRCCS Institute of Neurological Sciences, Bologna, Italy
| | | | | | - Michel Lecendreux
- Pediatric Sleep Center and National Reference Center for Narcolepsy and Idiopathic Hypersomnia Hospital Robert Debre, Paris, France
| | - Patrice Bourgin
- Department of Sleep Medicine, Strasbourg University Hospital, Strasbourg University, Strasbourg, France
| | - Takashi Kanbayashi
- Department of Neuropsychiatry, Akita University Graduate School of Medicine, Akita, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan
| | - Francisco J Martínez-Orozco
- Sleep Unit. Clinical Neurophysiology Service. San Carlos University Hospital. University Complutense of Madrid, Madrid, Spain
| | - Rosa Peraita-Adrados
- Sleep and Epilepsy Unit, Clinical Neurophysiology Service, Gregorio Marañón University General Hospital and Research Institute, University Complutense of Madrid (UCM), Madrid, Spain
| | | | - Jacques Montplaisir
- Center for Advanced Research in Sleep Medicine, Hôpital du Sacré-Coeur and Department of Neurosciences, University of Montréal, Montréal, QC, Canada
| | - Alex Desautels
- Center for Advanced Research in Sleep Medicine, Hôpital du Sacré-Coeur and Department of Neurosciences, University of Montréal, Montréal, QC, Canada
| | - Yu-Shu Huang
- Department of Child Psychiatry and Sleep Center, Chang Gung Memorial Hospital and University, Taoyuan, Taiwan
| | - Poul Jennum
- Danish Center for Sleep Medicine, Department of Clinical Neurophysiology, University of Copenhagen, Glostrup Hospital, Glostrup, Denmark
| | - Sona Nevsimalova
- Department of Neurology and Centre of Clinical Neurosciences, First Faculty of Medicine, Charles University and General University Hosptal, Prague, Czech Republic
| | - David Kemlink
- Department of Neurology and Centre of Clinical Neurosciences, First Faculty of Medicine, Charles University and General University Hosptal, Prague, Czech Republic
| | - Alex Iranzo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Department of Neurology, Barcelona, Spain
- Multidisciplinary Sleep Disorders Unit, Barcelona, Spain
| | - Sebastiaan Overeem
- Sleep Medicine Center Kempenhaeghe, P.O. Box 61, 5590 AB, Heeze, The Netherlands
- Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Aleksandra Wierzbicka
- Department of Clinical Neurophysiology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Peter Geisler
- Department of Psychiatry and Psychotherapy, University of Regensburg, Regensburg, Germany
| | - Karel Sonka
- Department of Neurology and Centre of Clinical Neurosciences, First Faculty of Medicine, Charles University and General University Hosptal, Prague, Czech Republic
| | - Makoto Honda
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Seiwa Hospital, Neuropsychiatric Research Institute, Tokyo, Japan
| | - Birgit Högl
- Department of Neurology, Medical University Innsbruck (MUI), Innsbruck, Austria
| | - Ambra Stefani
- Department of Neurology, Medical University Innsbruck (MUI), Innsbruck, Austria
| | | | - Vilma Mantovani
- Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Eva Feketeova
- Neurology Department, Medical Faculty of P. J. Safarik University, University Hospital of L. Pasteur Kosice, Kosice, Slovak Republic
| | - Mia Wadelius
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Niclas Eriksson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala, Sweden
| | - Hans Smedje
- Division of Child and Adolescent Psychiatry, Karolinska Institutet, Stockholm, Sweden
| | - Pär Hallberg
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - David Rye
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Zerrin Pelin
- Faculty of Health Sciences, Hasan Kalyoncu University, Gaziantep, Turkey
| | - Luigi Ferini-Strambi
- Sleep Disorders Center, Division of Neuroscience, Ospedale San Raffaele, Università Vita-Salute, Milan, Italy
| | - Claudio L Bassetti
- Neurology Department, EOC, Ospedale Regionale di Lugano, Lugano, Ticino, Switzerland
- Department of Neurology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
| | - Johannes Mathis
- Department of Neurology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
| | - Ramin Khatami
- Department of Neurology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Center for Sleep Medicine and Sleep Research, Clinic Barmelweid AG, Barmelweid, Switzerland
| | - Adi Aran
- Shaare Zedek Medical Center, Jerusalem, Israel
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Kerala, India
| | - Tomas Olsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Markku Partinen
- Helsinki Sleep Clinic, Vitalmed Research Centre, Helsinki, Finland
- Department of Clinical Neurosciences, University of Helsinki, Helsinki, Finland
| | - Markus Perola
- University of Helsinki, Institute for Molecular Medicine, Finland (FIMM) and Diabetes and Obesity Research Program. University of Tartu, Estonian Genome Center, Tartu, Estonia
| | - Birgitte R Kornum
- Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Sina Rueger
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Neurologische Klinik und Poliklinik, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Taku Miyagawa
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiromi Toyoda
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mihoko Shimada
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Manuel Rivas
- Department of Biomedical Data Science-Administration, Stanford University, Palo Alto, CA, USA
| | | | - Neil Risch
- Dept. Epidemiology and Biostatistics, UCSF, 513 Parnassus Avenue, San Francisco, CA, 94117, USA
| | - Zoltan Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland, Lausanne, 1010, Switzerland
| | - Ruth O'Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
- Mental Illness Research Education Clinical Centers (MIRECC), VA Palo Alto, Palo Alto, CA, USA
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
- Mental Illness Research Education Clinical Centers (MIRECC), VA Palo Alto, Palo Alto, CA, USA
| | - Chun Jimmie Ye
- Department of Epidemiology & Biostatistics, Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Emmanuel J Mignot
- Stanford University, Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, 94304, USA.
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12
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Carrette LL, Kimbrough A, Davoudian PA, Kwan AC, Collazo A, George O. Hyperconnectivity of two separate long-range cholinergic systems contributes to the reorganization of the brain functional connectivity during nicotine withdrawal in male mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534836. [PMID: 37034602 PMCID: PMC10081261 DOI: 10.1101/2023.03.29.534836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Chronic nicotine results in dependence with withdrawal symptoms upon discontinuation of use, through desensitization of nicotinic acetylcholine receptors and altered cholinergic neurotransmission. Nicotine withdrawal is associated with increased whole-brain functional connectivity and decreased network modularity, however, the role of cholinergic neurons in those changes is unknown. To identify the contribution of nicotinic receptors and cholinergic regions to changes in the functional network, we analyzed the contribution of the main cholinergic regions to brain-wide activation of the immediate early-gene FOS during withdrawal in male mice and correlated these changes with the expression of nicotinic receptor mRNA throughout the brain. We show that the main functional connectivity modules included the main long-range cholinergic regions, which were highly synchronized with the rest of the brain. However, despite this hyperconnectivity they were organized into two anticorrelated networks that were separated into basal forebrain projecting and brainstem-thalamic projecting cholinergic regions, validating a long-standing hypothesis of the organization of the brain cholinergic systems. Moreover, baseline (without nicotine) expression of Chrna2 , Chrna3 , Chrna10 , and Chrnd mRNA of each brain region correlated with withdrawal-induced changes in FOS expression. Finally, by mining the Allen Brain mRNA expression database, we were able to identify 1755 gene candidates and three pathways (Sox2-Oct4-Nanog, JAK-STAT, and MeCP2-GABA) that may contribute to nicotine withdrawal-induced FOS expression. These results identify the dual contribution of the basal forebrain and brainstem-thalamic cholinergic systems to whole-brain functional connectivity during withdrawal; and identify nicotinic receptors and novel cellular pathways that may be critical for the transition to nicotine dependence. Significance Statement Discontinuation of nicotine use in dependent users is associated with increased whole-brain activation and functional connectivity and leads to withdrawal symptoms. Here we investigated the contribution of the nicotinic cholinergic receptors and main cholinergic projecting brain areas in the whole-brain changes associated with withdrawal. This not only allowed us to visualize and confirm the previously described duality of the cholinergic brain system using this novel methodology, but also identify nicotinic receptors together with 1751 other genes that contribute, and could thus be targets for treatments against, nicotine withdrawal and dependence.
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Affiliation(s)
| | - Adam Kimbrough
- Department of Psychiatry, UC San Diego, La Jolla, CA, 92032, United States
| | - Pasha A. Davoudian
- Medical Scientist Training Program, Yale University School of Medicine, New Haven, CT, 06511, United States
- Interdepartmental Neuroscience Program, Yale University School of Medicine, New Haven, CT, 06511, United States
| | - Alex C. Kwan
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, United States
| | - Andres Collazo
- Beckman Institute, CalTech, Pasadena, CA, 91125, United States
| | - Olivier George
- Department of Psychiatry, UC San Diego, La Jolla, CA, 92032, United States
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13
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Sharma R, Rakshit B. Global burden of cancers attributable to tobacco smoking, 1990-2019: an ecological study. EPMA J 2023; 14:167-182. [PMID: 36866162 PMCID: PMC9971393 DOI: 10.1007/s13167-022-00308-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022]
Abstract
Aim and background Identifying risk factors for cancer initiation and progression is the cornerstone of the preventive approach to cancer management and control (EPMA J. 4(1):6, 2013). Tobacco smoking is a well-recognized risk factor for initiation and spread of several cancers. The predictive, preventive, and personalized medicine (PPPM) approach to cancer management and control focuses on smoking cessation as an essential cancer prevention strategy. Towards this end, this study examines the temporal patterns of cancer burden due to tobacco smoking in the last three decades at global, regional, and national levels. Data and methods The data pertaining to the burden of 16 cancers attributable to tobacco smoking at global, regional, and national levels were procured from the Global Burden of Disease 2019 Study. Two main indicators, deaths and disability-adjusted life years (DALYs), were used to describe the burden of cancers attributable to tobacco smoking. The socio-economic development of countries was measured using the socio-demographic index (SDI). Results Globally, deaths due to neoplasms caused by tobacco smoking increased from 1.5 million in 1990 to 2.5 million in 2019, whereas the age-standardized mortality rate (ASMR) decreased from 39.8/100,000 to 30.6/100,000 and the age-standardized DALY rate (ASDALR) decreased from 948.9/100,000 to 677.3/100,000 between 1990 and 2019. Males accounted for approximately 80% of global deaths and DALYs in 2019. Populous regions of Asia and a few regions of Europe account for the largest absolute burden, whereas countries in Europe and America have the highest age-standardized rates of cancers due to tobacco smoking. In 8 out of 21 regions, there were more than 100,000 deaths due to cancers attributable to tobacco smoking led by East Asia, followed by Western Europe in 2019. The regions of Sub-Saharan Africa (except southern region) had one of the lowest absolute counts of deaths, DALYs, and age-standardized rates. In 2019, tracheal, bronchus, and lung (TBL), esophageal, stomach, colorectal, and pancreatic cancer were the top 5 neoplasms attributable to tobacco smoking, with different burdens in regions as per their development status. The ASMR and ASDALR of neoplasms due to tobacco smoking were positively correlated with SDI, with pairwise correlation coefficient of 0.55 and 0.52, respectively. Conclusion As a preventive tool, tobacco smoking cessation has the biggest potential among all risk factors for preventing millions of cancer deaths every year. Cancer burden due to tobacco smoking is found to be higher in males and is positively associated with socio-economic development of countries. As tobacco smoking begins mostly at younger ages and the epidemic is unfolding in several parts of the world, more accelerated efforts are required towards tobacco cessation and preventing youth from entering this addiction. The PPPM approach to medicine suggests that not only personalized and precision medicine must be provided to cancer patients afflicted by tobacco smoking but personalized and targeted preventive solutions must be provided to prevent initiation and progression of smoking. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-022-00308-y.
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Affiliation(s)
- Rajesh Sharma
- Humanities and Social Sciences, National Institute of Technology Kurukshetra, Kurukshetra, India
| | - Bijoy Rakshit
- Economics and Business Environment, Indian Institute of Management Jammu, Jammu and Kashmir, India
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14
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Defo J, Awany D, Ramesar R. From SNP to pathway-based GWAS meta-analysis: do current meta-analysis approaches resolve power and replication in genetic association studies? Brief Bioinform 2023; 24:6972298. [PMID: 36611240 DOI: 10.1093/bib/bbac600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 01/09/2023] Open
Abstract
Genome-wide association studies (GWAS) have benefited greatly from enhanced high-throughput technology in recent decades. GWAS meta-analysis has become increasingly popular to highlight the genetic architecture of complex traits, informing about the replicability and variability of effect estimations across human ancestries. A wealth of GWAS meta-analysis methodologies have been developed depending on the input data and the outcome information of interest. We present a survey of current approaches from SNP to pathway-based meta-analysis by acknowledging the range of resources and methodologies in the field, and we provide a comprehensive review of different categories of Genome-Wide Meta-analysis methods employed. These methods highlight different levels at which GWAS meta-analysis may be done, including Single Nucleotide Polymorphisms, Genes and Pathways, for which we describe their framework outline. We also discuss the strengths and pitfalls of each approach and make suggestions regarding each of them.
