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Strober BJ, Zhang MJ, Amariuta T, Rossen J, Price AL. Fine-mapping causal tissues and genes at disease-associated loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.01.23297909. [PMID: 37961337 PMCID: PMC10635248 DOI: 10.1101/2023.11.01.23297909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Heritable diseases often manifest in a highly tissue-specific manner, with different disease loci mediated by genes in distinct tissues or cell types. We propose Tissue-Gene Fine-Mapping (TGFM), a fine-mapping method that infers the posterior probability (PIP) for each gene-tissue pair to mediate a disease locus by analyzing GWAS summary statistics (and in-sample LD) and leveraging eQTL data from diverse tissues to build cis-predicted expression models; TGFM also assigns PIPs to causal variants that are not mediated by gene expression in assayed genes and tissues. TGFM accounts for both co-regulation across genes and tissues and LD between SNPs (generalizing existing fine-mapping methods), and incorporates genome-wide estimates of each tissue's contribution to disease as tissue-level priors. TGFM was well-calibrated and moderately well-powered in simulations; unlike previous methods, TGFM was able to attain correct calibration by modeling uncertainty in cis-predicted expression models. We applied TGFM to 45 UK Biobank diseases/traits (average N = 316K) using eQTL data from 38 GTEx tissues. TGFM identified an average of 147 PIP > 0.5 causal genetic elements per disease/trait, of which 11% were gene-tissue pairs. Implicated gene-tissue pairs were concentrated in known disease-critical tissues, and causal genes were strongly enriched in disease-relevant gene sets. Causal gene-tissue pairs identified by TGFM recapitulated known biology (e.g., TPO-thyroid for Hypothyroidism), but also included biologically plausible novel findings (e.g., SLC20A2-artery aorta for Diastolic blood pressure). Further application of TGFM to single-cell eQTL data from 9 cell types in peripheral blood mononuclear cells (PBMC), analyzed jointly with GTEx tissues, identified 30 additional causal gene-PBMC cell type pairs at PIP > 0.5-primarily for autoimmune disease and blood cell traits, including the biologically plausible example of CD52 in classical monocyte cells for Monocyte count. In conclusion, TGFM is a robust and powerful method for fine-mapping causal tissues and genes at disease-associated loci.
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Affiliation(s)
- Benjamin J. Strober
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Jinye Zhang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tiffany Amariuta
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jordan Rossen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Chen Z, Dragan M, Sun P, Haensel D, Vu R, Cui L, Shi Y, Dai X. An AhR-Ovol1-Id1 regulatory axis in keratinocytes promotes skin homeostasis against atopic dermatitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577821. [PMID: 38352592 PMCID: PMC10862726 DOI: 10.1101/2024.01.29.577821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Skin is our outer permeability and immune defense barrier against myriad external assaults. Aryl hydrocarbon receptor (AhR) senses environmental factors and regulates barrier robustness and immune homeostasis. AhR agonist is in clinical trial for atopic dermatitis (AD) treatment, but the underlying mechanism of action remains ill-defined. Here we report OVOL1/Ovol1 as a conserved and direct transcriptional target of AhR in epidermal keratinocytes. We show that OVOL1/Ovol1 impacts AhR regulation of keratinocyte gene expression, and Ovol1 deletion in keratinocytes hampers AhR's barrier promotion function and worsens AD-like inflammation. Mechanistically, we identify Ovol1's direct downstream targets genome-wide, and provide in vivo evidence for Id1's critical role in barrier maintenance and disease suppression. Furthermore, our findings reveal an IL-1/dermal γδT cell axis exacerbating both type 2 and type 3 immune responses downstream of barrier perturbation in Ovol1 -deficient AD skin. Finally, we present data suggesting the clinical relevance of OVOL1 and ID1 function in human AD. Our study highlights a keratinocyte-intrinsic AhR-Ovol1-Id1 regulatory axis that promotes both epidermal and immune homeostasis against AD-like inflammation, implicating new therapeutic targets for AD.
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Dragan M, Chen Z, Li Y, Le J, Sun P, Haensel D, Sureshchandra S, Pham A, Lu E, Pham KT, Verlande A, Vu R, Gutierrez G, Li W, Jang C, Masri S, Dai X. Ovol1/2 loss-induced epidermal defects elicit skin immune activation and alter global metabolism. EMBO Rep 2023; 24:e56214. [PMID: 37249012 PMCID: PMC10328084 DOI: 10.15252/embr.202256214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 04/29/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023] Open
Abstract
Skin epidermis constitutes the outer permeability barrier that protects the body from dehydration, heat loss, and myriad external assaults. Mechanisms that maintain barrier integrity in constantly challenged adult skin and how epidermal dysregulation shapes the local immune microenvironment and whole-body metabolism remain poorly understood. Here, we demonstrate that inducible and simultaneous ablation of transcription factor-encoding Ovol1 and Ovol2 in adult epidermis results in barrier dysregulation through impacting epithelial-mesenchymal plasticity and inflammatory gene expression. We find that aberrant skin immune activation then ensues, featuring Langerhans cell mobilization and T cell responses, and leading to elevated levels of secreted inflammatory factors in circulation. Finally, we identify failure to gain body weight and accumulate body fat as long-term consequences of epidermal-specific Ovol1/2 loss and show that these global metabolic changes along with the skin barrier/immune defects are partially rescued by immunosuppressant dexamethasone. Collectively, our study reveals key regulators of adult barrier maintenance and suggests a causal connection between epidermal dysregulation and whole-body metabolism that is in part mediated through aberrant immune activation.
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Affiliation(s)
- Morgan Dragan
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
- The NSF‐Simons Center for Multiscale Cell Fate ResearchUniversity of CaliforniaIrvineCAUSA
| | - Zeyu Chen
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
- Present address:
Department of Dermatology, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
- Present address:
Institute of PsoriasisTongji University School of MedicineShanghaiChina
| | - Yumei Li
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Johnny Le
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Peng Sun
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Daniel Haensel
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
- Present address:
Program in Epithelial BiologyStanford University School of MedicineStanfordCAUSA
| | - Suhas Sureshchandra
- Department of Physiology and Biophysics, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Anh Pham
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Eddie Lu
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Katherine Thanh Pham
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Amandine Verlande
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Remy Vu
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
- The NSF‐Simons Center for Multiscale Cell Fate ResearchUniversity of CaliforniaIrvineCAUSA
| | - Guadalupe Gutierrez
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Wei Li
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Cholsoon Jang
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Selma Masri
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
| | - Xing Dai
- Department of Biological Chemistry, School of MedicineUniversity of CaliforniaIrvineCAUSA
- The NSF‐Simons Center for Multiscale Cell Fate ResearchUniversity of CaliforniaIrvineCAUSA
- Department of Dermatology, School of MedicineUniversity of CaliforniaIrvineCAUSA
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