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Virolainen SJ, Satish L, Biagini JM, Chaib H, Chang WC, Dexheimer PJ, Dixon MR, Dunn KA, Fletcher D, Forney C, Granitto M, Hestand MS, Hurd M, Kaufman K, Lawson LP, Martin LJ, Peña LD, Phelan KJ, Shook MS, Weirauch MT, Khurana Hershey GK, Kottyan LC. Filaggrin loss-of-function variants are associated with atopic dermatitis phenotypes in a diverse, early life prospective cohort. JCI Insight 2024:e178258. [PMID: 38564302 DOI: 10.1172/jci.insight.178258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Loss-of-Function (LoF) variants in the filaggrin (FLG) gene are the strongest known genetic risk factor for atopic dermatitis (AD), but the impact of these variants on AD outcomes is poorly understood. We comprehensively identified genetic variants through targeted region sequencing of FLG in children (n = 438) participating in the Mechanisms of Progression of Atopic Dermatitis to Asthma in Children (MPAACH) cohort. Twenty FLG LoF variants were identified, including one novel variant and nine variants not previously associated with AD. FLG LoF variants were found in 13.6% of the cohort. Among these children, the presence of one or more FLG LoF variants was associated with moderate/severe AD (odds ratio (OR) = 2.00 (95% CI, 1.23-3.68) compared to those with mild AD. Children with FLG LoF variants had a higher SCORAD (SCORing for Atopic Dermatitis (SCORAD); P = 0.012) and higher likelihood of food allergy within the first 2.5 years of life (OR = 2.81, 1.50-5.26). LoF variants were associated with higher transepidermal Water Loss (TEWL) in both lesional (P = 0.018) and non-lesional skin (P = 0.015). Collectively, our study identifies established and novel AD-associated FLG LoF variants and associates FLG LoF with higher TEWL in lesional and non-lesional skin.
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Affiliation(s)
- Samuel J Virolainen
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Latha Satish
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Jocelyn M Biagini
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Hassan Chaib
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Wan Chi Chang
- Division of Asthma Research, Cincinnati Children Hospital Medical Center, Cincinnati, United States of America
| | - Phillip J Dexheimer
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Michael R Dixon
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Katelyn A Dunn
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - David Fletcher
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Carmy Forney
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Marissa Granitto
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | | | - Makenna Hurd
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Kenneth Kaufman
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Lucinda P Lawson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Lisa J Martin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Loren Dm Peña
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Kieran J Phelan
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Molly S Shook
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Matthew T Weirauch
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Gurjit K Khurana Hershey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Leah C Kottyan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
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Shook MS, Lu X, Chen X, Parameswaran S, Edsall L, Trimarchi MP, Ernst K, Granitto M, Forney C, Donmez OA, Diouf AA, VonHandorf A, Rothenberg ME, Weirauch MT, Kottyan LC. Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis. Am J Hum Genet 2024; 111:280-294. [PMID: 38183988 PMCID: PMC10870143 DOI: 10.1016/j.ajhg.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 01/08/2024] Open
Abstract
Eosinophilic esophagitis (EoE) is a rare atopic disorder associated with esophageal dysfunction, including difficulty swallowing, food impaction, and inflammation, that develops in a small subset of people with food allergies. Genome-wide association studies (GWASs) have identified 9 independent EoE risk loci reaching genome-wide significance (p < 5 × 10-8) and 27 additional loci of suggestive significance (5 × 10-8 < p < 1 × 10-5). In the current study, we perform linkage disequilibrium (LD) expansion of these loci to nominate a set of 531 variants that are potentially causal. To systematically interrogate the gene regulatory activity of these variants, we designed a massively parallel reporter assay (MPRA) containing the alleles of each variant within their genomic sequence context cloned into a GFP reporter library. Analysis of reporter gene expression in TE-7, HaCaT, and Jurkat cells revealed cell-type-specific gene regulation. We identify 32 allelic enhancer variants, representing 6 genome-wide significant EoE loci and 7 suggestive EoE loci, that regulate reporter gene expression in a genotype-dependent manner in at least one cellular context. By annotating these variants with expression quantitative trait loci (eQTL) and chromatin looping data in related tissues and cell types, we identify putative target genes affected by genetic variation in individuals with EoE. Transcription factor enrichment analyses reveal possible roles for cell-type-specific regulators, including GATA3. Our approach reduces the large set of EoE-associated variants to a set of 32 with allelic regulatory activity, providing functional insights into the effects of genetic variation in this disease.