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Affiliation(s)
- Joel Defo
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 7925, Observatory, South Africa.,South African Medical Research Council Genomic and Personalized Medicine Research Unit
| | - Denis Awany
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, 7925, South Africa
| | - Raj Ramesar
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 7925, Observatory, South Africa.,South African Medical Research Council Genomic and Personalized Medicine Research Unit
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15
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Fernandez-Rozadilla C, Timofeeva M, Chen Z, Law P, Thomas M, Schmit S, Díez-Obrero V, Hsu L, Fernandez-Tajes J, Palles C, Sherwood K, Briggs S, Svinti V, Donnelly K, Farrington S, Blackmur J, Vaughan-Shaw P, Shu XO, Long J, Cai Q, Guo X, Lu Y, Broderick P, Studd J, Huyghe J, Harrison T, Conti D, Dampier C, Devall M, Schumacher F, Melas M, Rennert G, Obón-Santacana M, Martín-Sánchez V, Moratalla-Navarro F, Oh JH, Kim J, Jee SH, Jung KJ, Kweon SS, Shin MH, Shin A, Ahn YO, Kim DH, Oze I, Wen W, Matsuo K, Matsuda K, Tanikawa C, Ren Z, Gao YT, Jia WH, Hopper J, Jenkins M, Win AK, Pai R, Figueiredo J, Haile R, Gallinger S, Woods M, Newcomb P, Duggan D, Cheadle J, Kaplan R, Maughan T, Kerr R, Kerr D, Kirac I, Böhm J, Mecklin LP, Jousilahti P, Knekt P, Aaltonen L, Rissanen H, Pukkala E, Eriksson J, Cajuso T, Hänninen U, Kondelin J, Palin K, Tanskanen T, Renkonen-Sinisalo L, Zanke B, Männistö S, Albanes D, Weinstein S, Ruiz-Narvaez E, Palmer J, Buchanan D, Platz E, Visvanathan K, Ulrich C, Siegel E, Brezina S, Gsur A, Campbell P, Chang-Claude J, Hoffmeister M, Brenner H, Slattery M, Potter J, Tsilidis K, Schulze M, Gunter M, Murphy N, Castells A, Castellví-Bel S, Moreira L, Arndt V, Shcherbina A, Stern M, Pardamean B, Bishop T, Giles G, Southey M, Idos G, McDonnell K, Abu-Ful Z, Greenson J, Shulman K, Lejbkowicz F, Offit K, Su YR, Steinfelder R, Keku T, van Guelpen B, Hudson T, Hampel H, Pearlman R, Berndt S, Hayes R, Martinez ME, Thomas S, Corley D, Pharoah P, Larsson S, Yen Y, Lenz HJ, White E, Li L, Doheny K, Pugh E, Shelford T, Chan A, Cruz-Correa M, Lindblom A, Hunter D, Joshi A, Schafmayer C, Scacheri P, Kundaje A, Nickerson D, Schoen R, Hampe J, Stadler Z, Vodicka P, Vodickova L, Vymetalkova V, Papadopoulos N, Edlund C, Gauderman W, Thomas D, Shibata D, Toland A, Markowitz S, Kim A, Chanock S, van Duijnhoven F, Feskens E, Sakoda L, Gago-Dominguez M, Wolk A, Naccarati A, Pardini B, FitzGerald L, Lee SC, Ogino S, Bien S, Kooperberg C, Li C, Lin Y, Prentice R, Qu C, Bézieau S, Tangen C, Mardis E, Yamaji T, Sawada N, Iwasaki M, Haiman C, Le Marchand L, Wu A, Qu C, McNeil C, Coetzee G, Hayward C, Deary I, Harris S, Theodoratou E, Reid S, Walker M, Ooi LY, Moreno V, Casey G, Gruber S, Tomlinson I, Zheng W, Dunlop M, Houlston R, Peters U. Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nat Genet 2023; 55:89-99. [PMID: 36539618 PMCID: PMC10094749 DOI: 10.1038/s41588-022-01222-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 10/09/2022] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.
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Affiliation(s)
- Ceres Fernandez-Rozadilla
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
- Genomic Medicine Group, Instituto de Investigacion Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Danish Institute for Advanced Study, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Virginia Díez-Obrero
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Juan Fernandez-Tajes
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Kitty Sherwood
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sarah Briggs
- Department of Public Health, Richard Doll Building, University of Oxford, Oxford, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kevin Donnelly
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan Farrington
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James Blackmur
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Peter Vaughan-Shaw
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - James Studd
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Jeroen Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tabitha Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher Dampier
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Mathew Devall
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Fredrick Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Mireia Obón-Santacana
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
| | - Vicente Martín-Sánchez
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Biomedicine Institute, University of León, León, Spain
| | - Ferran Moratalla-Navarro
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, Gyeonggi-do, South Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi-do, South Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Keum Ji Jung
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Aesun Shin
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University, Seoul, South Korea
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, South Korea
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - John Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Rish Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Jane Figueiredo
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robert Haile
- Division of Oncology, Department of Medicine, Cedars-Sinai Cancer Research Center for Health Equity, Los Angeles, CA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Michael Woods
- Division of Biomedical Sciences, Memorial University of Newfoundland, St. John, Ontario, Canada
| | - Polly Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - David Duggan
- City of Hope National Medical Center, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jeremy Cheadle
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Richard Kaplan
- MRC Clinical Trials Unit, Medical Research Council, Cardiff, UK
| | - Timothy Maughan
- MRC Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - David Kerr
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Iva Kirac
- Department of Surgical Oncology, University Hospital for Tumors, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Jan Böhm
- Department of Pathology, Central Finland Health Care District, Jyväskylä, Finland
| | | | - Pekka Jousilahti
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Paul Knekt
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Lauri Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Harri Rissanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
- Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Johan Eriksson
- Folkhälsan Research Centre, University of Helsinki, Helsinki, Finland
- Human Potential Translational Research Programme, National University of Singapore, Singapore, Singapore
- Unit of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tatiana Cajuso
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Ulrika Hänninen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Tomas Tanskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Brent Zanke
- Department of Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Satu Männistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Edward Ruiz-Narvaez
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Julie Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Daniel Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Elizabeth Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Cornelia Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Erin Siegel
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Peter Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Martha Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - John Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Konstantinos Tsilidis
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Matthias Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Marc Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Anna Shcherbina
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mariana Stern
- Department of Population and Public Health Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Bens Pardamean
- Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, Indonesia
| | - Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Graham Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gregory Idos
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Kevin McDonnell
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Zomoroda Abu-Ful
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Joel Greenson
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Katerina Shulman
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Flavio Lejbkowicz
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Clalit Health Services, Personalized Genomic Service, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Yu-Ru Su
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Robert Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Temitope Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Bethany van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Thomas Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sonja Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Marie Elena Martinez
- Population Sciences, Disparities and Community Engagement, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Sushma Thomas
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Douglas Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
- Department of Gastroenterology, Kaiser Permanente Medical Center, San Francisco, CA, USA
| | - Paul Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Susanna Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yun Yen
- Taipei Medical University, Taipei, Taiwan
| | - Heinz-Josef Lenz
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Li Li
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Kimberly Doheny
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tameka Shelford
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marcia Cruz-Correa
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - David Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Amit Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Peter Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Deborah Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Robert Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Zsofia Stadler
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Pavel Vodicka
- 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
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- 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
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- 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
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Nickolas Papadopoulos
- Department of Oncology Ludwig Center at the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chistopher Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - William Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Duncan Thomas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amanda Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Sanford Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA
| | - Andre Kim
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Franzel van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Edith Feskens
- Division of Human Nutrition, Wageningen University and Research, Wageningen, The Netherlands
| | - Lori Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Public Foundation of Genomic Medicine, Servicio Galego de Saude, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine, Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
- Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine, Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
- Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy
| | - Liesel FitzGerald
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Soo Chin Lee
- National University Cancer Institute, Singapore, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ross Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, Nantes, France
| | - Catherine Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elaine Mardis
- Department of Pediatrics, Nationwide Children's Hospital, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Christopher Haiman
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | | | - Anna Wu
- Preventative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Caroline McNeil
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ian Deary
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sarah Harris
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Stuart Reid
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marion Walker
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Li Yin Ooi
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | - Victor Moreno
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Stephen Gruber
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK.
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Epidemiology, University of Washington, Seattle, WA, USA.
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16
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Caligiuri SPB, Howe WM, Wills L, Smith ACW, Lei Y, Bali P, Heyer MP, Moen JK, Ables JL, Elayouby KS, Williams M, Fillinger C, Oketokoun Z, Lehmann VE, DiFeliceantonio AG, Johnson PM, Beaumont K, Sebra RP, Ibanez-Tallon I, Kenny PJ. Hedgehog-interacting protein acts in the habenula to regulate nicotine intake. Proc Natl Acad Sci U S A 2022; 119:e2209870119. [PMID: 36346845 PMCID: PMC9674224 DOI: 10.1073/pnas.2209870119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/28/2022] [Indexed: 11/10/2023] Open
Abstract
Hedgehog-interacting protein (HHIP) sequesters Hedgehog ligands to repress Smoothened (SMO)-mediated recruitment of the GLI family of transcription factors. Allelic variation in HHIP confers risk of chronic obstructive pulmonary disease and other smoking-related lung diseases, but underlying mechanisms are unclear. Using single-cell and cell-type-specific translational profiling, we show that HHIP expression is highly enriched in medial habenula (MHb) neurons, particularly MHb cholinergic neurons that regulate aversive behavioral responses to nicotine. HHIP deficiency dysregulated the expression of genes involved in cholinergic signaling in the MHb and disrupted the function of nicotinic acetylcholine receptors (nAChRs) through a PTCH-1/cholesterol-dependent mechanism. Further, CRISPR/Cas9-mediated genomic cleavage of the Hhip gene in MHb neurons enhanced the motivational properties of nicotine in mice. These findings suggest that HHIP influences vulnerability to smoking-related lung diseases in part by regulating the actions of nicotine on habenular aversion circuits.
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Affiliation(s)
- Stephanie P B Caligiuri
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - William M Howe
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Lauren Wills
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Alexander C W Smith
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ye Lei
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Purva Bali
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Mary P Heyer
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Janna K Moen
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jessica L Ables
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Karim S Elayouby
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Maya Williams
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Clementine Fillinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Zainab Oketokoun
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Vanessa E Lehmann
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | - Paul M Johnson
- Department of Information Technology and Electrical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Kristin Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ines Ibanez-Tallon
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY 10065
| | - Paul J Kenny
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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17
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Briggs SEW, Law P, East JE, Wordsworth S, Dunlop M, Houlston R, Hippisley-Cox J, Tomlinson I. Integrating genome-wide polygenic risk scores and non-genetic risk to predict colorectal cancer diagnosis using UK Biobank data: population based cohort study. BMJ 2022; 379:e071707. [PMID: 36351667 PMCID: PMC9644277 DOI: 10.1136/bmj-2022-071707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To evaluate the benefit of combining polygenic risk scores with the QCancer-10 (colorectal cancer) prediction model for non-genetic risk to identify people at highest risk of colorectal cancer. DESIGN Population based cohort study. SETTING Data from the UK Biobank study, collected between March 2006 and July 2010. PARTICIPANTS 434 587 individuals with complete data for genetics and QCancer-10 predictions were included in the QCancer-10 plus polygenic risk score modelling and validation cohorts. MAIN OUTCOME MEASURES Prediction of colorectal cancer diagnosis by genetic, non-genetic, and combined risk models. Using data from UK Biobank, six different polygenic risk scores for colorectal cancer were developed using LDpred2 polygenic risk score software, clumping, and thresholding approaches, and a model based on genome-wide significant polymorphisms. The top performing genome-wide polygenic risk score and the score containing genome-wide significant polymorphisms were combined with QCancer-10 and performance was compared with QCancer-10 alone. Case-control (logistic regression) and time-to-event (Cox proportional hazards) analyses were used to evaluate risk model performance in men and women. RESULTS Polygenic risk scores derived using the LDpred2 program performed best, with an odds ratio per standard deviation of 1.584 (95% confidence interval 1.536 to 1.633), and top age and sex adjusted C statistic of 0.733 (95% confidence interval 0.710 to 0.753) in logistic regression models in the validation cohort. Integrated QCancer-10 plus polygenic risk score models out-performed QCancer-10 alone. In men, the integrated LDpred2 model produced a C statistic of 0.730 (0.720 to 0.741) and explained variation of 28.2% (26.3 to 30.1), compared with 0.693 (0.682 to 0.704) and 21.0% (18.9 to 23.1) for QCancer-10 alone. In women, the C statistic for the integrated LDpred2 model was 0.687 (0.673 to 0.702) and explained variation was 21.0% (18.7 to 23.7), compared with 0.645 (0.631 to 0.659) and 12.4% (10.3 to 14.6) for QCancer-10 alone. In the top 20% of individuals at highest absolute risk, the sensitivity and specificity of the integrated LDpred2 models for predicting colorectal cancer diagnosis was 47.8% and 80.3% respectively in men, and 42.7% and 80.1% respectively in women, with increases in absolute risk in the top 5% of risk in men of 3.47-fold and in women of 2.77-fold compared with the median. Illustrative decision curve analysis indicated a small incremental improvement in net benefit with QCancer-10 plus polygenic risk score models compared with QCancer-10 alone. CONCLUSIONS Integrating polygenic risk scores with QCancer-10 modestly improves risk prediction over use of QCancer-10 alone. Given that QCancer-10 data can be obtained relatively easily from health records, use of polygenic risk score in risk stratified population screening for colorectal cancer currently has no clear justification. The added benefit, cost effectiveness, and acceptability of polygenic risk scores should be carefully evaluated in a real life screening setting before implementation in the general population.
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Affiliation(s)
- Sarah E W Briggs
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - James E East
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Sarah Wordsworth
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Julia Hippisley-Cox
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Ian Tomlinson
- Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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18
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Chmielowiec K, Chmielowiec J, Strońska-Pluta A, Trybek G, Śmiarowska M, Suchanecka A, Woźniak G, Jaroń A, Grzywacz A. Association of Polymorphism CHRNA5 and CHRNA3 Gene in People Addicted to Nicotine. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10478. [PMID: 36078193 PMCID: PMC9517777 DOI: 10.3390/ijerph191710478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Smoking is a chronic and relapsing addictive trait that harms public health. Among the many identified genetic variants of nicotine dependence, the variants in the CHRNA5/A3/B4 gene cluster on chromosome 15 that encode the α5, α3, and β4 subunits have recently received a lot of attention. Importantly, variants in this gene cluster have been associated with nicotine addiction. Among the many significant variants in this cluster, the polymorphism SNP rs16969968 seems to be the most interesting factor in nicotine addiction. This polymorphism causes an amino acid change from aspartate to asparagine at position 398 of the α5 nicotinic receptor protein sequence. Our study aimed to analyze three polymorphic variants: the rs16969968 located in the CHRNA5 gene, the rs578776 and rs1051730 located in the CHRNA3 gene in nicotine-addicted subjects, and in controls. Our study encompasses an association analysis of genotypes and haplotypes. A group of 401 volunteers was recruited for the study and divided into two groups: the study group consisted of addicted smokers and a control group of 200 unrelated non-smokers who were not dependent on any substance and healthy. A statistically significant difference was observed in the frequency of genotypes of the rs1051730 polymorphism of the CHRNA3 gene (χ2 = 6.704 p = 0.035). The T/T genotype was statistically significantly more frequent in the group of nicotine-dependent subjects. The haplotypes rs16969968, rs578776, and rs1051730 were distinguished, of which the G-T-T and G-C-T haplotypes were present only in the study group. With differences in frequencies, statistical significance was noted-for the G-T-T haplotype p = 0.01284 and the G-C-T haplotype p = 0.00775. The research stated that novel haplotypes G-T-T and G-C-T, though with very low-frequency variants in CHRNA3, were associated with nicotine addiction.
