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Jennings MV, Martínez-Magaña JJ, Courchesne-Krak NS, Cupertino RB, Vilar-Ribó L, Bianchi SB, Hatoum AS, Atkinson EG, Giusti-Rodriguez P, Montalvo-Ortiz JL, Gelernter J, Artigas MS, Elson SL, Edenberg HJ, Fontanillas P, Palmer AA, Sanchez-Roige S. A phenome-wide association and Mendelian randomisation study of alcohol use variants in a diverse cohort comprising over 3 million individuals. EBioMedicine 2024; 103:105086. [PMID: 38580523 PMCID: PMC11121167 DOI: 10.1016/j.ebiom.2024.105086] [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: 12/13/2022] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Alcohol consumption is associated with numerous negative social and health outcomes. These associations may be direct consequences of drinking, or they may reflect common genetic factors that influence both alcohol consumption and other outcomes. METHODS We performed exploratory phenome-wide association studies (PheWAS) of three of the best studied protective single nucleotide polymorphisms (SNPs) in genes encoding ethanol metabolising enzymes (ADH1B: rs1229984-T, rs2066702-A; ADH1C: rs698-T) using up to 1109 health outcomes across 28 phenotypic categories (e.g., substance-use, mental health, sleep, immune, cardiovascular, metabolic) from a diverse 23andMe cohort, including European (N ≤ 2,619,939), Latin American (N ≤ 446,646) and African American (N ≤ 146,776) populations to uncover new and perhaps unexpected associations. These SNPs have been consistently implicated by both candidate gene studies and genome-wide association studies of alcohol-related behaviours but have not been investigated in detail for other relevant phenotypes in a hypothesis-free approach in such a large cohort of multiple ancestries. To provide insight into potential causal effects of alcohol consumption on the outcomes significant in the PheWAS, we performed univariable two-sample and one-sample Mendelian randomisation (MR) analyses. FINDINGS The minor allele rs1229984-T, which is protective against alcohol behaviours, showed the highest number of PheWAS associations across the three cohorts (N = 232, European; N = 29, Latin American; N = 7, African American). rs1229984-T influenced multiple domains of health. We replicated associations with alcohol-related behaviours, mental and sleep conditions, and cardio-metabolic health. We also found associations with understudied traits related to neurological (migraines, epilepsy), immune (allergies), musculoskeletal (fibromyalgia), and reproductive health (preeclampsia). MR analyses identified evidence of causal effects of alcohol consumption on liability for 35 of these outcomes in the European cohort. INTERPRETATION Our work demonstrates that polymorphisms in genes encoding alcohol metabolising enzymes affect multiple domains of health beyond alcohol-related behaviours. Understanding the underlying mechanisms of these effects could have implications for treatments and preventative medicine. FUNDING MVJ, NCK, SBB, SSR and AAP were supported by T32IR5226 and 28IR-0070. SSR was also supported by NIDA DP1DA054394. NCK and RBC were also supported by R25MH081482. ASH was supported by funds from NIAAA K01AA030083. JLMO was supported by VA 1IK2CX002095. JLMO and JJMM were also supported by NIDA R21DA050160. JJMM was also supported by the Kavli Postdoctoral Award for Academic Diversity. EGA was supported by K01MH121659 from the NIMH/NIH, the Caroline Wiess Law Fund for Research in Molecular Medicine and the ARCO Foundation Young Teacher-Investigator Fund at Baylor College of Medicine. MSA was supported by the Instituto de Salud Carlos III and co-funded by the European Union Found: Fondo Social Europeo Plus (FSE+) (P19/01224, PI22/00464 and CP22/00128).