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Affiliation(s)
- Molly S Shook
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lee Edsall
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael P Trimarchi
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kevin Ernst
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Omer A Donmez
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Arame A Diouf
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrew VonHandorf
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Marc E Rothenberg
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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Matsui S, Granitto M, Buckley M, Ludwig K, Koigi S, Shiley J, Zacharias WJ, Mayhew CN, Lim HW, Iwafuchi M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Mol Cell 2024; 84:476-489.e10. [PMID: 38211589 PMCID: PMC10872272 DOI: 10.1016/j.molcel.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024]
Abstract
Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative-lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF FOXA coordinates with PRDM1 TF to recruit nucleosome remodeling and deacetylation (NuRD) complexes and Polycomb repressive complexes (PRCs), which establish highly occupied, accessible nucleosome conformation with bivalent epigenetic states, thereby preventing precocious and alternative-lineage gene expression during human endoderm differentiation. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to form bivalent enhancers and repress cell differentiation programs in human pluripotent stem cells, suggesting that this may be a common and critical function of pioneer TFs. We propose that pioneer and PRDM TFs coordinate to safeguard cell fate through epigenetic repression mechanisms.
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Affiliation(s)
- Satoshi Matsui
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Morgan Buckley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Katie Ludwig
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Sandra Koigi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joseph Shiley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - William J Zacharias
- Division of Pulmonary Biology and Pulmonary and Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
| | - Makiko Iwafuchi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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Eapen AA, Parameswaran S, Forney C, Edsall LE, Miller D, Donmez O, Dunn K, Lu X, Granitto M, Rowden H, Magier AZ, Pujato M, Chen X, Kaufman K, Bernstein DI, Devonshire AL, Rothenberg ME, Weirauch MT, Kottyan LC. Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis. PLoS Genet 2022; 18:e1009973. [PMID: 35576187 PMCID: PMC9135339 DOI: 10.1371/journal.pgen.1009973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/26/2022] [Accepted: 04/20/2022] [Indexed: 12/30/2022] Open
Abstract
Atopic dermatitis (AD) is one of the most common skin disorders among children. Disease etiology involves genetic and environmental factors, with 29 independent AD risk loci enriched for risk allele-dependent gene expression in the skin and CD4+ T cell compartments. We investigated the potential epigenetic mechanisms responsible for the genetic susceptibility of CD4+ T cells. To understand the differences in gene regulatory activity in peripheral blood T cells in AD, we measured chromatin accessibility (an assay based on transposase-accessible chromatin sequencing, ATAC-seq), nuclear factor kappa B subunit 1 (NFKB1) binding (chromatin immunoprecipitation with sequencing, ChIP-seq), and gene expression levels (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD, as well as in age-matched non-allergic controls. Open chromatin regions in stimulated CD4+ T cells were highly enriched for AD genetic risk variants, with almost half of the AD risk loci overlapping AD-dependent ATAC-seq peaks. AD-specific open chromatin regions were strongly enriched for NF-κB DNA-binding motifs. ChIP-seq identified hundreds of NFKB1-occupied genomic loci that were AD- or control-specific. As expected, the AD-specific ChIP-seq peaks were strongly enriched for NF-κB DNA-binding motifs. Surprisingly, control-specific NFKB1 ChIP-seq peaks were not enriched for NFKB1 motifs, but instead contained motifs for other classes of human transcription factors, suggesting a mechanism involving altered indirect NFKB1 binding. Using DNA sequencing data, we identified 63 instances of altered genotype-dependent chromatin accessibility at 36 AD risk variant loci (30% of AD risk loci) that might lead to genotype-dependent gene expression. Based on these findings, we propose that CD4+ T cells respond to stimulation in an AD-specific manner, resulting in disease- and genotype-dependent chromatin accessibility alterations involving NFKB1 binding.
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Affiliation(s)
- Amy A. Eapen
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Allergy and Clinical Immunology, Henry Ford Health System, Detroit, Michigan, United States of America
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Lee E. Edsall
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Daniel Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Omer Donmez
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Katelyn Dunn
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Marissa Granitto
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Hope Rowden
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Adam Z. Magier
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Mario Pujato
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Kenneth Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Cincinnati Veterans Administration, Cincinnati, Ohio, United States of America
| | - David I. Bernstein
- Division of Immunology, Allergy, and Rheumatology, University of Cincinnati, College of Medicine, Cincinnati, Ohio, United States of America
| | - Ashley L. Devonshire
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Marc E. Rothenberg
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Matthew T. Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Leah C. Kottyan
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
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Eapen A, Kottyan L, Parameswaran S, Forney C, Edsall L, Miller D, Donmez O, Weirauch M, Dunn K, Lu X, Granitto M, Rowden H, Magier A, Pujato M, Chen X, Bernstein D, Devonshire A, Rothenberg M. Epigenetic and Transcriptional Dysregulation in T cells of Patients with Atopic Dermatitis. J Allergy Clin Immunol 2022. [DOI: 10.1016/j.jaci.2021.12.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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