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Affiliation(s)
- Krzysztof Chmielowiec
- Department of Hygiene and Epidemiology, Collegium Medicum, University of Zielona Góra, 28 Zyty St., 65-046 Zielona Gora, Poland
| | - Jolanta Chmielowiec
- Department of Hygiene and Epidemiology, Collegium Medicum, University of Zielona Góra, 28 Zyty St., 65-046 Zielona Gora, Poland
| | - Aleksandra Strońska-Pluta
- Independent Laboratory of Health Promotion, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
| | - Grzegorz Trybek
- Department of Oral Surgery, Pomeranian Medical University in Szczecin, 72 Powstanców Wlkp. St., 70-111 Szczecin, Poland
| | - Małgorzata Śmiarowska
- Department of Pharmacokinetics and Therapeutic Drug Monitoring, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Aleksandra Suchanecka
- Independent Laboratory of Health Promotion, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
| | - Grzegorz Woźniak
- Private Dental Practice, 9 Bahnhofstrasse, 3940 Steg, Switzerland
| | - Aleksandra Jaroń
- Department of Oral Surgery, Pomeranian Medical University in Szczecin, 72 Powstanców Wlkp. St., 70-111 Szczecin, Poland
| | - Anna Grzywacz
- Independent Laboratory of Health Promotion, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
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19
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Long E, Patel H, Byun J, Amos CI, Choi J. Functional studies of lung cancer GWAS beyond association. Hum Mol Genet 2022; 31:R22-R36. [PMID: 35776125 DOI: 10.1093/hmg/ddac140] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
Fourteen years after the first genome-wide association study (GWAS) of lung cancer was published, approximately forty-five genomic loci have now been significantly associated with lung cancer risk. While functional characterization was performed for several of these loci, a comprehensive summary of current molecular understanding of lung cancer risk has been lacking. Further, many novel computational and experimental tools now became available to accelerate the functional assessment of disease-associated variants, moving beyond locus-by-locus approaches. In this review, we first highlight the heterogeneity of lung cancer GWAS findings across histological subtypes, ancestries, and smoking status, which poses unique challenges to follow-up studies. We then summarize the published lung cancer post-GWAS studies for each risk-associated locus to assess the current understanding of biological mechanisms beyond the initial statistical association. We further summarize strategies for GWAS functional follow-up studies considering cutting-edge functional genomics tools and providing a catalog of available resources relevant to lung cancer. Overall, we aim to highlight the importance of integrating computational and experimental approaches to draw biological insights from the lung cancer GWAS results beyond association.
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Affiliation(s)
- Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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20
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CHRNA5 rs16969968 and CHRNA3 rs578776 polymorphisms are associated with multiple nicotine dependence phenotypes in Bangladeshi smokers. Heliyon 2022; 8:e09947. [PMID: 35865987 PMCID: PMC9293740 DOI: 10.1016/j.heliyon.2022.e09947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/14/2021] [Accepted: 07/08/2022] [Indexed: 11/23/2022] Open
Abstract
Background A recent study has identified the role of CHRNA5-A3-B4 gene cluster variants rs16969968 and rs578776 of nicotinic acetylcholine receptors (nAChRs) on smoking status in Bengali ethnicity. The aim of the current study was to investigate whether these rs16969968-rs578776-rs11072768 single nucleotide polymorphisms (SNPs) of CHRNA5-A3-B4 gene cluster were associated with nicotine dependence (ND) and related phenotypes. Methods The Fagerstrom Test for Nicotine Dependence (FTND) and Cigarette Dependence Scale (CDS-12) were used to assess the degree of ND, and genotyping was done using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method on a cohort of 129 male smokers participating in a structured questionnaire-based survey. Results Smokers with AA genotype of CHRNA5 rs16969968 SNP were at significantly increased risk of developing ND compared to its wild type variant with odds ratio (ORs) of 1.20 (FTND: 95% CI 0.25–5.37, p = 0.253) and 2.48 (CDS-12: 95% CI 0.46–13.26, p = 0.081), respectively. Conversely, smokers with AA genotype of CHRNA3 rs578776 variant had a strong protective effect against ND development (ORs = 0.27, 95% CI 0.09–0.80, p = 0.076). There was no such link reported in CHRNB4 rs11072768 variant carriers. Similarly, G-A/G-A diplotype of rs16969968_rs578776 variants was discovered to be a protective factor against ND. Moreover, demographic features such as age, occupation and dwelling status were found to be significantly associated with ND. Conclusion Taken together, CHRNA5-A3-B4 gene cluster variants rs16969968 and rs578776 as well as specific demographic characteristics regulate ND and related smoking phenotypes in Bangladeshi male smokers. Further studies with large sample sizes are required to substantially validate the significance.
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21
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Munday RM, Haque R, Jan NJ, Wojcik GL, Marie C, Duchen D, Mentzer AJ, Nayak U, Korpe P, Kirkpatrick BD, Petri WA, Duggal P. Genome-Wide Association Study of Campylobacter -Positive Diarrhea Identifies Genes Involved in Toxin Processing and Inflammatory Response. mBio 2022; 13:e0055622. [PMID: 35420468 PMCID: PMC9239263 DOI: 10.1128/mbio.00556-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Diarrhea is responsible for the deaths of more than 500,000 children each year, many of whom reside in low-to-middle-income countries (LMICs). Additionally, children with multiple diarrheal infections early in life have increased growth stunting and malnutrition and decreased vaccine efficacy. Two bacteria that contribute to the burden of diarrhea are Campylobacter jejuni and Campylobacter coli, both are endemic in Bangladesh. However, not all children that are exposed to these pathogens, including Campylobacter, will experience diarrhea. We hypothesized that host genetics may influence susceptibility to Campylobacter infections and performed a genome-wide association study in 534 children from two independent birth cohorts in Dhaka, Bangladesh. Infants were monitored for diarrhea for the first 2 years of life and only defined as controls if all diarrheal samples in the first year were negative for Campylobacter jejuni/C. coli. Each cohort was analyzed separately under an additive model and adjusted for length-for-age z-scores at birth and 12 months, sex, water treatment, and ancestry. In a fixed effect inverse-variance weighted meta-analysis of these two cohorts, we identified a genome-wide significant region on chromosome 8 in intron 4 of the rho guanine nucleotide exchange factor 10 gene (ARHGEF10). Individuals with the G allele (rs13281104) had a 2-fold lower risk of having a Campylobacter-associated diarrheal episode than individuals with the A allele (OR 0.41, 95% CI 0.29 to 0.58, P = 3.6 × 10-7). This SNP is associated with decreased expression of the neighboring gene, CLN8, which may be involved in the transport of the cytolethal distending toxin produced by Campylobacter. IMPORTANCE Children in low-to-middle-income countries often suffer from multiple enteric infections in their first few years of life, many of which have the potential for long-lasting effects. These children are already likely to be malnourished and underweight, and chronic intestinal disturbances exacerbate these conditions. Despite public health interventions aimed at improving water, sanitation, and hygiene, enteric infections are still a leading cause of death for children under five. Previous work has included transmission dynamics, pathogen characteristics, and evaluation of interventions. Here, we examined the role of host genetic variation in susceptibility to diarrhea-associated Campylobacter infection. In our meta-analysis of two independent birth cohorts from Dhaka, Bangladesh, we found that children carrying a specific genetic variant (rs13281104, in an intron of ARHGEF10) were half as likely to have a diarrhea-associated Campylobacter infection in their first year of life. This protective effect may be achieved by decreasing gene expression and thereby impacting host-pathogen interactions and host immune response.
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Affiliation(s)
- Rebecca M. Munday
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Ning-Jiun Jan
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Genevieve L. Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Chelsea Marie
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Alexander J. Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, UK
| | - Uma Nayak
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Poonum Korpe
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Beth D. Kirkpatrick
- University of Vermont College of Medicine and Vaccine Testing Center, Burlington, Vermont, USA
| | - William A. Petri
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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22
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Zhu P, Kang G, Jiao Y, Gui C, Fan H, Li X, Jia Y, Zhang L, Ma X. The α5-nAChR/PD-L1 axis facilitates lung adenocarcinoma cell migration and invasion. Hum Cell 2022; 35:1207-1218. [PMID: 35593989 DOI: 10.1007/s13577-022-00709-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/21/2022] [Indexed: 12/17/2022]
Abstract
α5 nicotinic acetylcholine receptor (α5-nAChR) is associated with the progression of smoking-related lung adenocarcinoma (LUAD), but the molecular mechanism is unclear. Programmed death ligand 1 (PD-L1) is encoded by the CD274 gene, which not only inhibits the immune system, but also plays a unique role in tumor growth and metastasis. Here, we gained important insights into the underlying mechanism between α5-nAChR and PD-L1 in LUAD progression. α5-nAChR was overexpressed in various histological subtypes, cancer stages and metastasis statuses of LUAD. The group that coexpressed α5-nAChR and PD-L1 had a worse prognosis than the other subgroups at different stages of LUAD lymph node metastasis. The expression of α5-nAChR and PD-L1 was associated with epithelial-mesenchymal transition (EMT) marker CDH2. In vitro, α5-nAChR mediated nicotine-induced PD-L1 expression via STAT3 and the expression of EMT markers. Downregulation of α5-nAChR and/or PD-L1 inhibited EMT marker expression, cell proliferation, migration and invasion compared to silencing α5-nAChR or PD-L1 alone in LUAD cells. Furthermore, α5-nAChR expression was associated with PD-L1 and EMT marker expression in mouse xenograft models. These results highlight that α5-nAChR mediates STAT3/PD-L1 signaling, which contributes to cell migration and invasion. Therefore, our study may reveal a new interaction between α5-nAChR and PD-L1 that is involved in tumor cell growth and progression in LUAD, which may be a promising target for NSCLC diagnosis and immunotherapy.
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Affiliation(s)
- Ping Zhu
- Department of Medical Laboratory, Weifang Medical University, Weifang, 261053, China
| | - Guiyu Kang
- Department of Medical Laboratory, Weifang Medical University, Weifang, 261053, China
| | - Yang Jiao
- Jinan Central Hospital, Shandong University, Jinan, 250013, China
| | - Chengzhi Gui
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, China
| | - Huiping Fan
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, China
| | - Xiangying Li
- Jinan Central Hospital, Shandong University, Jinan, 250013, China
| | - Yanfei Jia
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, China
| | - Lulu Zhang
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, China
| | - Xiaoli Ma
- Department of Medical Laboratory, Weifang Medical University, Weifang, 261053, China.
- Jinan Central Hospital, Shandong University, Jinan, 250013, China.
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, China.
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23
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Chang X, Zhou YF, Wang L, Liu J, Yuan JM, Khor CC, Heng CK, Pan A, Koh WP, Dorajoo R. Genetic associations with healthy ageing among Chinese adults. NPJ AGING 2022; 8:6. [PMID: 35927272 PMCID: PMC9158790 DOI: 10.1038/s41514-022-00086-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 04/04/2022] [Indexed: 12/15/2022]
Abstract
The genetic basis of overall healthy ageing, especially among the East-Asian population is understudied. We conducted a genome-wide association study among 1618 Singapore Chinese elderly participants (65 years or older) ascertained to have aged healthily and compared their genome-wide genotypes to 6221 participants who did not age healthily, after a 20-year follow-up. Two genetic variants were identified (PMeta < 2.59 × 10-8) to be associated with healthy aging, including the LRP1B locus previously associated in long-lived individuals without cognitive decline. Our study sheds additional insights on the genetic basis of healthy ageing.
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Affiliation(s)
- Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, 119074, Singapore
| | - Yan-Feng Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Ling Wang
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, 119074, Singapore
| | - An Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore.
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore, 117609, Singapore.
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore.
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore.
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24
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Flatby HM, Rasheed H, Ravi A, Thomas LF, Liyanarachi KV, Afset JE, DeWan AT, Brumpton BM, Hveem K, Åsvold BO, Simonsen GS, Furberg AS, Damås JK, Solligård E, Rogne T. Risk of lower respiratory tract infections: a genome-wide association study with Mendelian randomization analysis in three independent European populations. Clin Microbiol Infect 2022; 28:732.e1-732.e7. [PMID: 34763054 DOI: 10.1016/j.cmi.2021.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality worldwide. Few studies have previously investigated genetic susceptibility and potential risk factors for LRTI. METHODS We used data from the UK Biobank, Trøndelag Health Study (HUNT), and FinnGen to conduct a genome-wide association study (GWAS). Cases were subjects hospitalized with LRTI, and controls were subjects with no such hospitalization. We conducted stratification and interaction analyses to evaluate whether the genetic effect of LRTI differed by sex or smoking. Mendelian randomization (MR) analyses were conducted to identify the unconfounded relationship between cardiometabolic risk factors and LRTI. RESULTS A total of 25 320 cases and 575 294 controls were included. The 15q25.1 locus reached genome-wide significance in the meta-analysis (rs10519203: OR 0.94, p 3.87e-11). The protective effect of effect allele of rs10519203 was present among smokers (OR 0.90, 95%CI 0.87-0.92, p 1.38e-15) but not among never-smokers (OR 1.01, 95%CI 0.97-1.06, p 5.20e-01). In MR analyses, we found that increasing body mass index (OR 1.31, 95%CI 1.24-1.40, p 3.78e-18), lifetime smoking (OR 2.83, 95%CI 2.34-3.42, p 6.56e-27), and systolic blood pressure robustly increased the risk of LRTIs (OR 1.11, 95%CI 1.02-1.22, p 1.48e-02). CONCLUSION A region in 15q25.1 was strongly associated with LRTI susceptibility. Reduction in the prevalence of smoking, overweight, obesity, and hypertension may reduce the disease burden of LRTIs.
