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Gautam Y, Satish L, Ramirez S, Grashel B, Biagini JM, Martin LJ, Rothenberg ME, Khurana Hershey GK, Mersha TB. Joint genotype and ancestry analysis identify novel loci associated with atopic dermatitis in African American population. HGG ADVANCES 2024; 5:100350. [PMID: 39245941 PMCID: PMC11470243 DOI: 10.1016/j.xhgg.2024.100350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/10/2024] Open
Abstract
Atopic dermatitis (AD) is a chronic itchy inflammatory disease of the skin. Genetic studies have identified multiple risk factors linked to the disease; however, most of the studies have been derived from European and East Asian populations. The admixed African American (AA) genome may provide an opportunity to discovery ancestry-specific loci involved in AD susceptibility. Herein, we present joint analysis of ancestry and genotype effects followed by validation using differential gene expression analysis on AD using 726 AD-affected individuals and 999 non-AD control individuals from the AA population, genotyped using Multi-Ethnic Global Array (MEGA) followed by imputation using the Consortium on Asthma among African Ancestry Populations in the Americas (CAAPA) reference panel. The joint analysis identified two novel AD-susceptibility loci, rs2195989 in gene ANGPT1 (8q23.1) and rs62538818 in the intergenic region between genes LURAP1L and MPDZ (9p23). Admixture mapping (AM) results showed potential genomic inflation, and we implemented genomic control and identified five ancestry-of-origin loci with European ancestry effects. The multi-omics functional prioritization of variants in AM signals prioritized the loci SLAIN2, RNF39, and FOXA2. Genome-wide association study (GWAS) identified variants significantly associated with AD in the AA population, including SGK1 (rs113357522, odds ratio [OR] = 2.81), EFR3A (rs16904552, OR = 1.725), and MMP14 (rs911912, OR = 1.791). GWAS variants were common in the AA but rare in the European population, which suggests an African-ancestry-specific risk of AD. Four genes (ANGPT1, LURAP1L, EFR3A, and SGK1) were further validated using qPCR from AD and healthy skin. This study highlighted the importance of genetic studies on admixed populations, as well as local ancestry and genotype-ancestry joint effects to identify risk loci for AD.
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Affiliation(s)
- Yadu Gautam
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Latha Satish
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Stephen Ramirez
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Brittany Grashel
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Jocelyn M Biagini
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Lisa J Martin
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA.
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Herrera-Luis E, Martin-Almeida M, Pino-Yanes M. Asthma-Genomic Advances Toward Risk Prediction. Clin Chest Med 2024; 45:599-610. [PMID: 39069324 PMCID: PMC11284279 DOI: 10.1016/j.ccm.2024.03.002] [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] [Indexed: 07/30/2024]
Abstract
Asthma is a common complex airway disease whose prediction of disease risk and most severe outcomes is crucial in clinical practice for adequate clinical management. This review discusses the latest findings in asthma genomics and current obstacles faced in moving forward to translational medicine. While genome-wide association studies have provided valuable insights into the genetic basis of asthma, there are challenges that must be addressed to improve disease prediction, such as the need for diverse representation, the functional characterization of genetic variants identified, variant selection for genetic testing, and refining prediction models using polygenic risk scores.
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Affiliation(s)
- Esther Herrera-Luis
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, 615 N Wolfe Street, Baltimore, MD 21205, USA.
| | - Mario Martin-Almeida
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez, s/n. Facultad de Ciencias, San Cristóbal de La Laguna, S/C de Tenerife La Laguna 38200, Tenerife, Spain
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez, s/n. Facultad de Ciencias, San Cristóbal de La Laguna, S/C de Tenerife La Laguna 38200, Tenerife, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain; Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), San Cristóbal de La Laguna 38200, Tenerife, Spain
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3
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Amri O, Madore AM, Boucher-Lafleur AM, Laprise C. Genomic analysis of severe COVID-19 considering or not asthma comorbidity: GWAS insights from the BQC19 cohort. BMC Genomics 2024; 25:482. [PMID: 38750426 PMCID: PMC11097529 DOI: 10.1186/s12864-024-10342-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND The severity of COVID-19 is influenced by various factors including the presence of respiratory diseases. Studies have indicated a potential relationship between asthma and COVID-19 severity. OBJECTIVE This study aimed to conduct a genome-wide association study (GWAS) to identify genetic and clinical variants associated with the severity of COVID-19, both among patients with and without asthma. METHODS We analyzed data from 2131 samples sourced from the Biobanque québécoise de la COVID-19 (BQC19), with 1499 samples from patients who tested positive for COVID-19. Among these, 1110 exhibited mild-to-moderate symptoms, 389 had severe symptoms, and 58 had asthma. We conducted a comparative analysis of clinical data from individuals in these three groups and GWAS using a logistic regression model. Phenotypic data analysis resulted in the refined covariates integrated into logistic models for genetic studies. RESULTS Considering a significance threshold of 1 × 10-6, seven genetic variants were associated with severe COVID-19. These variants were located proximal to five genes: sodium voltage-gated channel alpha subunit 1 (SCN10A), desmoplakin (DSP), RP1 axonemal microtubule associated (RP1), IGF like family member 1 (IGFL1), and docking protein 5 (DOK5). The GWAS comparing individuals with severe COVID-19 with asthma to those without asthma revealed four genetic variants in transmembrane protein with EGF like and two follistatin like domains 2 (TMEFF2) and huntingtin interacting protein-1 (HIP1) genes. CONCLUSION This study provides significant insights into the genetic profiles of patients with severe forms of the disease, whether accompanied by asthma or not. These findings enhance our comprehension of the genetic factors that affect COVID-19 severity. KEY MESSAGES Seven genetic variants were associated with the severe form of COVID-19; Four genetic variants were associated with the severe form of COVID-19 in individuals with comorbid asthma; These findings help define the genetic component of the severe form of COVID-19 in relation to asthma as a comorbidity.