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Affiliation(s)
- Mariela V Jennings
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - José Jaime Martínez-Magaña
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, Orange, West Haven, CT, USA
| | | | - Renata B Cupertino
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Laura Vilar-Ribó
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
| | - Sevim B Bianchi
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Alexander S Hatoum
- Department of Psychology & Brain Sciences, Washington University in St. Louis, St Louis, MO, USA
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Paola Giusti-Rodriguez
- Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL, USA
| | - Janitza L Montalvo-Ortiz
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, Orange, West Haven, CT, USA; National Center of Posttraumatic Stress Disorder, VA CT Healthcare Center, West Haven, CT, USA
| | - Joel Gelernter
- VA CT Healthcare Center, Department Psychiatry, West Haven, CT, USA; Departments Psychiatry, Genetics, and Neuroscience, Yale Univ. School of Medicine, New Haven, CT, USA
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain; Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | | | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA.
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Sanchez-Roige S, Jennings MV, Thorpe HHA, Mallari JE, van der Werf LC, Bianchi SB, Huang Y, Lee C, Mallard TT, Barnes SA, Wu JY, Barkley-Levenson AM, Boussaty EC, Snethlage CE, Schafer D, Babic Z, Winters BD, Watters KE, Biederer T, Mackillop J, Stephens DN, Elson SL, Fontanillas P, Khokhar JY, Young JW, Palmer AA. CADM2 is implicated in impulsive personality and numerous other traits by genome- and phenome-wide association studies in humans and mice. Transl Psychiatry 2023; 13:167. [PMID: 37173343 PMCID: PMC10182097 DOI: 10.1038/s41398-023-02453-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Impulsivity is a multidimensional heritable phenotype that broadly refers to the tendency to act prematurely and is associated with multiple forms of psychopathology, including substance use disorders. We performed genome-wide association studies (GWAS) of eight impulsive personality traits from the Barratt Impulsiveness Scale and the short UPPS-P Impulsive Personality Scale (N = 123,509-133,517 23andMe research participants of European ancestry), and a measure of Drug Experimentation (N = 130,684). Because these GWAS implicated the gene CADM2, we next performed single-SNP phenome-wide studies (PheWAS) of several of the implicated variants in CADM2 in a multi-ancestral 23andMe cohort (N = 3,229,317, European; N = 579,623, Latin American; N = 199,663, African American). Finally, we produced Cadm2 mutant mice and used them to perform a Mouse-PheWAS ("MouseWAS") by testing them with a battery of relevant behavioral tasks. In humans, impulsive personality traits showed modest chip-heritability (~6-11%), and moderate genetic correlations (rg = 0.20-0.50) with other personality traits, and various psychiatric and medical traits. We identified significant associations proximal to genes such as TCF4 and PTPRF, and also identified nominal associations proximal to DRD2 and CRHR1. PheWAS for CADM2 variants identified associations with 378 traits in European participants, and 47 traits in Latin American participants, replicating associations with risky behaviors, cognition and BMI, and revealing novel associations including allergies, anxiety, irritable bowel syndrome, and migraine. Our MouseWAS recapitulated some of the associations found in humans, including impulsivity, cognition, and BMI. Our results further delineate the role of CADM2 in impulsivity and numerous other psychiatric and somatic traits across ancestries and species.