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Affiliation(s)
- Helene M Flatby
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.
| | - Humaira Rasheed
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Anuradha Ravi
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Laurent F Thomas
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; BioCore-Bioinformatics Core Facility, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Laboratory Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Kristin V Liyanarachi
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Infectious Diseases, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan E Afset
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Laboratory Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway; Department of Medical Microbiology, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Andrew T DeWan
- Department of Chronic Disease Epidemiology and Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, USA; Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ben M Brumpton
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway; HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Kristian Hveem
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Research, Innovation, and Education, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Bjørn O Åsvold
- Department of Endocrinology, Clinic of Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway; HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway; K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gunnar S Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research Group for Host-Microbe Interaction, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Anne-Sofie Furberg
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Faculty of Health and Social Sciences, Molde University College, Molde, Norway
| | - Jan K Damås
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Infectious Diseases, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Erik Solligård
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Tormod Rogne
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Chronic Disease Epidemiology and Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, USA; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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25
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Li J, Liu B, Banaschewski T, Bokde ALW, Quinlan EB, Desrivières S, Flor H, Frouin V, Garavan H, Gowland P, Heinz A, Ittermann B, Martinot JL, Artiges E, Nees F, Papadopoulos Orfanos D, Paus T, Poustka L, Hohmann S, Fröhner JH, Smolka MN, Walter H, Whelan R, Schumann G, Jiang T. Orbitofrontal cortex volume links polygenic risk for smoking with tobacco use in healthy adolescents. Psychol Med 2022; 52:1175-1182. [PMID: 32878661 DOI: 10.1017/s0033291720002962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Tobacco smoking remains one of the leading causes of preventable illness and death and is heritable with complex underpinnings. Converging evidence suggests a contribution of the polygenic risk for smoking to the use of tobacco and other substances. Yet, the underlying brain mechanisms between the genetic risk and tobacco smoking remain poorly understood. METHODS Genomic, neuroimaging, and self-report data were acquired from a large cohort of adolescents from the IMAGEN study (a European multicenter study). Polygenic risk scores (PGRS) for smoking were calculated based on a genome-wide association study meta-analysis conducted by the Tobacco and Genetics Consortium. We examined the interrelationships among the genetic risk for smoking initiation, brain structure, and the number of occasions of tobacco use. RESULTS A higher smoking PGRS was significantly associated with both an increased number of occasions of tobacco use and smaller cortical volume of the right orbitofrontal cortex (OFC). Furthermore, reduced cortical volume within this cluster correlated with greater tobacco use. A subsequent path analysis suggested that the cortical volume within this cluster partially mediated the association between the genetic risk for smoking and the number of occasions of tobacco use. CONCLUSIONS Our data provide the first evidence for the involvement of the OFC in the relationship between smoking PGRS and tobacco use. Future studies of the molecular mechanisms underlying tobacco smoking should consider the mediation effect of the related neural structure.
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Affiliation(s)
- Jin Li
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190, China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190, China
| | - Bing Liu
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190, China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Tobias Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, 68159 Mannheim, Germany
| | - Arun L W Bokde
- Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Erin Burke Quinlan
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute of Psychiatry, Psychology & Neuroscience, SGDP Centre, King's College London, London, UK
| | - Sylvane Desrivières
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute of Psychiatry, Psychology & Neuroscience, SGDP Centre, King's College London, London, UK
| | - Herta Flor
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, Mannheim, Germany
- Department of Psychology, School of Social Sciences, University of Mannheim, 68131 Mannheim, Germany
| | - Vincent Frouin
- NeuroSpin, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Hugh Garavan
- Departments of Psychiatry and Psychology, University of Vermont, 05405 Burlington, Vermont, USA
| | - Penny Gowland
- Sir Peter Mansfield Imaging Centre School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, UK
| | - Andreas Heinz
- Department of Psychiatry and Psychotherapy CCM, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Bernd Ittermann
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
| | - Jean-Luc Martinot
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1000 'Neuroimaging & Psychiatry', University Paris-Saclay, University Paris Descartes - Sorbonne Paris Cité; and Maison de Solenn, Paris, France
| | - Eric Artiges
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1000 'Neuroimaging & Psychiatry', University Paris-Saclay, University Paris Descartes - Sorbonne Paris Cité; and Psychiatry Department 91G16, Orsay Hospital, Orsay, France
| | - Frauke Nees
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, 68159 Mannheim, Germany
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, Mannheim, Germany
| | | | - Tomáš Paus
- Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, Ontario, M6A 2E1, Canada
| | - Luise Poustka
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Medical Centre Göttingen, von-Siebold-Str. 5, 37075, Göttingen, Germany
| | - Sarah Hohmann
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, 68159 Mannheim, Germany
| | - Juliane H Fröhner
- Department of Psychiatry and Neuroimaging Center, Technische Universität Dresden, Dresden, Germany
| | - Michael N Smolka
- Department of Psychiatry and Neuroimaging Center, Technische Universität Dresden, Dresden, Germany
| | - Henrik Walter
- Department of Psychiatry and Psychotherapy CCM, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Robert Whelan
- School of Psychology and Global Brain Health Institute, Trinity College Dublin, Dublin, Ireland
| | - Gunter Schumann
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute of Psychiatry, Psychology & Neuroscience, SGDP Centre, King's College London, London, UK
- PONS Research Group, Department of Psychiatry and Psychotherapy, Campus Charite Mitte, Humboldt University, Berlin, Germany
- Leibniz Institute for Neurobiology, Magdeburg, Germany
- Institute for Science and Technology of Brain-inspired Intelligence (ISTBI), Fudan University, Shanghai, P.R. China
| | - Tianzi Jiang
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190, China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
- The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
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26
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Jordi SBU, Lang BM, Auschra B, von Känel R, Biedermann L, Greuter T, Schreiner P, Rogler G, Krupka N, Sulz MC, Misselwitz B, Begré S. Depressive Symptoms Predict Clinical Recurrence of Inflammatory Bowel Disease. Inflamm Bowel Dis 2022; 28:560-571. [PMID: 34096587 DOI: 10.1093/ibd/izab136] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) patients are at high risk for depression, and depression has been shown to affect disease course. We examined interrelations between depression, genetic risk factors for depression, and IBD flares. METHOD In 1973 patients (1137 Crohn's disease, 836 ulcerative colitis) of the Swiss IBD Cohort Study (SIBDCS), depressive status (hospital anxiety and depression subscale for depression, HADS-D ≥11) was assessed on a yearly basis. We investigated the impact of depression on IBD-relevant clinical outcomes in Cox proportional hazards models. We used active disease (CDAI ≥150 or MTWAI ≥10) and 2 published composite flare definitions-FNCE (physician-reported flare, nonresponse to therapy, new complication, or extraintestinal manifestation) and AFFSST (active disease, physician-reported flare, fistula, stenosis, and new systemic therapy)-as clinical end points. Additionally, 62 preselected single nucleotide polymorphisms (SNPs) were screened for cross-sectional associations with depression, and if present, their predictive value for future depression and clinical deterioration was assessed. RESULTS Depression was a strong risk factor for disease-related end points, including active disease (adjusted hazard ratio [aHR], 3.55; P < 0.001), AFFSST (aHR, 1.62; P < 0.001), and FNCE (aHR, 1.35; P = 0.019). The SNP rs2522833 was significantly associated with depression at enrollment (q = 0.059). The TC allele of rs588765 was negatively associated with the presence of depression at enrollment (q = 0.050) and after enrollment (aHR, 0.67; P = 0.035) and with fewer active disease states (aHR, 0.72; P = 0.045) during follow-up. CONCLUSION In IBD, depressive symptoms and inflammatory activity are intimately related. Depressive symptoms were a strong predictor of clinical deterioration, and genetic markers may play a role in this relationship.
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Affiliation(s)
- Sebastian Bruno Ulrich Jordi
- Clinic for Visceral Surgery and Medicine, Inselspital Bern and Bern University, Bern, Switzerland.,Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Brian Matthew Lang
- Clinic for Transplantation Immunology and Nephrology (Swiss Transplant Cohort Study), University Hospital of Basel, Basel, Switzerland
| | - Bianca Auschra
- Department of Consultation-Liaison Psychiatry and Psychosomatic Medicine, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Roland von Känel
- Department of Consultation-Liaison Psychiatry and Psychosomatic Medicine, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Luc Biedermann
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Thomas Greuter
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Philipp Schreiner
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Niklas Krupka
- Clinic for Visceral Surgery and Medicine, Inselspital Bern and Bern University, Bern, Switzerland
| | - Michael Christian Sulz
- Department of Gastroenterology and Hepatology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Benjamin Misselwitz
- Clinic for Visceral Surgery and Medicine, Inselspital Bern and Bern University, Bern, Switzerland.,Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Stefan Begré
- Neurology, Department of Biomedical Research, Bern University Hospital, University of Bern, Bern, Switzerland.,Institute of Stress Diseases and Stressmanagement (ISFOM), Zurich, Switzerland
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27
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Zhang WL, Zhang JB, Wang TM, Wu YX, He YQ, Xue WQ, Liao Y, Deng CM, Li DH, Wu ZY, Yang DW, Zheng XH, Li XZ, Zhou T, Zhang PF, Zhang SD, Hu YZ, Jia WH. Genomic landscape of Epstein–Barr virus in familial nasopharyngeal carcinoma. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To better understand the genomic characteristics of Epstein–Barr virus (EBV) in familial nasopharyngeal carcinoma (NPC), we sequenced the EBV genomes by whole-genome capture in 38 unrelated patients with NPC family history in first-degree relatives and 47 healthy controls, including 13 with family history and 34 without. Compared with type 1 reference genome, mutation hotspots were observed in the latent gene regions of EBV in familial NPC cases. Population structure analysis showed that one cluster has a higher frequency in familial cases than in controls (OR=5.33, 95 % CI 2.50–11.33, P=1.42×10−5), and similar population structure composition was observed among familial and sporadic NPC cases in high-endemic areas. By genome-wide association analysis, four variants were found to be significantly associated with familial NPC. Consistent results were observed in the meta-analysis integrating two published case-control EBV sequencing studies in NPC high-endemic areas. High-risk haplotypes of EBV composed of 34 variants were associated with familial NPC risk (OR=13.85, 95 % CI 4.13–46.44, P=2.06×10−5), and higher frequency was observed in healthy blood-relative controls with NPC family history (9/13, 69.23 %) than those without family history (16/34, 47.06%). This study suggested the potential contribution of EBV high-risk subtypes to familial aggregation of NPC.
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Affiliation(s)
- Wen-Li Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jiang-Bo Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Dan-Hua Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Zi-Yi Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Da-Wei Yang
- School of Public Health, Sun Yat-sen University, Guangzhou, PR China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Shao-Dan Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ye-Zhu Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Wei-Hua Jia
- School of Public Health, Sun Yat-sen University, Guangzhou, PR China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
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28
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Zhang P, Chen PL, Li ZH, Zhang A, Zhang XR, Zhang YJ, Liu D, Mao C. Association of smoking and polygenic risk with the incidence of lung cancer: a prospective cohort study. Br J Cancer 2022; 126:1637-1646. [PMID: 35194190 PMCID: PMC9130319 DOI: 10.1038/s41416-022-01736-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 01/23/2022] [Accepted: 02/02/2022] [Indexed: 12/24/2022] Open
Abstract
Background Genetic variation increases the risk of lung cancer, but the extent to which smoking amplifies this effect remains unknown. Therefore, we aimed to investigate the risk of lung cancer in people with different genetic risks and smoking habits. Methods This prospective cohort study included 345,794 European ancestry participants from the UK Biobank and followed up for 7.2 [6.5–7.8] years. Results Overall, 26.2% of the participants were former smokers, and 9.8% were current smokers. During follow-up, 1687 (0.49%) participants developed lung cancer. High genetic risk and smoking were independently associated with an increased risk of incident lung cancer. Compared with never-smokers, HR per standard deviation of the PRS increase was 1.16 (95% CI, 1.11–1.22), and HR of heavy smokers (≥40 pack-years) was 17.89 (95% CI, 15.31–20.91). There were no significant interactions between the PRS and the smoking status or pack-years. Population-attributable fraction analysis showed that smoking cessation might prevent 76.4% of new lung cancers. Conclusions Both high genetic risk and smoking were independently associated with higher lung cancer risk, but the increased risk of smoking was much more significant than heredity. The combination of traditional risk factors and additional PRS provides realistic application prospects for precise prevention.
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Affiliation(s)
- Peidong Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Pei-Liang Chen
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhi-Hao Li
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Ao Zhang
- State Key Laboratory of Molecular Neuroscience and Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xi-Ru Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu-Jie Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Dan Liu
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Chen Mao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China. .,Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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29
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Melbourne CA, Mesut Erzurumluoglu A, Shrine N, Chen J, Tobin MD, Hansell AL, Wain LV. Genome-wide gene-air pollution interaction analysis of lung function in 300,000 individuals. ENVIRONMENT INTERNATIONAL 2022; 159:107041. [PMID: 34923368 PMCID: PMC8739564 DOI: 10.1016/j.envint.2021.107041] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/25/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Impaired lung function is predictive of mortality and is a key component of chronic obstructive pulmonary disease. Lung function has a strong genetic component but is also affected by environmental factors such as increased exposure to air pollution, but the effect of their interactions is not well understood. OBJECTIVES To identify interactions between genetic variants and air pollution measures which affect COPD risk and lung function. Additionally, to determine whether previously identified lung function genetic association signals showed evidence of interaction with air pollution, considering both individual effects and combined effects using a genetic risk score (GRS). METHODS We conducted a genome-wide gene-air pollution interaction analysis of spirometry measures with three measures of air pollution at home address: particulate matter (PM2.5 & PM10) and nitrogen dioxide (NO2), in approximately 300,000 unrelated European individuals from UK Biobank. We explored air pollution interactions with previously identified lung function signals and determined their combined interaction effect using a GRS. RESULTS We identified seven new genome-wide interaction signals (P<5×10-8), and a further ten suggestive interaction signals (P<5×10-7). Additionally, we found statistical evidence of interaction for FEV1/FVC between PM2.5 and previously identified lung function signal, rs10841302, near AEBP2, suggesting increased susceptibility as copies of the G allele increased (but size of the impact was small - interaction beta: -0.363 percentage points, 95% CI: -0.523, -0.203 per 5 µg/m3). There was no observed interaction between air pollutants and the weighted GRS. DISCUSSION We carried out the largest genome-wide gene-air pollution interaction study of lung function and identified potential effects of clinically relevant size and significance. We observed up to 440 ml lower lung function for certain genotypes when exposed to mean levels of outdoor air pollution, which is approximately equivalent to nine years of average normal loss of lung function in adults.
