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Clay S, Alladina J, Smith NP, Visness CM, Wood RA, O'Connor GT, Cohen RT, Khurana Hershey GK, Kercsmar CM, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Rivera-Spoljaric K, Robison RG, Gergen PJ, Busse WW, Villani AC, Cho JL, Medoff BD, Gern JE, Jackson DJ, Ober C, Dapas M. Gene-based association study of rare variants in children of diverse ancestries implicates TNFRSF21 in the development of allergic asthma. J Allergy Clin Immunol 2024; 153:809-820. [PMID: 37944567 PMCID: PMC10939893 DOI: 10.1016/j.jaci.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Most genetic studies of asthma and allergy have focused on common variation in individuals primarily of European ancestry. Studying the role of rare variation in quantitative phenotypes and in asthma phenotypes in populations of diverse ancestries can provide additional, important insights into the development of these traits. OBJECTIVE We sought to examine the contribution of rare variants to different asthma- or allergy-associated quantitative traits in children with diverse ancestries and explore their role in asthma phenotypes. METHODS We examined whole-genome sequencing data from children participants in longitudinal studies of asthma (n = 1035; parent-identified as 67% Black and 25% Hispanic) to identify rare variants (minor allele frequency < 0.01). We assigned variants to genes and tested for associations using an omnibus variant-set test between each of 24,902 genes and 8 asthma-associated quantitative traits. On combining our results with external data on predicted gene expression in humans and mouse knockout studies, we identified 3 candidate genes. A burden of rare variants in each gene and in a combined 3-gene score was tested for its associations with clinical phenotypes of asthma. Finally, published single-cell gene expression data in lower airway mucosal cells after allergen challenge were used to assess transcriptional responses to allergen. RESULTS Rare variants in USF1 were significantly associated with blood neutrophil count (P = 2.18 × 10-7); rare variants in TNFRSF21 with total IgE (P = 6.47 × 10-6) and PIK3R6 with eosinophil count (P = 4.10 × 10-5) reached suggestive significance. These 3 findings were supported by independent data from human and mouse studies. A burden of rare variants in TNFRSF21 and in a 3-gene score was associated with allergy-related phenotypes in cohorts of children with mild and severe asthma. Furthermore, TNFRSF21 was significantly upregulated in bronchial basal epithelial cells from adults with allergic asthma but not in adults with allergies (but not asthma) after allergen challenge. CONCLUSIONS We report novel associations between rare variants in genes and allergic and inflammatory phenotypes in children with diverse ancestries, highlighting TNFRSF21 as contributing to the development of allergic asthma.
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Affiliation(s)
- Selene Clay
- Department of Human Genetics, University of Chicago, Chicago, Ill.
| | - Jehan Alladina
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass
| | - Neal P Smith
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Mass; Massachusetts General Hospital Cancer Center, Boston, Mass
| | | | - Robert A Wood
- Pediatric Allergy and Immunology Department, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md
| | - George T O'Connor
- Department of Pediatrics, Boston University School of Medicine, Boston, Mass
| | - Robyn T Cohen
- Department of Pediatrics, Boston University School of Medicine, Boston, Mass
| | | | - Carolyn M Kercsmar
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Rebecca S Gruchalla
- Internal Medicine and Pediatrics, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Michelle A Gill
- Pediatric Infectious Diseases, St. Louis Children's Hospital, St Louis, Mo
| | - Andrew H Liu
- Breathing Institute, Children's Hospital Colorado, Aurora, Colo
| | - Haejin Kim
- Allergy and Immunology, Henry Ford Health, Detroit, Mich
| | - Meyer Kattan
- Department of Pediatrics, Columbia University Medical Center, New York, NY
| | - Leonard B Bacharier
- Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt University Medical Center, Nashville, Tenn
| | - Deepa Rastogi
- Division of Pulmonology and Sleep Medicine, Children's National Hospital, Washington, DC
| | - Katherine Rivera-Spoljaric
- Department of Pediatric Allergy, Immunology, and Pulmonary Medicine, Washington University School of Medicine, St Louis, Mo
| | - Rachel G Robison
- Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt University Medical Center, Nashville, Tenn; Ann & Robert H. Lurie Children's Hospital, Chicago, Ill
| | - Peter J Gergen
- National Institute of Allergy and Infectious Diseases, Rockville, Md