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Affiliation(s)
- Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Mariela V Jennings
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Hayley H A Thorpe
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Jazlene E Mallari
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | - Sevim B Bianchi
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Yuye Huang
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Calvin Lee
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Samuel A Barnes
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jin Yi Wu
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | - Ely C Boussaty
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Cedric E Snethlage
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Danielle Schafer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Zeljana Babic
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Boyer D Winters
- Department of Psychology, University of Guelph, Guelph, ON, Canada
| | - Katherine E Watters
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Thomas Biederer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA
| | - James Mackillop
- Peter Boris Centre for Addictions Research, McMaster University and St. Joseph's Healthcare Hamilton, Hamilton, ON, Canada and Homewood Research Institute, Guelph, ON, Canada
| | - David N Stephens
- Laboratory of Behavioural and Clinical Neuroscience, School of Psychology, University of Sussex, Brighton, UK
| | | | | | - Jibran Y Khokhar
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Jared W Young
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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3
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Kerley CI, Chaganti S, Nguyen TQ, Bermudez C, Cutting LE, Beason-Held LL, Lasko T, Landman BA. pyPheWAS: A Phenome-Disease Association Tool for Electronic Medical Record Analysis. Neuroinformatics 2022; 20:483-505. [PMID: 34981404 PMCID: PMC9250547 DOI: 10.1007/s12021-021-09553-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
Along with the increasing availability of electronic medical record (EMR) data, phenome-wide association studies (PheWAS) and phenome-disease association studies (PheDAS) have become a prominent, first-line method of analysis for uncovering the secrets of EMR. Despite this recent growth, there is a lack of approachable software tools for conducting these analyses on large-scale EMR cohorts. In this article, we introduce pyPheWAS, an open-source python package for conducting PheDAS and related analyses. This toolkit includes 1) data preparation, such as cohort censoring and age-matching; 2) traditional PheDAS analysis of ICD-9 and ICD-10 billing codes; 3) PheDAS analysis applied to a novel EMR phenotype mapping: current procedural terminology (CPT) codes; and 4) novelty analysis of significant disease-phenotype associations found through PheDAS. The pyPheWAS toolkit is approachable and comprehensive, encapsulating data prep through result visualization all within a simple command-line interface. The toolkit is designed for the ever-growing scale of available EMR data, with the ability to analyze cohorts of 100,000 + patients in less than 2 h. Through a case study of Down Syndrome and other intellectual developmental disabilities, we demonstrate the ability of pyPheWAS to discover both known and potentially novel disease-phenotype associations across different experiment designs and disease groups. The software and user documentation are available in open source at https://github.com/MASILab/pyPheWAS .
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Affiliation(s)
- Cailey I Kerley
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA.
| | - Shikha Chaganti
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Tin Q Nguyen
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.,Department of Special Education, Peabody College of Education and Human Development, Nashville, TN, USA
| | - Camilo Bermudez
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Laurie E Cutting
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.,Department of Special Education, Peabody College of Education and Human Development, Nashville, TN, USA.,Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
| | - Lori L Beason-Held
- Laboratory of Behavioral Neuroscience, National Institute On Aging, NIH, Baltimore, MD, USA
| | - Thomas Lasko
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bennett A Landman
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA.,Department of Computer Science, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
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4
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The Immunogenetics of Acne. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:137-154. [DOI: 10.1007/978-3-030-92616-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Wilson PA, Santos Franco S, He L, Galwey NW, Meakin J, McIntyre R, McHugh SM, Nolan MA, Spain SL, Carlson T, Lobera M, Rubio JP, Davis B, McCarthy LC. Transcriptomic effects of rs4845604, an IBD and allergy-associated RORC variant, in stimulated ex vivo CD4+ T cells. PLoS One 2021; 16:e0258316. [PMID: 34673799 PMCID: PMC8530322 DOI: 10.1371/journal.pone.0258316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/23/2021] [Indexed: 11/18/2022] Open
Abstract
RORγt is an isoform of RORC, preferentially expressed in Th17 cells, that functions as a critical regulator of type 3 immunity. As murine Th17-driven inflammatory disease models were greatly diminished in RORC knock-out mice, this receptor was prioritised as an attractive therapeutic target for the treatment of several autoimmune diseases. Human genetic studies indicate a significant contributory role for RORC in several human disease conditions. Furthermore, genome-wide association studies (GWAS) report a significant association between inflammatory bowel disease (IBD) and the RORC regulatory variant rs4845604. To investigate if the rs4845604 variant may affect CD4+ T cell differentiation events, naïve CD4+ T cells were isolated from eighteen healthy subjects homozygous for the rs4845604 minor (A) or major (G) allele). Isolated cells from each subject were differentiated into distinct T cell lineages by culturing in either T cell maintenance medium or Th17 driving medium conditions for six days in the presence of an RORC inverse agonist (to prevent constitutive receptor activity) or an inactive diastereomer (control). Our proof of concept study indicated that genotype had no significant effect on the mean number of naïve CD4 T cells isolated, nor the frequency of Th1-like and Th17-like cells following six days of culture in any of the four culture conditions. Analysis of the derived RNA-seq count data identified genotype-driven transcriptional effects in each of the four culture conditions. Subsequent pathway enrichment analysis of these profiles reported perturbation of metabolic signalling networks, with the potential to affect the cellular detoxification response. This investigation reveals that rs4845604 genotype is associated with transcriptional effects in CD4+ T cells that may perturb immune and metabolic pathways. Most significantly, the rs4845604 GG, IBD risk associated, genotype may be associated with a differential detoxification response. This observation justifies further investigation in a larger cohort of both healthy and IBD-affected individuals.