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Affiliation(s)
- Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Jing Chen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Anna L Hansell
- Centre for Environmental Health and Sustainability, University of Leicester, Leicester, UK; National Institute for Health Research Health Protection Research Unit in Environmental Exposures and Health at the University of Leicester, Leicester, UK.
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
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30
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OUP accepted manuscript. Hum Mol Genet 2022; 31:3934-3944. [DOI: 10.1093/hmg/ddac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/14/2022] Open
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31
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Jung S, Ye BD, Lee HS, Baek J, Kim G, Park D, Park SH, Yang SK, Han B, Liu J, Song K. Identification of Three Novel Susceptibility Loci for Inflammatory Bowel Disease in Koreans in an Extended Genome-Wide Association Study. J Crohns Colitis 2021; 15:1898-1907. [PMID: 33853113 DOI: 10.1093/ecco-jcc/jjab060] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Genome-wide association studies [GWAS] of inflammatory bowel disease [IBD] in multiple populations have identified over 240 susceptibility loci. We previously performed a largest-to-date Asian-specific IBD GWAS to identify two new IBD risk loci and confirm associations with 28 established loci. To identify additional susceptibility loci in Asians, we expanded our previous study design by doubling the case size with an additional dataset of 1726 cases and 378 controls. METHODS An inverse-variance fixed-effects meta-analysis was performed between the previous and the new GWAS dataset, comprising a total of 3195 cases and 4419 controls, followed by replication in an additional 1088 cases and 845 controls. RESULTS The meta-analysis of Korean GWAS identified one novel locus for ulcerative colitis at rs76227733 on 10q24 [pcombined = 6.56 × 10-9] and two novel loci for Crohn's disease [CD] at rs2240751 on 19p13 [pcombined = 3.03 × 10-8] and rs6936629 on 6q22 [pcombined = 3.63 × 10-8]. Pathway-based analysis of GWAS data using MAGMA showed that the MHC and antigenic stimulus-related pathways were more significant in Korean CD, whereas cytokine and transcription factor-related pathways were more significant in European CD. Phenotype variance explained by the polygenic risk scores derived from Korean data explained up to 14% of the variance of CD whereas those derived from European data explained 10%, emphasizing the need for large-scale genetic studies in this population. CONCLUSIONS The identification of novel loci not previously associated with IBD suggests the importance of studying IBD genetics in diverse populations.
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Affiliation(s)
- Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Gyeonghoon Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Dohoon Park
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Jianjun Liu
- Human Genetics Group, Genome Institute of Singapore, Singapore
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
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32
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Chenoweth MJ, Cox LS, Nollen NL, Ahluwalia JS, Benowitz NL, Lerman C, Knight J, Tyndale RF. Analyses of nicotine metabolism biomarker genetics stratified by sex in African and European Americans. Sci Rep 2021; 11:19572. [PMID: 34599228 PMCID: PMC8486765 DOI: 10.1038/s41598-021-98883-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 09/08/2021] [Indexed: 12/01/2022] Open
Abstract
Nicotine is inactivated by the polymorphic CYP2A6 enzyme to cotinine and then to 3′hydroxycotinine. The Nicotine Metabolite Ratio (NMR; 3′hydroxycotinine/cotinine) is a heritable nicotine metabolism biomarker, varies with sex and ancestry, and influences smoking cessation and disease risk. We conducted sex-stratified genome-wide association studies of the NMR in European American (EA) and African American (AA) smokers (NCT01314001, NCT00666978). In EA females (n = 389) and males (n = 541), one significant (P < 5e−8) chromosome 19 locus was found (top variant: rs56113850, CYP2A6 (intronic), for C vs. T: females: beta = 0.67, P = 7.5e−22, 21.8% variation explained; males: beta = 0.75, P = 1.2e−37, 26.1% variation explained). In AA females (n = 503) and males (n = 352), the top variant was found on chromosome 19 but differed by sex (females: rs11878604, CYP2A6 (~ 16 kb 3′), for C vs. T: beta = − 0.71, P = 6.6e−26, 16.2% variation explained; males: rs3865454, CYP2A6 (~ 7 kb 3′), for G vs. T: beta = 0.64, P = 1.9e−19, 18.9% variation explained). In AA females, a significant region was found on chromosome 12 (top variant: rs12425845: P = 5.0e−9, TMEM132C (~ 1 Mb 5′), 6.1% variation explained) which was not significant in AA males. In AA males, significant regions were found on chromosomes 6 (top variant: rs9379805: P = 4.8e−9, SLC17A2 (~ 8 kb 5′), 8.0% variation explained) and 16 (top variant: rs77368288: P = 3.5e−8, ZNF469 (~ 92 kb 5′), 7.1% variation explained) which were not significant in AA females. Further investigation of these associations outside of chromosome 19 is required, as they did not replicate. Understanding how sex and ancestry influence nicotine metabolism genetics may improve personalized approaches for smoking cessation and risk prediction for tobacco-related diseases.
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Affiliation(s)
- Meghan J Chenoweth
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Lisa Sanderson Cox
- Department of Population Health, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Nikki L Nollen
- Department of Population Health, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Jasjit S Ahluwalia
- Departments of Behavioral and Social Sciences and Medicine, Brown University, Providence, Rhode Island, USA
| | - Neal L Benowitz
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Caryn Lerman
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jo Knight
- Data Science Institute and Lancaster University Medical School, Lancaster, UK.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada. .,Department of Psychiatry, University of Toronto, Toronto, ON, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Medical Sciences Building Room 4326, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
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Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MAR, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byan J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF. An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs. J Hepatol 2021; 75:572-581. [PMID: 34033851 PMCID: PMC8811537 DOI: 10.1016/j.jhep.2021.04.055] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/11/2021] [Accepted: 04/07/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUNDS & AIMS Primary biliary cholangitis (PBC) is a chronic liver disease in which autoimmune destruction of the small intrahepatic bile ducts eventually leads to cirrhosis. Many patients have inadequate response to licensed medications, motivating the search for novel therapies. Previous genome-wide association studies (GWAS) and meta-analyses (GWMA) of PBC have identified numerous risk loci for this condition, providing insight into its aetiology. We undertook the largest GWMA of PBC to date, aiming to identify additional risk loci and prioritise candidate genes for in silico drug efficacy screening. METHODS We combined new and existing genotype data for 10,516 cases and 20,772 controls from 5 European and 2 East Asian cohorts. RESULTS We identified 56 genome-wide significant loci (20 novel) including 46 in European, 13 in Asian, and 41 in combined cohorts; and a 57th genome-wide significant locus (also novel) in conditional analysis of the European cohorts. Candidate genes at newly identified loci include FCRL3, INAVA, PRDM1, IRF7, CCR6, CD226, and IL12RB1, which each play key roles in immunity. Pathway analysis reiterated the likely importance of pattern recognition receptor and TNF signalling, JAK-STAT signalling, and differentiation of T helper (TH)1 and TH17 cells in the pathogenesis of this disease. Drug efficacy screening identified several medications predicted to be therapeutic in PBC, some of which are well-established in the treatment of other autoimmune disorders. CONCLUSIONS This study has identified additional risk loci for PBC, provided a hierarchy of agents that could be trialled in this condition, and emphasised the value of genetic and genomic approaches to drug discovery in complex disorders. LAY SUMMARY Primary biliary cholangitis (PBC) is a chronic liver disease that eventually leads to cirrhosis. In this study, we analysed genetic information from 10,516 people with PBC and 20,772 healthy individuals recruited in Canada, China, Italy, Japan, the UK, or the USA. We identified several genetic regions associated with PBC. Each of these regions contains several genes. For each region, we used diverse sources of evidence to help us choose the gene most likely to be involved in causing PBC. We used these 'candidate genes' to help us identify medications that are currently used for treatment of other conditions, which might also be useful for treatment of PBC.
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Affiliation(s)
- Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James J Fryett
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Brian D Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Angela Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Julie Horowitz
- Regeneron Genetics Center, Tarrytown, New York, United States
| | | | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - David E Jones
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steven Flack
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ann Spicer
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Victoria L Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jinyoung Byan
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Richard N Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Gideon M Hirschfield
- Toronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, Canada
| | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Katherine A Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada; Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan; Department of Hepatology, Nagasaki Graduate School of Biomedical Sciences, Japan
| | - George F Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.
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Vaughan-Shaw PG, Timofeeva M, Ooi LY, Svinti V, Grimes G, Smillie C, Blackmur JP, Donnelly K, Theodoratou E, Campbell H, Zgaga L, Din FVN, Farrington SM, Dunlop MG. Differential genetic influences over colorectal cancer risk and gene expression in large bowel mucosa. Int J Cancer 2021; 149:1100-1108. [PMID: 33937989 DOI: 10.1002/ijc.33616] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/05/2021] [Accepted: 03/31/2021] [Indexed: 12/30/2022]
Abstract
Site-specific variation in colorectal cancer (CRC) incidence, biology and prognosis are poorly understood. We sought to determine whether common genetic variants influencing CRC risk might exhibit topographical differences on CRC risk through regional differences in effects on gene expression in the large bowel mucosa. We conducted a site-specific genetic association study (10 630 cases, 31 331 controls) to identify whether established risk variants exert differential effects on risk of proximal, compared to distal CRC. We collected normal colorectal mucosa and blood from 481 subjects and assessed mucosal gene expression using Illumina HumanHT-12v4 arrays in relation to germline genotype. Expression quantitative trait loci (eQTLs) were explored by anatomical location of sampling. The rs3087967 genotype (chr11q23.1 risk variant) exhibited significant site-specific effects-risk of distal CRC (odds ratio [OR] = 1.20, P = 8.20 × 10-20 ) with negligible effects on proximal CRC risk (OR = 1.05, P = .10). Expression of 1261 genes differed between proximal and distal colonic mucosa (top hit PRAC gene, fold-difference = 10, P = 3.48 × 10-57 ). In eQTL studies, rs3087967 genotype was associated with expression of 8 cis- and 21 trans-genes. Four of these (AKAP14, ADH5P4, ASGR2, RP11-342M1.7) showed differential effects by site, with strongest trans-eQTL signals in proximal colonic mucosa (eg, AKAP14, beta = 0.61, P = 5.02 × 10-5 ) and opposite signals in distal mucosa (AKAP14, beta = -0.17, P = .04). In summary, genetic variation at the chr11q23.1 risk locus imparts greater risk of distal rather than proximal CRC and exhibits site-specific differences in eQTL effects in normal mucosa. Topographical differences in genomic control over gene expression relevant to CRC risk may underlie site-specific variation in CRC. Results may inform individualised CRC screening programmes.
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Affiliation(s)
- Peter G Vaughan-Shaw
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Maria Timofeeva
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Public Health, D-IAS, Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Li-Yin Ooi
- Department of Pathology, National University Hospital, Singapore
| | - Victoria Svinti
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Claire Smillie
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James P Blackmur
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kevin Donnelly
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Evi Theodoratou
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Lina Zgaga
- Department of Public Health and Primary Care, Trinity College Dublin, Dublin, Ireland
| | - Farhat V N Din
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan M Farrington
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Dunlop
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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35
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Sanyal N, Napolioni V, de Rochemonteix M, Belloy ME, Caporaso NE, Landi MT, Greicius MD, Chatterjee N, Han SS. A Robust Test for Additive Gene-Environment Interaction Under the Trend Effect of Genotype Using an Empirical Bayes-Type Shrinkage Estimator. Am J Epidemiol 2021; 190:1948-1960. [PMID: 33942053 DOI: 10.1093/aje/kwab124] [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: 07/01/2020] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 11/12/2022] Open
Abstract
Evaluating gene by environment (G × E) interaction under an additive risk model (i.e., additive interaction) has gained wider attention. Recently, statistical tests have been proposed for detecting additive interaction, utilizing an assumption on gene-environment (G-E) independence to boost power, that do not rely on restrictive genetic models such as dominant or recessive models. However, a major limitation of these methods is a sharp increase in type I error when this assumption is violated. Our goal was to develop a robust test for additive G × E interaction under the trend effect of genotype, applying an empirical Bayes-type shrinkage estimator of the relative excess risk due to interaction. The proposed method uses a set of constraints to impose the trend effect of genotype and builds an estimator that data-adaptively shrinks an estimator of relative excess risk due to interaction obtained under a general model for G-E dependence using a retrospective likelihood framework. Numerical study under varying levels of departures from G-E independence shows that the proposed method is robust against the violation of the independence assumption while providing an adequate balance between bias and efficiency compared with existing methods. We applied the proposed method to the genetic data of Alzheimer disease and lung cancer.