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Affiliation(s)
- Omayma Amri
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
| | - Anne-Marie Madore
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
| | - Anne-Marie Boucher-Lafleur
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
| | - Catherine Laprise
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada.
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada.
- Centre de recherche du Centre intégré universitaire de santé et de services sociaux du Saguenay-Lac-Saint-Jean, Saguenay, Québec, G7H 7K9, Canada.
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Margaritte-Jeannin P, Vernet R, Budu-Aggrey A, Ege M, Madore AM, Linhard C, Mohamdi H, von Mutius E, Granell R, Demenais F, Laprise C, Bouzigon E, Dizier MH. TNS1 and NRXN1 Genes Interacting With Early-Life Smoking Exposure in Asthma-Plus-Eczema Susceptibility. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2023; 15:779-794. [PMID: 37957795 PMCID: PMC10643854 DOI: 10.4168/aair.2023.15.6.779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 11/15/2023]
Abstract
PURPOSE Numerous genes have been associated with allergic diseases (asthma, allergic rhinitis, and eczema), but they explain only part of their heritability. This is partly because most previous studies ignored complex mechanisms such as gene-environment (G-E) interactions and complex phenotypes such as co-morbidity. However, it was recently evidenced that the co-morbidity of asthma-plus-eczema appears as a sub-entity depending on specific genetic factors. Besides, evidence also suggest that gene-by-early life environmental tobacco smoke (ETS) exposure interactions play a role in asthma, but were never investigated for asthma-plus-eczema. To identify genetic variants interacting with ETS exposure that influence asthma-plus-eczema susceptibility. METHODS To conduct a genome-wide interaction study (GWIS) of asthma-plus-eczema according to ETS exposure, we applied a 2-stage strategy with a first selection of single nucleotide polymorphisms (SNPs) from genome-wide association meta-analysis to be tested at a second stage by interaction meta-analysis. All meta-analyses were conducted across 4 studies including a total of 5,516 European-ancestry individuals, of whom 1,164 had both asthma and eczema. RESULTS Two SNPs showed significant interactions with ETS exposure. They were located in 2 genes, NRXN1 (2p16) and TNS1 (2q35), never reported associated and/or interacting with ETS exposure for asthma, eczema or more generally for allergic diseases. TNS1 is a promising candidate gene because of its link to lung and skin diseases with possible interactive effect with tobacco smoke exposure. CONCLUSIONS This first GWIS of asthma-plus-eczema with ETS exposure underlines the importance of studying sub-phenotypes such as co-morbidities as well as G-E interactions to detect new susceptibility genes.
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Affiliation(s)
- Patricia Margaritte-Jeannin
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Raphaël Vernet
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Ashley Budu-Aggrey
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Markus Ege
- Dr von Hauner Children's Hospital, Ludwig Maximilian University; Institute of Asthma and Allergy prevention, Helmholtz Centre Munich; Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research, Munich, Germany
| | - Anne-Marie Madore
- Département des sciences fondamentales, Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Christophe Linhard
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Hamida Mohamdi
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Erika von Mutius
- Dr von Hauner Children's Hospital, Ludwig Maximilian University; Institute of Asthma and Allergy prevention, Helmholtz Centre Munich; Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research, Munich, Germany
| | - Raquell Granell
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Florence Demenais
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Cathrine Laprise
- Département des sciences fondamentales, Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Emmanuelle Bouzigon
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Marie-Hélène Dizier
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France.
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Tengvall K, Sundström E, Wang C, Bergvall K, Wallerman O, Pederson E, Karlsson Å, Harvey ND, Blott SC, Olby N, Olivry T, Brander G, Meadows JRS, Roosje P, Leeb T, Hedhammar Å, Andersson G, Lindblad-Toh K. Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis. Commun Biol 2022; 5:1348. [PMID: 36482174 PMCID: PMC9731970 DOI: 10.1038/s42003-022-04279-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Canine atopic dermatitis is an inflammatory skin disease with clinical similarities to human atopic dermatitis. Several dog breeds are at increased risk for developing this disease but previous genetic associations are poorly defined. To identify additional genetic risk factors for canine atopic dermatitis, we here apply a Bayesian mixture model adapted for mapping complex traits and a cross-population extended haplotype test to search for disease-associated loci and selective sweeps in four dog breeds at risk for atopic dermatitis. We define 15 associated loci and eight candidate regions under selection by comparing cases with controls. One associated locus is syntenic to the major genetic risk locus (Filaggrin locus) in human atopic dermatitis. One selection signal in common type Labrador retriever cases positions across the TBC1D1 gene (body weight) and one signal of selection in working type German shepherd controls overlaps the LRP1B gene (brain), near the KYNU gene (psoriasis). In conclusion, we identify candidate genes, including genes belonging to the same biological pathways across multiple loci, with potential relevance to the pathogenesis of canine atopic dermatitis. The results show genetic similarities between dog and human atopic dermatitis, and future across-species genetic comparisons are hereby further motivated.
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Affiliation(s)
- Katarina Tengvall
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Elisabeth Sundström
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kerstin Bergvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ola Wallerman
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Eric Pederson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Åsa Karlsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Naomi D Harvey
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - Sarah C Blott
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - Natasha Olby
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Thierry Olivry
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Gustaf Brander
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Petra Roosje
- Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Boyle RJ, Shamji MH. Milk allergy over-diagnosis. Clin Exp Allergy 2022; 52:4-6. [PMID: 34978736 DOI: 10.1111/cea.14076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert J Boyle
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Mohamed H Shamji
- National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Imperial Biomedical Research Centre, London, UK
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