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Affiliation(s)
- Paul A. Wilson
- Human Genetics, GlaxoSmithKline Medicine Research Centre, Stevenage, England
| | - Sara Santos Franco
- Clinical Unit Cambridge, Addenbrooke’s Centre for Clinical Investigation, GlaxoSmithKline, Cambridge, England
| | - Liu He
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Nicholas W. Galwey
- Research Statistics, GlaxoSmithKline Medicines Research Centre, Stevenage, England
| | - Jackie Meakin
- Functional Genomics, GlaxoSmithKline Medicines Research Centre, Stevenage, England
| | | | - Simon M. McHugh
- Clinical Unit Cambridge, Addenbrooke’s Centre for Clinical Investigation, GlaxoSmithKline, Cambridge, England
| | | | | | - Thaddeus Carlson
- Adaptive Immunity, GSK Pharma Research & Development, Cambridge, MA, United States of America
| | - Mercedes Lobera
- Adaptive Immunity, GSK Pharma Research & Development, Cambridge, MA, United States of America
| | - Justin P. Rubio
- Department of Pharmacology and Therapeutics, The University of Melbourne, Victoria, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia
| | - Bill Davis
- Clinical Unit Cambridge, Addenbrooke’s Centre for Clinical Investigation, GlaxoSmithKline, Cambridge, England
| | - Linda C. McCarthy
- Human Genetics, GlaxoSmithKline Medicine Research Centre, Stevenage, England
- * E-mail:
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Heng AHS, Say YH, Sio YY, Ng YT, Chew FT. Gene variants associated with acne vulgaris presentation and severity: a systematic review and meta-analysis. BMC Med Genomics 2021; 14:103. [PMID: 33849530 PMCID: PMC8045239 DOI: 10.1186/s12920-021-00953-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/29/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Multiple factors have been attributed to acne vulgaris predisposition and individual variations in the severity of skin symptoms, and genetics stood out as one of the major factors. METHODS We performed a systematic review on the genes and their variants that have been investigated for association with acne presentation and severity. A random-effect meta-analysis using the allele model (minor allele vs. major allele) was also conducted to provide an overall estimation of risk effects of frequently reported gene variants. This included a subset data of 982 acne cases and 846 controls extracted from our existing GWAS database on various allergic and skin diseases among Singapore Chinese. RESULTS Systematic review of 51 articles covering Asians and Caucasians found 60 genes/loci and their 100 variants implicated in acne; majority of them were in the intron, coding region/missense, and promoter regions. The commonly studied candidate genes/gene families include tumor necrosis factor (TNF), and the interleukin (IL) and cytochrome P450 (CYP) gene families. Our meta-analysis showed that most of the analyzed gene variants exhibited insignificant pooled odds ratio (pOR) and significant heterogeneity between studies. Nevertheless, we found that TNF rs1800629 A allele carriers and CYP17A1 rs743572 T allele carriers had significantly reduced mild acne risk [pOR: 0.60; 95% Confidence Interval (CI): 0.33-0.86] and severe acne risk (pOR: 0.59; 95% CI: 0.40-0.79), respectively, across populations. Overall, FST (follistatin) rs629725 A allele poses a significantly modest increased risk for acne presentation (pOR: 1.19, 95% CI: 1.14, 1.23), but neither TIMP2 (TIMP metallopeptidase inhibitor 2) rs8179090 nor CYP1A1 rs4646903 (pOR: 0.96, 95% CI: 0.80-1.12; pOR: 0.95, 95% CI: 0.83, 1.08), respectively. We discovered 15 novel SNPs in the 3' UTR region of the Toll-like Receptor 4 gene (TLR4) associated with acne presentation. CONCLUSIONS This systematic review and meta-analysis suggest that genes influencing inflammatory responses, specifically TNF, and genes influencing the function and activity of sebaceous glands, specifically CYP17A1 and FST, have potential risk variants for acne presentation and severity across populations. Understanding the genetic susceptibility factors and biological pathways involved in the pathogenesis of acne will help us to gain insights into developing effective acne treatments.