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36
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Cheng S, Wen Y, Liu L, Cheng B, Liang C, Ye J, Chu X, Yao Y, Jia Y, Kafle OP, Zhang F. Traumatic events during childhood and its risks to substance use in adulthood: an observational and genome-wide by environment interaction study in UK Biobank. Transl Psychiatry 2021; 11:431. [PMID: 34417442 PMCID: PMC8379203 DOI: 10.1038/s41398-021-01557-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
We aimed to explore the underlying genetic mechanisms of traumatic events during childhood affecting the risks of adult substance use in present study. Using UK Biobank cohort, linear regression model was first applied to assess the relationships between cigarette smoking and alcohol drinking in adults with traumatic events during childhood, including felt hated by family member (41,648-111,465), felt loved (46,394-124,481) and sexually molested (47,598-127,766). Using traumatic events as exposure variables, genome-wide by environment interaction study was then performed by PLINK 2.0 to identify cigarette smoking and alcohol drinking associated genes interacting with traumatic events during childhood. We found that the frequency of cigarette smoking was significantly associated with felt hated by family member (coefficient = 0.42, P < 1.0 × 10-9), felt loved (coefficient = -0.31, P < 1.0 × 10-9) and sexually molested (coefficient = 0.46, P < 1.0 × 10-9). We also observed weaker associations of alcohol drinking with felt hated by family member (coefficient = 0.08, P = 3.10 × 10-6) and felt loved (coefficient = -0.06, P = 3.15 × 10-7). GWEIS identified multiple candidate loci interacting with traumatic events, such as CTNNA3 (rs189142060, P = 4.23 × 10-8) between felt hated by family member and the frequency of cigarette smoking, GABRG3 (rs117020886, P = 2.77 × 10-8) between felt hated by family member and the frequency of alcohol drinking. Our results suggested the significant impact of traumatic events during childhood on the risk of cigarette smoking and alcohol drinking.
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Affiliation(s)
- Shiqiang Cheng
- grid.43169.390000 0001 0599 1243Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Yan Wen
- grid.43169.390000 0001 0599 1243Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Li Liu
- grid.43169.390000 0001 0599 1243Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Bolun Cheng
- grid.43169.390000 0001 0599 1243Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Chujun Liang
- grid.43169.390000 0001 0599 1243Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Jing Ye
- grid.43169.390000 0001 0599 1243Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Xiaomeng Chu
- grid.43169.390000 0001 0599 1243Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Yao Yao
- grid.43169.390000 0001 0599 1243Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Yumeng Jia
- grid.43169.390000 0001 0599 1243Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Om Prakash Kafle
- grid.43169.390000 0001 0599 1243Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.
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Zhang Z, Xiao X, Zhou W, Zhu D, Amos CI. False positive findings during genome-wide association studies with imputation: Influence of allele frequency and imputation accuracy. Hum Mol Genet 2021; 31:146-155. [PMID: 34368847 DOI: 10.1093/hmg/ddab203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 11/12/2022] Open
Abstract
Genotype imputation is widely used in genetic studies to boost the power of GWAS, to combine multiple studies for meta-analysis and to perform fine mapping. With advances of imputation tools and large reference panels, genotype imputation has become mature and accurate. However, the uncertain nature of imputed genotypes can cause bias in the downstream analysis. Many studies have compared the performance of popular imputation approaches, but few investigated bias characteristics of downstream association analyses. Herein, we showed that the imputation accuracy is diminished if the real genotypes contain minor alleles. Although these genotypes are less common, which is particularly true for loci with low minor allele frequency, a large discordance between imputed and observed genotypes significantly inflated the association results, especially in data with a large portion of uncertain SNPs. The significant discordance of p-values happened as the p-value approached 0 or the imputation quality was poor. Although elimination of poorly imputed SNPs can remove false positive (FP) SNPs, it sacrificed, sometimes, more than 80% true positive (TP) SNPs. For top ranked SNPs, removing variants with moderate imputation quality cannot reduce the proportion of FP SNPs, and increasing sample size in reference panels did not greatly benefit the results as well. Additionally, samples with a balanced ratio between cases and controls can dramatically improve the number of TP SNPs observed in the imputation based GWAS. These results raise concerns about results from analysis of association studies when rare variants are studied, particularly when case-control studies are unbalanced.
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Affiliation(s)
- Zhihui Zhang
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030.,Institute of Clinical and Translational Medicine, Department of Medicine, Baylor College of Medicine, Houston, TX 77030
| | - Xiangjun Xiao
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Wen Zhou
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Dakai Zhu
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Christopher I Amos
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030.,Institute of Clinical and Translational Medicine, Department of Medicine, Baylor College of Medicine, Houston, TX 77030
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El-Boraie A, Tyndale RF. The Role of Pharmacogenetics in Smoking. Clin Pharmacol Ther 2021; 110:599-606. [PMID: 34165800 DOI: 10.1002/cpt.2345] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/21/2021] [Indexed: 11/09/2022]
Abstract
Smoking continues to be the leading preventable contributor to death worldwide. Twin studies have suggested a significant genetic contribution underlying most smoking behaviors (40-70% heritability estimates). Candidate gene studies of smoking phenotypes have identified several pharmacogenes implicated in nicotine's pharmacokinetics (CYP2A6, CYP2B6, CYP2A13, FMOs, UGTs, and OCT2), and nicotine's pharmacodynamic response in the central nervous system (nicotinic acetylcholine receptors, as well as through the dopaminergic and serotonergic systems). Subsequent genome-wide association studies (GWAS) have confirmed the role of certain pharmacogenes through hypothesis-free approaches. Furthermore, pharmacogenes that alter the efficacy of smoking cessation pharmacotherapies, including nicotine replacement therapies, bupropion, and varenicline, may also impact quitting success. In this brief review we highlight the role of pharmacogenes in smoking behaviors, such as smoking status, consumption, nicotine dependence, spontaneous quitting, and altered abstinence to pharmacotherapies; We provide examples from initial candidate gene associations and subsequent GWAS. The genes CYP2A6 and the CHRNA5-A3-B4 confer the most replicated sources of genetic variation in smoking behaviors, likely due to their importance in nicotine's pharmacology. We will also provide examples of genetic scoring approaches, and the role of rare variants in explaining a portion of the missing heritability in smoking behaviors.
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Affiliation(s)
- Ahmed El-Boraie
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.,Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Rachel F Tyndale
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.,Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
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39
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Chung RH, Chiu YF, Wang WC, Hwu CM, Hung YJ, Lee IT, Chuang LM, Quertermous T, Rotter JI, Chen YDI, Chang IS, Hsiung CA. Multi-omics analysis identifies CpGs near G6PC2 mediating the effects of genetic variants on fasting glucose. Diabetologia 2021; 64:1613-1625. [PMID: 33842983 DOI: 10.1007/s00125-021-05449-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/08/2021] [Indexed: 10/21/2022]
Abstract
AIMS/HYPOTHESIS An elevated fasting glucose level in non-diabetic individuals is a key predictor of type 2 diabetes. Genome-wide association studies (GWAS) have identified hundreds of SNPs for fasting glucose but most of their functional roles in influencing the trait are unclear. This study aimed to identify the mediation effects of DNA methylation between SNPs identified as significant from GWAS and fasting glucose using Mendelian randomisation (MR) analyses. METHODS We first performed GWAS analyses for three cohorts (Taiwan Biobank with 18,122 individuals, the Healthy Aging Longitudinal Study in Taiwan with 1989 individuals and the Stanford Asia-Pacific Program for Hypertension and Insulin Resistance with 416 individuals) with individuals of Han Chinese ancestry in Taiwan, followed by a meta-analysis for combining the three GWAS analysis results to identify significant and independent SNPs for fasting glucose. We determined whether these SNPs were methylation quantitative trait loci (meQTLs) by testing their associations with DNA methylation levels at nearby CpG sites using a subsample of 1775 individuals from the Taiwan Biobank. The MR analysis was performed to identify DNA methylation with causal effects on fasting glucose using meQTLs as instrumental variables based on the 1775 individuals. We also used a two-sample MR strategy to perform replication analysis for CpG sites with significant MR effects based on literature data. RESULTS Our meta-analysis identified 18 significant (p < 5 × 10-8) and independent SNPs for fasting glucose. Interestingly, all 18 SNPs were meQTLs. The MR analysis identified seven CpGs near the G6PC2 gene that mediated the effects of a significant SNP (rs2232326) in the gene on fasting glucose. The MR effects for two CpGs were replicated using summary data based on the European population, using an exonic SNP rs2232328 in G6PC2 as the instrument. CONCLUSIONS/INTERPRETATION Our analysis results suggest that rs2232326 and rs2232328 in G6PC2 may affect DNA methylation at CpGs near the gene and that the methylation may have downstream effects on fasting glucose. Therefore, SNPs in G6PC2 and CpGs near G6PC2 may reside along the pathway that influences fasting glucose levels. This is the first study to report CpGs near G6PC2, an important gene for regulating insulin secretion, mediating the effects of GWAS-significant SNPs on fasting glucose.
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Affiliation(s)
- Ren-Hua Chung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan.
| | - Yen-Feng Chiu
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Wen-Chang Wang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Jen Hung
- Division of Endocrine and Metabolism, Tri-Service General Hospital, Taipei, Taiwan
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
| | - I-Te Lee
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Lee-Ming Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Institutes of Molecular Medicine, Collage of Medicine, National Taiwan University, Taipei, Taiwan
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and Stanford Cardiovascular Institute, Falk Cardiovascular Research Center, Stanford University, Stanford, CA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, the Lundquist Institute, Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, the Lundquist Institute, Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chao A Hsiung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan.
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Genome-wide association study of stimulant dependence. Transl Psychiatry 2021; 11:363. [PMID: 34226506 PMCID: PMC8257618 DOI: 10.1038/s41398-021-01440-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 11/08/2022] Open
Abstract
Stimulant dependence is heritable, but specific genetic factors underlying the trait have not been identified. A genome-wide association study for stimulant dependence was performed in a discovery cohort of African- (AA) and European-ancestry (EA) subjects ascertained for genetic studies of alcohol, opioid, and cocaine use disorders. The sample comprised individuals with DSM-IV stimulant dependence (393 EA cases, 5288 EA controls; 155 AA cases, 5603 AA controls). An independent cohort from the family-based Collaborative Study on the Genetics of Alcoholism (532 EA cases, 7635 EA controls; 53 AA cases, AA 3352 controls) was used for replication. One variant in SLC25A16 (rs2394476, p = 3.42 × 10-10, odds ratio [OR] = 3.70) was GWS in AAs. Four other loci showed suggestive evidence, including KCNA4 in AAs (rs11500237, p = 2.99 × 10-7, OR = 2.31) which encodes one of the potassium voltage-gated channel protein that has been linked to several other substance use disorders, and CPVL in the combined population groups (rs1176440, p = 3.05 × 10-7, OR = 1.35), whose expression was previously shown to be upregulated in the prefrontal cortex from users of cocaine, cannabis, and phencyclidine. Analysis of the top GWAS signals revealed a significant enrichment with nicotinic acetylcholine receptor genes (adjusted p = 0.04) and significant pleiotropy between stimulant dependence and alcohol dependence in EAs (padj = 3.6 × 10-3), an anxiety disorder in EAs (padj = 2.1 × 10-4), and ADHD in both AAs (padj = 3.0 × 10-33) and EAs (padj = 6.7 × 10-35). Our results implicate novel genes and pathways as having roles in the etiology of stimulant dependence.
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Zhang PD, Zhang XR, Zhang A, Li ZH, Liu D, Zhang YJ, Mao C. Associations of genetic risk and smoking with incident chronic obstructive pulmonary disease. Eur Respir J 2021; 59:13993003.01320-2021. [PMID: 34172472 DOI: 10.1183/13993003.01320-2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/14/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Genetic and smoking contribute to chronic obstructive pulmonary disease (COPD), but whether a combined polygenic risk score (PRS) is associated with incident COPD and whether it has a synergistic effect on the smoking remains unclear. We aimed to investigate the association of PRS with COPD and explore whether smoking behaviors could modify such association. METHODS Multivariable Cox proportional models were used to estimate hazard ratios (HRs) and 95% confidence intervals (95% CIs) for the association of the PRS and smoking with COPD. RESULTS The study included 439 255 participants (mean age 56.5; 53.9% female), with a median follow-up of 9.0 years. The PRSlasso containing 2.5 million variants showed better discrimination and a stronger association for incident COPD than the PRS279 containing 279 genome-wide significance variants. Compared with the low genetic risk, the HRs of the medium and high genetic risk were 1.39 (95% CI, 1.31-1.48) and 2.40 (95% CI, 2.24-2.56), respectively. The HR of high genetic risk and current smoking was 11.62 (95% CI, 10.31-13.10) times of low genetic risk and never smoking. There were significant interactions between the PRSlasso and smoking status for incident COPD (p for interaction<0.001). From low genetic risk to high genetic risk, the HRs of current smoking increased from 4.32 (95% CI, 3.69-5.06) to 6.89 (95% CI, 6.21-7.64), and the population-attributable risks of smoking increased from 42.7% to 61.1%. CONCLUSION PRS constructed from millions of variants below genome-wide significance showed significant associations with incident COPD. Participants with a high genetic risk may be more susceptible to developing COPD when exposed to smoking.
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Affiliation(s)
- Pei-Dong Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Pei-Dong Zhang and Xi-Ru Zhang contributed to the work equally
| | - Xi-Ru Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Pei-Dong Zhang and Xi-Ru Zhang contributed to the work equally
| | - Ao Zhang
- State Key Laboratory of Molecular Neuroscience and Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhi-Hao Li
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Dan Liu
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu-Jie Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Chen Mao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China .,Department of Laboratory Medicine, Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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From Stem Cells to Populations-Using hiPSC, Next-Generation Sequencing, and GWAS to Explore the Genetic and Molecular Mechanisms of Congenital Heart Defects. Genes (Basel) 2021; 12:genes12060921. [PMID: 34208537 PMCID: PMC8235101 DOI: 10.3390/genes12060921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/01/2021] [Accepted: 06/12/2021] [Indexed: 01/16/2023] Open
Abstract
Congenital heart defects (CHD) are developmental malformations affecting the heart and the great vessels. Early heart development requires temporally regulated crosstalk between multiple cell types, signaling pathways, and mechanical forces of early blood flow. While both genetic and environmental factors have been recognized to be involved, identifying causal genes in non-syndromic CHD has been difficult. While variants following Mendelian inheritance have been identified by linkage analysis in a few families with multiple affected members, the inheritance pattern in most familial cases is complex, with reduced penetrance and variable expressivity. Furthermore, most non-syndromic CHD are sporadic. Improved sequencing technologies and large biobank collections have enabled genome-wide association studies (GWAS) in non-syndromic CHD. The ability to generate human to create human induced pluripotent stem cells (hiPSC) and further differentiate them to organotypic cells enables further exploration of genotype–phenotype correlations in patient-derived cells. Here we review how these technologies can be used in unraveling the genetics and molecular mechanisms of heart development.