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Alexandra-Chloe Villani
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Mass; Massachusetts General Hospital Cancer Center, Boston, Mass
| | - Josalyn L Cho
- Division of Pulmonary, Critical Care and Occupational Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Benjamin D Medoff
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago, Ill
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Cha J, Choi S. Gene-Smoking Interaction Analysis for the Identification of Novel Asthma-Associated Genetic Factors. Int J Mol Sci 2023; 24:12266. [PMID: 37569643 PMCID: PMC10419280 DOI: 10.3390/ijms241512266] [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: 07/01/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
Asthma is a complex heterogeneous disease caused by gene-environment interactions. Although numerous genome-wide association studies have been conducted, these interactions have not been systemically investigated. We sought to identify genetic factors associated with the asthma phenotype in 66,857 subjects from the Health Examination Study, Cardiovascular Disease Association Study, and Korea Association Resource Study cohorts. We investigated asthma-associated gene-environment (smoking status) interactions at the level of single nucleotide polymorphisms, genes, and gene sets. We identified two potentially novel (SETDB1 and ZNF8) and five previously reported (DM4C, DOCK8, MMP20, MYL7, and ADCY9) genes associated with increased asthma risk. Numerous gene ontology processes, including regulation of T cell differentiation in the thymus (GO:0033081), were significantly enriched for asthma risk. Functional annotation analysis confirmed the causal relationship between five genes (two potentially novel and three previously reported genes) and asthma through genome-wide functional prediction scores (combined annotation-dependent depletion, deleterious annotation of genetic variants using neural networks, and RegulomeDB). Our findings elucidate the genetic architecture of asthma and improve the understanding of its biological mechanisms. However, further studies are necessary for developing preventive treatments based on environmental factors and understanding the immune system mechanisms that contribute to the etiology of asthma.
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Affiliation(s)
- Junho Cha
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea;
| | - Sungkyoung Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea;
- Department of Mathematical Data Science, College of Science and Convergence Technology, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea
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Inamoto I, Sheoran I, Popa SC, Hussain M, Shin JA. Combining Rational Design and Continuous Evolution on Minimalist Proteins That Target the E-box DNA Site. ACS Chem Biol 2021; 16:35-44. [PMID: 33370105 DOI: 10.1021/acschembio.0c00684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-based therapeutics are part of the next-generation arsenal of drugs being developed against proto-oncoprotein Myc. We designed protein MEF to mimic the basic region/helix-loop-helix/leucine zipper (bHLHZ) domain of Max and Myc, which bind to the E-box motif (enhancer box, CACGTG). To make MEF, we started with our rationally designed ME47, a hybrid of the Max basic region and E47 HLH, that effectively inhibited tumor growth in a mouse model of breast cancer. We used phage-assisted continuous evolution (PACE), which uncovered mutations at Arg12 that contact the DNA phosphodiester backbone. The Arg12 mutations improved ME47's stability. We replaced Cys29 with Ala to eliminate potential undesired disulfide formation and fused the designed FosW leucine zipper to mutated ME47 to increase the dimerization interface and E-box targeting activity. This "franken-protein" MEF comprises the Max basic region, E47 HLH, and FosW leucine zipper. Compared with ME47, MEF gives 2-fold stronger binding to E-box and 4-fold increased specificity for E-box over nonspecific DNA. The synergistic combination of rational design and PACE allowed us to make MEF and demonstrates the power and utility of our two-pronged approach toward development of promising protein drugs with robust structure and DNA-binding function.
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Affiliation(s)
- Ichiro Inamoto
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Inder Sheoran
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Serban C. Popa
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Montdher Hussain
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Jumi A. Shin
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
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