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Affiliation(s)
- Anna Hwee Sing Heng
- Allergy and Molecular Immunology Laboratory, Lee Hiok Kwee Functional Genomics Laboratories, Department of Biological Sciences, Faculty of Science, National University of Singapore, Block S2, Level 5, 14 Science Drive 4, Lower Kent Ridge Road, Singapore, 117543, Singapore
| | - Yee-How Say
- Allergy and Molecular Immunology Laboratory, Lee Hiok Kwee Functional Genomics Laboratories, Department of Biological Sciences, Faculty of Science, National University of Singapore, Block S2, Level 5, 14 Science Drive 4, Lower Kent Ridge Road, Singapore, 117543, Singapore
| | - Yang Yie Sio
- Allergy and Molecular Immunology Laboratory, Lee Hiok Kwee Functional Genomics Laboratories, Department of Biological Sciences, Faculty of Science, National University of Singapore, Block S2, Level 5, 14 Science Drive 4, Lower Kent Ridge Road, Singapore, 117543, Singapore
| | - Yu Ting Ng
- Allergy and Molecular Immunology Laboratory, Lee Hiok Kwee Functional Genomics Laboratories, Department of Biological Sciences, Faculty of Science, National University of Singapore, Block S2, Level 5, 14 Science Drive 4, Lower Kent Ridge Road, Singapore, 117543, Singapore
| | - Fook Tim Chew
- Allergy and Molecular Immunology Laboratory, Lee Hiok Kwee Functional Genomics Laboratories, Department of Biological Sciences, Faculty of Science, National University of Singapore, Block S2, Level 5, 14 Science Drive 4, Lower Kent Ridge Road, Singapore, 117543, Singapore.
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Li QS, Tian C, Hinds D, Seabrook GR. The association of clinical phenotypes to known AD/FTD genetic risk loci and their inter-relationship. PLoS One 2020; 15:e0241552. [PMID: 33152005 PMCID: PMC7644002 DOI: 10.1371/journal.pone.0241552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 10/18/2020] [Indexed: 11/25/2022] Open
Abstract
To elucidate how variants in genetic risk loci previously implicated in Alzheimer’s Disease (AD) and/or frontotemporal dementia (FTD) contribute to expression of disease phenotypes, a phenome-wide association study was performed in two waves. In the first wave, we explored clinical traits associated with thirteen genetic variants previously reported to be linked to disease risk using both the 23andMe and UKB cohorts. We tested 30 additional AD variants in UKB cohort only in the second wave. APOE variants defining ε2/ε3/ε4 alleles and rs646776 were identified to be significantly associated with metabolic/cardiovascular and longevity traits. APOE variants were also significantly associated with neurological traits. ABI3 variant rs28394864 was significantly associated with cardiovascular (e.g. (hypertension, ischemic heart disease, coronary atherosclerosis, angina) and immune-related trait asthma. Both APOE variants and CLU variant were significantly associated with nearsightedness. HLA- DRB1 variant was associated with diseases with immune-related traits. Additionally, variants from 10+ AD genes (BZRAP1-AS1, ADAMTS4, ADAM10, APH1B, SCIMP, ABI3, SPPL2A, ZNF232, GRN, CD2AP, and CD33) were associated with hematological measurements such as white blood cell (leukocyte) count, monocyte count, neutrophill count, platelet count, and/or mean platelet (thrombocyte) volume (an autoimmune disease biomarker). Many of these genes are expressed specifically in microglia. The associations of ABI3 variant with cardiovascular and immune-related traits are one of the novel findings from this study. Taken together, it is evidenced that at least some AD and FTD variants are associated with multiple clinical phenotypes and not just dementia. These findings were discussed in the context of causal relationship versus pleiotropy via Mendelian randomization analysis.