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Yu X, Megens HJ, Mengistu SB, Bastiaansen JWM, Mulder HA, Benzie JAH, Groenen MAM, Komen H. Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus). BMC Genomics 2021; 22:426. [PMID: 34107887 PMCID: PMC8188787 DOI: 10.1186/s12864-021-07486-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/25/2021] [Indexed: 11/18/2022] Open
Abstract
Background Tilapia is one of the most abundant species in aquaculture. Hypoxia is known to depress growth rate, but the genetic mechanism by which this occurs is unknown. In this study, two groups consisting of 3140 fish that were raised in either aerated (normoxia) or non-aerated pond (nocturnal hypoxia). During grow out, fish were sampled five times to determine individual body weight (BW) gains. We applied a genome-wide association study to identify SNPs and genes associated with the hypoxic and normoxic environments in the 16th generation of a Genetically Improved Farmed Tilapia population. Results In the hypoxic environment, 36 SNPs associated with at least one of the five body weight measurements (BW1 till BW5), of which six, located between 19.48 Mb and 21.04 Mb on Linkage group (LG) 8, were significant for body weight in the early growth stage (BW1 to BW2). Further significant associations were found for BW in the later growth stage (BW3 to BW5), located on LG1 and LG8. Analysis of genes within the candidate genomic region suggested that MAPK and VEGF signalling were significantly involved in the later growth stage under the hypoxic environment. Well-known hypoxia-regulated genes such as igf1rb, rora, efna3 and aurk were also associated with growth in the later stage in the hypoxic environment. Conversely, 13 linkage groups containing 29 unique significant and suggestive SNPs were found across the whole growth period under the normoxic environment. A meta-analysis showed that 33 SNPs were significantly associated with BW across the two environments, indicating a shared effect independent of hypoxic or normoxic environment. Functional pathways were involved in nervous system development and organ growth in the early stage, and oocyte maturation in the later stage. Conclusions There are clear genotype-growth associations in both normoxic and hypoxic environments, although genome architecture involved changed over the growing period, indicating a transition in metabolism along the way. The involvement of pathways important in hypoxia especially at the later growth stage indicates a genotype-by-environment interaction, in which MAPK and VEGF signalling are important components. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07486-5.
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Affiliation(s)
- Xiaofei Yu
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.
| | - Hendrik-Jan Megens
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Samuel Bekele Mengistu
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.,School of Animal and Range Sciences, College of Agriculture, Hawassa University, Hawassa, Ethiopia
| | - John W M Bastiaansen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Han A Mulder
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - John A H Benzie
- WorldFish Centre, Jalan Batu Maung, Bayan Lepas, Penang, Malaysia.,School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Martien A M Groenen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Hans Komen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
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Buchwald J, Chenoweth MJ, Palviainen T, Zhu G, Benner C, Gordon S, Korhonen T, Ripatti S, Madden PAF, Lehtimäki T, Raitakari OT, Salomaa V, Rose RJ, George TP, Lerman C, Pirinen M, Martin NG, Kaprio J, Loukola A, Tyndale RF. Genome-wide association meta-analysis of nicotine metabolism and cigarette consumption measures in smokers of European descent. Mol Psychiatry 2021; 26:2212-2223. [PMID: 32157176 PMCID: PMC7483250 DOI: 10.1038/s41380-020-0702-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022]
Abstract
Smoking behaviors, including amount smoked, smoking cessation, and tobacco-related diseases, are altered by the rate of nicotine clearance. Nicotine clearance can be estimated using the nicotine metabolite ratio (NMR) (ratio of 3'hydroxycotinine/cotinine), but only in current smokers. Advancing the genomics of this highly heritable biomarker of CYP2A6, the main metabolic enzyme for nicotine, will also enable investigation of never and former smokers. We performed the largest genome-wide association study (GWAS) to date of the NMR in European ancestry current smokers (n = 5185), found 1255 genome-wide significant variants, and replicated the chromosome 19 locus. Fine-mapping of chromosome 19 revealed 13 putatively causal variants, with nine of these being highly putatively causal and mapping to CYP2A6, MAP3K10, ADCK4, and CYP2B6. We also identified a putatively causal variant on chromosome 4 mapping to TMPRSS11E and demonstrated an association between TMPRSS11E variation and a UGT2B17 activity phenotype. Together the 14 putatively causal SNPs explained ~38% of NMR variation, a substantial increase from the ~20 to 30% previously explained. Our additional GWASs of nicotine intake biomarkers showed that cotinine and smoking intensity (cotinine/cigarettes per day (CPD)) shared chromosome 19 and chromosome 4 loci with the NMR, and that cotinine and a more accurate biomarker, cotinine + 3'hydroxycotinine, shared a chromosome 15 locus near CHRNA5 with CPD and Pack-Years (i.e., cumulative exposure). Understanding the genetic factors influencing smoking-related traits facilitates epidemiological studies of smoking and disease, as well as assists in optimizing smoking cessation support, which in turn will reduce the enormous personal and societal costs associated with smoking.
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Affiliation(s)
- Jadwiga Buchwald
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Meghan J. Chenoweth
- Campbell Family Mental Health Research Institute, CAMH, and Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Gu Zhu
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Christian Benner
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Scott Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Tellervo Korhonen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland,Department of Public Health, University of Helsinki, Helsinki, Finland,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Pamela A. F. Madden
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, United States
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center, Tampere, Finland,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli T. Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland,Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland,Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Veikko Salomaa
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Richard J. Rose
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, United States
| | - Tony P. George
- Division of Addictions, Centre for Addiction and Mental Health, Toronto, Ontario, Canada and Division of Brain and Therapeutics, Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Caryn Lerman
- USC Norris Comprehensive Cancer Center at Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland,Department of Public Health, University of Helsinki, Helsinki, Finland,Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | | | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland,Department of Pathology, Medicum, University of Helsinki, Helsinki, Finland
| | - Rachel F. Tyndale
- Campbell Family Mental Health Research Institute, CAMH, and Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada,Division of Addictions, Centre for Addiction and Mental Health, Toronto, Ontario, Canada and Division of Brain and Therapeutics, Department of Psychiatry, University of Toronto, Toronto, Canada
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Host Genome-Wide Association Study of Infant Susceptibility to Shigella-Associated Diarrhea. Infect Immun 2021; 89:IAI.00012-21. [PMID: 33649051 PMCID: PMC8316060 DOI: 10.1128/iai.00012-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
Shigella is a leading cause of moderate-to-severe diarrhea globally and the causative agent of shigellosis and bacillary dysentery. Associated with 80 to 165 million cases of diarrhea and >13% of diarrheal deaths, in many regions, Shigella exposure is ubiquitous while infection is heterogenous. To characterize host-genetic susceptibility to Shigella-associated diarrhea, we performed two independent genome-wide association studies (GWAS) including Bangladeshi infants from the PROVIDE and CBC birth cohorts in Dhaka, Bangladesh. Cases were infants with Shigella-associated diarrhea (n = 143) and controls were infants with no Shigella-associated diarrhea in the first 13 months of life (n = 446). Shigella-associated diarrhea was identified via quantitative PCR (qPCR) threshold cycle (CT ) distributions for the ipaH gene, carried by all four Shigella species and enteroinvasive Escherichia coli Host GWAS were performed under an additive genetic model. A joint analysis identified protective loci on chromosomes 11 (rs582240, within the KRT18P59 pseudogene; P = 6.40 × 10-8; odds ratio [OR], 0.43) and 8 (rs12550437, within the lincRNA RP11-115J16.1; P = 1.49 × 10-7; OR, 0.48). Conditional analyses identified two previously suggestive loci, a protective locus on chromosome 7 (rs10266841, within the 3' untranslated region [UTR] of CYTH3; P conditional = 1.48 × 10-7; OR, 0.44) and a risk-associated locus on chromosome 10 (rs2801847, an intronic variant within MPP7; P conditional = 8.37 × 10-8; OR, 5.51). These loci have all been indirectly linked to bacterial type 3 secretion system (T3SS) activity, its components, and bacterial effectors delivered into host cells. Host genetic factors that may affect bacterial T3SS activity and are associated with the host response to Shigella-associated diarrhea may provide insight into vaccine and drug development efforts for Shigella-associated diarrheal disease.
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Probst-Hensch N, Jeong A, Stolz D, Pons M, Soccal PM, Bettschart R, Jarvis D, Holloway JW, Kronenberg F, Imboden M, Schindler C, Lovison GF. Causal Effects of Body Mass Index on Airflow Obstruction and Forced Mid-Expiratory Flow: A Mendelian Randomization Study Taking Interactions and Age-Specific Instruments Into Consideration Toward a Life Course Perspective. Front Public Health 2021; 9:584955. [PMID: 34046380 PMCID: PMC8144328 DOI: 10.3389/fpubh.2021.584955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/01/2021] [Indexed: 11/22/2022] Open
Abstract
Obesity has complex links to respiratory health. Mendelian randomization (MR) enables assessment of causality of body mass index (BMI) effects on airflow obstruction and mid-expiratory flow. In the adult SAPALDIA cohort, recruiting 9,651 population-representative samples aged 18–60 years at baseline (female 51%), BMI and the ratio of forced expiratory volume in 1 second (FEV1) to forced vital capacity (FVC) as well as forced mid-expiratory flow (FEF25–75%) were measured three times over 20 follow-up years. The causal effects of BMI in childhood and adulthood on FEV1/FVC and FEF25–75% were assessed in predictive (BMI averaged over 1st and 2nd, lung function (LF) averaged over 2nd and 3rd follow-up; N = 2,850) and long-term cross-sectional models (BMI and LF averaged over all follow-ups; N = 2,728) by Mendelian Randomization analyses with the use of weighted BMI allele score as an instrument variable and two-stage least squares (2SLS) method. Three different BMI allele scores were applied to specifically capture the part of BMI in adulthood that likely reflects tracking of genetically determined BMI in childhood. The main causal effects were derived from models containing BMI (instrumented by BMI genetic score), age, sex, height, and packyears smoked as covariates. BMI interactions were instrumented by the product of the instrument (BMI genetic score) and the relevant concomitant variable. Causal effects of BMI on FEV1/FVC and FEF25–75% were observed in both the predictive and long-term cross-sectional models. The causal BMI- LF effects were negative and attenuated with increasing age, and stronger if instrumented by gene scores associated with childhood BMI. This non-standard MR approach interrogating causal effects of multiplicative interaction suggests that the genetically rooted part of BMI patterns in childhood may be of particular relevance for the level of small airway function and airflow obstruction later in life. The methodological relevance of the results is first to point to the importance of a life course perspective in studies on the etiological role of BMI in respiratory health, and second to point out novel methodological aspects to be considered in future MR studies on the causal effects of obesity related phenotypes.
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Affiliation(s)
- Nicole Probst-Hensch
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Public Health, University of Basel, Basel, Switzerland
| | - Ayoung Jeong
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Public Health, University of Basel, Basel, Switzerland
| | - Daiana Stolz
- Clinic of Pulmonary Medicine and Respiratory Cell Research, University Hospital Basel, Basel, Switzerland
| | - Marco Pons
- Division of Pulmonary Medicine, Regional Hospital of Lugano, Lugano, Switzerland
| | - Paola M Soccal
- Division of Pulmonary Medicine, Geneva University Hospitals, Geneva, Switzerland
| | | | - Deborah Jarvis
- Medical Research Council-Public Health England, Centre for Environment and Health, Imperial College London, London, United Kingdom.,Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Medea Imboden
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Public Health, University of Basel, Basel, Switzerland
| | - Christian Schindler
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Public Health, University of Basel, Basel, Switzerland
| | - Gianfranco F Lovison
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Public Health, University of Basel, Basel, Switzerland.,Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy
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Labreche K, Daniau M, Sud A, Law PJ, Royer-Perron L, Holroyd A, Broderick P, Went M, Benazra M, Ahle G, Soubeyran P, Taillandier L, Chinot OL, Casasnovas O, Bay JO, Jardin F, Oberic L, Fabbro M, Damaj G, Brion A, Mokhtari K, Philippe C, Sanson M, Houillier C, Soussain C, Hoang-Xuan K, Houlston RS, Alentorn A. A genome-wide association study identifies susceptibility loci for primary central nervous system lymphoma at 6p25.3 and 3p22.1: a LOC Network study. Neuro Oncol 2021; 21:1039-1048. [PMID: 31102405 DOI: 10.1093/neuonc/noz088] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Primary central nervous system lymphoma (PCNSL) is a rare form of extra-nodal non-Hodgkin lymphoma. PCNSL is a distinct subtype of non-Hodgkin lymphoma, with over 95% of tumors belonging to the diffuse large B-cell lymphoma (DLBCL) group. We have conducted a genome-wide association study (GWAS) on immunocompetent patients to address the possibility that common genetic variants influence the risk of developing PCNSL. METHODS We performed a meta-analysis of 2 new GWASs of PCNSL totaling 475 cases and 1134 controls of European ancestry. To increase genomic resolution, we imputed >10 million single nucleotide polymorphisms using the 1000 Genomes Project combined with UK10K as reference. In addition we performed a transcription factor binding disruption analysis and investigated the patterns of local chromatin by Capture Hi-C data. RESULTS We identified independent risk loci at 3p22.1 (rs41289586, ANO10, P = 2.17 × 10-8) and 6p25.3 near EXOC2 (rs116446171, P = 1.95 x 10-13). In contrast, the lack of an association between rs41289586 and DLBCL suggests distinct germline predisposition to PCNSL and DLBCL. We found looping chromatin interactions between noncoding regions at 6p25.3 (rs11646171) with the IRF4 promoter and at 8q24.21 (rs13254990) with the MYC promoter, both genes with strong relevance to B-cell tumorigenesis. CONCLUSION To our knowledge this is the first study providing insight into the genetic predisposition to PCNSL. Our findings represent an important step in defining the contribution of common genetic variation to the risk of developing PCNSL.