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Affiliation(s)
- Qingqin S. Li
- Janssen Research & Development, LLC, Titusville, NJ, United States of America
- * E-mail:
| | - Chao Tian
- 23andMe, Inc., Mountain View, CA, United States of America
| | | | - David Hinds
- 23andMe, Inc., Mountain View, CA, United States of America
| | - Guy R. Seabrook
- Johnson & Johnson Innovation, South San Francisco, CA, United States of America
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Michelini S, Ricci M, Serrani R, Stuppia L, Beccari T, Veselenyiova D, Kenanoglu S, Barati S, Kurti D, Baglivo M, Basha SH, Krajcovic J, Dundar M, Bertelli M. Possible Role of the RORC Gene in Primary and Secondary Lymphedema: Review of the Literature and Genetic Study of Two Rare Causative Variants. Lymphat Res Biol 2020; 19:129-133. [PMID: 32960152 DOI: 10.1089/lrb.2020.0030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: RAR-related Orphan Receptor C (RORC) is a DNA-binding transcription factor and the key transcription factor responsible for differentiation of T helper 17 cells. The RORC gene plays a role in lymphoid organogenesis, thymopoiesis, and lymph node organogenesis. The aim of our study was to determine the possible role of RORC in the development of lymphatic system malformations by combining data from the scientific literature and next-generation sequencing of RORC in lymphedema patients negative for known causative genes. Methods and Results: We sequenced RORC in 235 lymphedema patients negative for known lymphedema-associated genes. We found two probands carrying nonsense RORC variants. Conclusions: We show that RORC is important for normal function of the lymphatic system and that a rare variant with a possible causative effect may imply predisposition for lymphedema.
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Affiliation(s)
- Sandro Michelini
- Department of Vascular Rehabilitation, San Giovanni Battista Hospital, Rome, Italy
| | - Maurizio Ricci
- Rehabilitative Medicine, University Hospital, Ospedali Riuniti of Ancona, Torrette, Italy
| | - Roberta Serrani
- Rehabilitative Medicine, University Hospital, Ospedali Riuniti of Ancona, Torrette, Italy
| | - Liborio Stuppia
- Aging and Translational Medicine Research Center (CeSI-MeT), University "G. d'Annunzio," Chieti-Pescara, Italy
| | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti 48, Perugia, Italy
| | - Dominika Veselenyiova
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
- MAGI Euregio, Bolzano, Italy
| | - Sercan Kenanoglu
- MAGI Euregio, Bolzano, Italy
- Department of Medical Genetics, Erciyes University, Kayseri, Turkey
| | | | - Danjela Kurti
- MAGI Euregio, Bolzano, Italy
- MAGI-Balkan, Tirana, Albania
| | | | | | - Juraj Krajcovic
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Munis Dundar
- Department of Medical Genetics, Erciyes University, Kayseri, Turkey
| | - Matteo Bertelli
- MAGI Euregio, Bolzano, Italy
- EBTNA-Lab, Rovereto, TN, Italy
- MAGI's Lab, Rovereto, TN, Italy
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Sparber F, Ruchti F, LeibundGut-Landmann S. Host Immunity to Malassezia in Health and Disease. Front Cell Infect Microbiol 2020; 10:198. [PMID: 32477963 PMCID: PMC7232612 DOI: 10.3389/fcimb.2020.00198] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/15/2020] [Indexed: 12/23/2022] Open
Abstract
The microbiota plays an integral role in shaping physical and functional aspects of the skin. While a healthy microbiota contributes to the maintenance of immune homeostasis, dysbiosis can result in the development of diverse skin pathologies. This dichotomous feature of the skin microbiota holds true not only for bacteria, but also for fungi that colonize the skin. As such, the yeast Malassezia, which is by far the most abundant component of the skin mycobiota, is associated with a variety of skin disorders, of which some can be chronic and severe and have a significant impact on the quality of life of those affected. Understanding the causative relationship between Malassezia and the development of such skin disorders requires in-depth knowledge of the mechanism by which the immune system interacts with and responds to the fungus. In this review, we will discuss recent advances in our understanding of the immune response to Malassezia and how the implicated cells and cytokine pathways prevent uncontrolled fungal growth to maintain commensalism in the mammalian skin. We also review how the antifungal response is currently thought to affect the development and severity of inflammatory disorders of the skin and at distant sites.
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Affiliation(s)
- Florian Sparber
- Section of Immunology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Fiorella Ruchti
- Section of Immunology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Salomé LeibundGut-Landmann
- Section of Immunology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
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10
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Wu P, Gifford A, Meng X, Li X, Campbell H, Varley T, Zhao J, Carroll R, Bastarache L, Denny JC, Theodoratou E, Wei WQ. Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation. JMIR Med Inform 2019; 7:e14325. [PMID: 31553307 PMCID: PMC6911227 DOI: 10.2196/14325] [Citation(s) in RCA: 259] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/03/2019] [Accepted: 09/24/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The phecode system was built upon the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) for phenome-wide association studies (PheWAS) using the electronic health record (EHR). OBJECTIVE The goal of this paper was to develop and perform an initial evaluation of maps from the International Classification of Diseases, 10th Revision (ICD-10) and the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) codes to phecodes. METHODS We mapped ICD-10 and ICD-10-CM codes to phecodes using a number of methods and resources, such as concept relationships and explicit mappings from the Centers for Medicare & Medicaid Services, the Unified Medical Language System, Observational Health Data Sciences and Informatics, Systematized Nomenclature of Medicine-Clinical Terms, and the National Library of Medicine. We assessed the coverage of the maps in two databases: Vanderbilt University Medical Center (VUMC) using ICD-10-CM and the UK Biobank (UKBB) using ICD-10. We assessed the fidelity of the ICD-10-CM map in comparison to the gold-standard ICD-9-CM phecode map by investigating phenotype reproducibility and conducting a PheWAS. RESULTS We mapped >75% of ICD-10 and ICD-10-CM codes to phecodes. Of the unique codes observed in the UKBB (ICD-10) and VUMC (ICD-10-CM) cohorts, >90% were mapped to phecodes. We observed 70-75% reproducibility for chronic diseases and <10% for an acute disease for phenotypes sourced from the ICD-10-CM phecode map. Using the ICD-9-CM and ICD-10-CM maps, we conducted a PheWAS with a Lipoprotein(a) genetic variant, rs10455872, which replicated two known genotype-phenotype associations with similar effect sizes: coronary atherosclerosis (ICD-9-CM: P<.001; odds ratio (OR) 1.60 [95% CI 1.43-1.80] vs ICD-10-CM: P<.001; OR 1.60 [95% CI 1.43-1.80]) and chronic ischemic heart disease (ICD-9-CM: P<.001; OR 1.56 [95% CI 1.35-1.79] vs ICD-10-CM: P<.001; OR 1.47 [95% CI 1.22-1.77]). CONCLUSIONS This study introduces the beta versions of ICD-10 and ICD-10-CM to phecode maps that enable researchers to leverage accumulated ICD-10 and ICD-10-CM data for PheWAS in the EHR.