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Affiliation(s)
- Karim Labreche
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK.,(i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France
| | - Mailys Daniau
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,ICM, iGenSeq Platform, Paris, France
| | - Amit Sud
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Louis Royer-Perron
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
| | - Amy Holroyd
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Molly Went
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Marion Benazra
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,ICM, iGenSeq Platform, Paris, France
| | - Guido Ahle
- Department of Neurology, Colmar Civil Hospitals, Colmar Cedex, France
| | - Pierre Soubeyran
- Department of Medical Oncology, Bergnoié Institute, Bordeaux, France.,Inserm Research Unit U1218, Bordeaux, France
| | - Luc Taillandier
- Neuro-oncology Department, Nancy University Hospital and The Center of Research in Automatic Control of Nancy, Joint Research Unit 7039, National Center for Scientific Research, SBS BEAM Department, Nancy University, Vandoeuvre-lès-Nancy, France
| | - Olivier L Chinot
- Department of Pathology and Neuropathology, Timone Hospital, Aix-Marseille University (AMU), Public Assistance-Hospitals of Marseille, Marseille, France.,AMU Research Center in Oncology Biology and Oncopharmacology, Marseille, France
| | | | - Jacques-Olivier Bay
- Department of Hematology, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Fabrice Jardin
- Department of Hematology, Henri Becquerel Cancer Center, Rouen, France and Inserm U1245, Henri Becquerel Cancer Center, Institute of Research and Innovation in Biomedicine, University of Normandy, Rouen, France
| | - Lucie Oberic
- Department of Hematology, University Cancer Institute of Toulouse-Oncopole, Toulouse, France
| | | | - Gandhi Damaj
- Department of Hematology, University Hospital of Caen, Caen, France
| | - Annie Brion
- Department of Hematology, Regional and University Hospitals Besançon, Besançon, France
| | - Karima Mokhtari
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Raymond Escourolle Department of Neuropathology, Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France.,OncoNeuroTek, ICM, Paris, France
| | | | - Marc Sanson
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France.,OncoNeuroTek, ICM, Paris, France
| | - Caroline Houillier
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France
| | - Carole Soussain
- Department of Hematology, René Huguenin Hospital, Curie Institute, Saint-Cloud, France
| | - Khê Hoang-Xuan
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Agusti Alentorn
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
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Verhulst B, Clark SL, Chen J, Maes HH, Chen X, Neale MC. Clarifying the Genetic Influences on Nicotine Dependence and Quantity of Use in Cigarette Smokers. Behav Genet 2021; 51:375-384. [PMID: 33884518 DOI: 10.1007/s10519-021-10056-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/30/2021] [Indexed: 11/29/2022]
Abstract
Nicotine dependence and smoking quantity are both robustly associated with the CHRNA5-A3-B4 gene cluster in the 15q25 region, and SNP rs16969968 in particular. The purpose of this paper is to use structural equation modeling techniques (SEM) to disentangle the complex pattern of relationships between rs16969968, nicotine quantity (as measured by the number of cigarettes an individual smokes per day; CPD) and nicotine dependence (as measured by the Fagerström Test for Nicotine Dependence; FTND). CPD is an indicator, but also a potential cause, of FTND, complicating the interpretation of associations between these constructs and requires a more detailed investigation than standard GWAS or general linear regression models can provide. FTND items and genotypes were collected in four samples, with a combined sample size of 5,373 respondents. A mega-analysis was conducted using a multiple group SEM approach to test competing hypotheses regarding the relationships between the SNP rs16969968, FTND and CPD. In the best fitting model, the FTND items loaded onto two correlated factors. The first, labeled "maintenance," assesses the motivation to maintain constant levels of nicotine through out the day. The second was labeled "urgency" as its items concern the urgency to restore nicotine levels after abstinence. We focus our attention on the "maintenance" factor, of which CPD was an indicator. The best fitting model included a negative feedback loop between the Maintenance factor and CPD. Accordingly, the motivation to maintain higher levels of nicotine increased the quantity of nicotine consumed, which subsequently decreases the maintenance motivation. The fact that the Maintenance-CPD feedback model fits the data best implies that there are at least two biological pathways that lead from rs16969968 to smoking behaviors. The model is consistent with a supply and demand system, which allows individuals to achieve a homeostatic equilibrium for their nicotine concentration.
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Affiliation(s)
- Brad Verhulst
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, 8447 Riverside Pkwy, Bryan, TX, 77807, USA.
| | - Shaunna L Clark
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, 8447 Riverside Pkwy, Bryan, TX, 77807, USA
| | - Jingchun Chen
- Nevada Institute of Personalized Medicine, University of Nevada, Reno, USA
| | | | - Xiangning Chen
- Nevada Institute of Personalized Medicine, University of Nevada, Reno, USA
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49
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Whitton AE, Rabinovich NE, Lindt JD, Pergadia ML, Pizzagalli DA, Gilbert DG. Genetic and Depressive Traits Moderate the Reward-Enhancing Effects of Acute Nicotine in Young Light Smokers. Nicotine Tob Res 2021; 23:1779-1786. [PMID: 33844007 DOI: 10.1093/ntr/ntab072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/11/2021] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Rates of light smoking have increased in recent years and are associated with adverse health outcomes. Reducing light smoking is a challenge because it is unclear why some but not others, progress to heavier smoking. Nicotine has profound effects on brain reward systems and individual differences in nicotine's reward-enhancing effects may drive variability in smoking trajectories. Therefore, we examined whether a genetic risk factor and personality traits known to moderate reward processing, also moderate the reward-enhancing effects of nicotine. METHODS Light smokers (n = 116) performed a Probabilistic Reward Task to assess reward responsiveness after receiving nicotine or placebo (order counterbalanced). Individuals were classified as nicotine dependence 'risk' allele carriers (rs16969968 A-allele carriers) or non-carriers (non-A-allele carriers), and self-reported negative affective traits were also measured. RESULTS Across the sample, reward responsiveness was greater following nicotine compared to placebo (p = 0.045). For Caucasian A-allele carriers but not non-A-allele carriers, nicotine enhanced reward responsiveness compared to placebo for those who received placebo first (p = 0.010). Furthermore, for A-allele carriers but not non-A-allele carriers who received nicotine first, the enhanced reward responsiveness in the nicotine condition carried over to the placebo condition (p < 0.001). Depressive traits also moderated the reward-enhancing effects of nicotine (p = 0.010) and were associated with blunted reward responsiveness following placebo but enhanced reward responsiveness following nicotine. CONCLUSION These findings suggest that individual differences in a genetic risk factor and depressive traits alter nicotine's effect on reward responsiveness in light smokers and may be important factors underpinning variability in smoking trajectories in this growing population. IMPLICATIONS Individuals carrying genetic risk factors associated with nicotine dependence(rs16969968 A-allele carriers) and those with higher levels of depressive personality traits, showmore pronounced increases in reward learning following acute nicotine exposure. These findingssuggest that genetic and personality factors may drive individual differences in smoking trajectoriesin young light smokers by altering the degree to which nicotine enhances reward processing. CLINICAL TRIAL REGISTRATION NCT02129387 (pre-registered hypothesis: www.clinicaltrials.gov).
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Affiliation(s)
- Alexis E Whitton
- McLean Hospital & Harvard Medical School, Boston, MA, USA.,Black Dog Institute, University of New South Wales, Sydney, NSW, Australia
| | - Norka E Rabinovich
- Department of Psychology, Southern Illinois University, Carbondale, IL, USA
| | - John D Lindt
- Department of Psychology, Southern Illinois University, Carbondale, IL, USA
| | - Michele L Pergadia
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | | | - David G Gilbert
- Department of Psychology, Southern Illinois University, Carbondale, IL, USA
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50
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Eldafashi N, Darlay R, Shukla R, McCain MV, Watson R, Liu YL, McStraw N, Fathy M, Fawzy MA, Zaki MYW, Daly AK, Maurício JP, Burt AD, Haugk B, Cordell HJ, Bianco C, Dufour JF, Valenti L, Anstee QM, Reeves HL. A PDCD1 Role in the Genetic Predisposition to NAFLD-HCC? Cancers (Basel) 2021; 13:1412. [PMID: 33808740 PMCID: PMC8003582 DOI: 10.3390/cancers13061412] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Obesity and non-alcoholic fatty liver disease (NAFLD) are contributing to the global rise in deaths from hepatocellular carcinoma (HCC). The pathogenesis of NAFLD-HCC is not well understood. The severity of hepatic steatosis, steatohepatitis and fibrosis are key pathogenic mechanisms, but animal studies suggest altered immune responses are also involved. Genetic studies have so far highlighted a major role of gene variants promoting fat deposition in the liver (PNPLA3 rs738409; TM6SF2 rs58542926). Here, we have considered single-nucleotide polymorphisms (SNPs) in candidate immunoregulatory genes (MICA rs2596542; CD44 rs187115; PDCD1 rs7421861 and rs10204525), in 594 patients with NAFLD and 391 with NAFLD-HCC, from three European centres. Associations between age, body mass index, diabetes, cirrhosis and SNPs with HCC development were explored. PNPLA3 and TM6SF2 SNPs were associated with both progression to cirrhosis and NAFLD-HCC development, while PDCD1 SNPs were specifically associated with NAFLD-HCC risk, regardless of cirrhosis. PDCD1 rs7421861 was independently associated with NAFLD-HCC development, while PDCD1 rs10204525 acquired significance after adjusting for other risks, being most notable in the smaller numbers of women with NAFLD-HCC. The study highlights the potential impact of inter individual variation in immune tolerance induction in patients with NAFLD, both in the presence and absence of cirrhosis.
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Affiliation(s)
- Nardeen Eldafashi
- Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (N.E.); (M.V.M.); (R.W.); (Y.L.L.); (M.Y.W.Z.); (A.K.D.); (J.P.M.); (A.D.B.); (Q.M.A.)
- Biochemistry Department, Faculty of Pharmacy, Minia University, Minia 61519, Egypt; (M.F.); (M.A.F.)
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK; (R.D.); (H.J.C.)
| | - Ruchi Shukla
- Biosciences Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (R.S.); (N.M.)
| | - Misti Vanette McCain
- Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (N.E.); (M.V.M.); (R.W.); (Y.L.L.); (M.Y.W.Z.); (A.K.D.); (J.P.M.); (A.D.B.); (Q.M.A.)
| | - Robyn Watson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (N.E.); (M.V.M.); (R.W.); (Y.L.L.); (M.Y.W.Z.); (A.K.D.); (J.P.M.); (A.D.B.); (Q.M.A.)
| | - Yang Lin Liu
- Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (N.E.); (M.V.M.); (R.W.); (Y.L.L.); (M.Y.W.Z.); (A.K.D.); (J.P.M.); (A.D.B.); (Q.M.A.)
| | - Nikki McStraw
- Biosciences Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (R.S.); (N.M.)
| | - Moustafa Fathy
- Biochemistry Department, Faculty of Pharmacy, Minia University, Minia 61519, Egypt; (M.F.); (M.A.F.)
| | - Michael Atef Fawzy
- Biochemistry Department, Faculty of Pharmacy, Minia University, Minia 61519, Egypt; (M.F.); (M.A.F.)
| | - Marco Y. W. Zaki
- Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (N.E.); (M.V.M.); (R.W.); (Y.L.L.); (M.Y.W.Z.); (A.K.D.); (J.P.M.); (A.D.B.); (Q.M.A.)
- Biochemistry Department, Faculty of Pharmacy, Minia University, Minia 61519, Egypt; (M.F.); (M.A.F.)
| | - Ann K. Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (N.E.); (M.V.M.); (R.W.); (Y.L.L.); (M.Y.W.Z.); (A.K.D.); (J.P.M.); (A.D.B.); (Q.M.A.)
| | - João P. Maurício
- Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (N.E.); (M.V.M.); (R.W.); (Y.L.L.); (M.Y.W.Z.); (A.K.D.); (J.P.M.); (A.D.B.); (Q.M.A.)
| | - Alastair D. Burt
- Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (N.E.); (M.V.M.); (R.W.); (Y.L.L.); (M.Y.W.Z.); (A.K.D.); (J.P.M.); (A.D.B.); (Q.M.A.)
| | - Beate Haugk
- Department of Cellular Pathology, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle NE1 4LP, UK;
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK; (R.D.); (H.J.C.)
| | - Cristiana Bianco
- Translational Medicine, Department of Transfusion Medicine and Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (C.B.); (L.V.)
| | - Jean-François Dufour
- University Clinic for Visceral Surgery and Medicine, University Hospital of Bern, 3010 Bern, Switzerland;
- Hepatology, Department of Biomedical Research, University of Bern, 3012 Bern, Switzerland
| | - Luca Valenti
- Translational Medicine, Department of Transfusion Medicine and Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (C.B.); (L.V.)
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Quentin M. Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (N.E.); (M.V.M.); (R.W.); (Y.L.L.); (M.Y.W.Z.); (A.K.D.); (J.P.M.); (A.D.B.); (Q.M.A.)
- The Liver Unit, Freeman Hospital, Freeman Road, Newcastle upon Tyne Hospitals NHS Foundation Trust, Heaton NE7 7DN, UK
| | - Helen L. Reeves
- Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; (N.E.); (M.V.M.); (R.W.); (Y.L.L.); (M.Y.W.Z.); (A.K.D.); (J.P.M.); (A.D.B.); (Q.M.A.)
- The Liver Unit, Freeman Hospital, Freeman Road, Newcastle upon Tyne Hospitals NHS Foundation Trust, Heaton NE7 7DN, UK
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