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Affiliation(s)
- Patrick Wu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Aliya Gifford
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Xiangrui Meng
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Xue Li
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Varley
- Public Health and Intelligence Strategic Business Unit, National Services Scotland, Edinburgh, United Kingdom
| | - Juan Zhao
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Robert Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Evropi Theodoratou
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
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11
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Whitehead GS, Kang HS, Thomas SY, Medvedev A, Karcz TP, Izumi G, Nakano K, Makarov SS, Nakano H, Jetten AM, Cook DN. Therapeutic suppression of pulmonary neutrophilia and allergic airway hyperresponsiveness by a RORγt inverse agonist. JCI Insight 2019; 5:125528. [PMID: 31184998 DOI: 10.1172/jci.insight.125528] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Airway neutrophilia occurs in approximately 50% of patients with asthma and is associated with particularly severe disease. Unfortunately, this form of asthma is usually refractory to corticosteroid treatment, and there is an unmet need for new therapies. Pulmonary neutrophilic inflammation is associated with Th17 cells, whose differentiation is controlled by the nuclear receptor, RORγt. Here, we tested whether VTP-938, a selective inverse agonist of this receptor, can reduce disease parameters in animal models of neutrophilic asthma. When administered prior to allergic sensitization through the airway, the RORγt inverse agonist blunted allergen-specific Th17 cell development in lung-draining lymph nodes and attenuated allergen-induced production of IL-17. VTP-938 also reduced pulmonary production of IL-17 and airway neutrophilia when given during the allergen challenge of the model. Finally, in an environmentally relevant model of allergic responses to house dust extracts, VTP-938 suppressed production of IL-17 and neutrophilic inflammation, and also markedly diminished airway hyperresponsiveness. Together, these findings suggest that orally available inverse agonists of RORγt might provide an effective therapy to treat glucocorticoid-resistant neutrophilic asthma.
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Affiliation(s)
- Gregory S Whitehead
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Hong Soon Kang
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Seddon Y Thomas
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | | | - Tadeusz P Karcz
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Gentaro Izumi
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Keiko Nakano
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | | | - Hideki Nakano
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Anton M Jetten
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Donald N Cook
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
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12
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Fox CS. Using Human Genetics to Drive Drug Discovery: A Perspective. Am J Kidney Dis 2019; 74:111-119. [PMID: 30898364 DOI: 10.1053/j.ajkd.2018.12.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/24/2018] [Indexed: 12/11/2022]
Abstract
The probability of success of developing medicines to treat human disease can be improved by leveraging human genetics. Different types of genetic data and techniques, including genome-wide association, whole-exome sequencing, and whole-genome sequencing, can be used to gain insight into human disease. Layering different types of genetic evidence from Mendelian disease, coding variants, and common variation can bolster support for a genetic target. Human knockouts offer the potential to perform reverse genetic screens in humans to identify physiologically relevant targets. Other components of a good genetic target include protective loss-of-function mutations, some degree of known biology, tractability, and a clean on-target safety profile. In addition to using human genetics to inspire new drug programs, phenome-wide association studies can be used to identify alternative indications or repurposing opportunities. This information can be combined into a 5-step approach for selecting a genetic target for validation, which is presented in detail in this review. Finally, current challenges in leveraging human genetics are highlighted, including the difficulties translating certain types of genetic data, relatively small number of bona fide disease-associated coding rare variants, and current sample sizes of large well-curated biobanks linked to comprehensive genetic information.
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Genomic and Phenomic Research in the 21st Century. Trends Genet 2018; 35:29-41. [PMID: 30342790 DOI: 10.1016/j.tig.2018.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 02/06/2023]
Abstract
The field of human genomics has changed dramatically over time. Initial genomic studies were predominantly restricted to rare disorders in small families. Over the past decade, researchers changed course from family-based studies and instead focused on common diseases and traits in populations of unrelated individuals. With further advancements in biobanking, computer science, electronic health record (EHR) data, and more affordable high-throughput genomics, we are experiencing a new paradigm in human genomic research. Rapidly changing technologies and resources now make it possible to study thousands of diseases simultaneously at the genomic level. This review will focus on these advancements as scientists begin to incorporate phenome-wide strategies in human genomic research to understand the etiology of human diseases and develop new drugs to treat them.
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