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Glunk V, Laber S, Sinnott-Armstrong N, Sobreira DR, Strobel SM, Batista TM, Kubitz P, Moud BN, Ebert H, Huang Y, Brandl B, Garbo G, Honecker J, Stirling DR, Abdennur N, Calabuig-Navarro V, Skurk T, Ocvirk S, Stemmer K, Cimini BA, Carpenter AE, Dankel SN, Lindgren CM, Hauner H, Nobrega MA, Claussnitzer M. A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes. Nat Metab 2023; 5:861-879. [PMID: 37253881 DOI: 10.1038/s42255-023-00807-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/12/2023] [Indexed: 06/01/2023]
Abstract
Recent large-scale genomic association studies found evidence for a genetic link between increased risk of type 2 diabetes and decreased risk for adiposity-related traits, reminiscent of metabolically obese normal weight (MONW) association signatures. However, the target genes and cellular mechanisms driving such MONW associations remain to be identified. Here, we systematically identify the cellular programmes of one of the top-scoring MONW risk loci, the 2q24.3 risk locus, in subcutaneous adipocytes. We identify a causal genetic variant, rs6712203, an intronic single-nucleotide polymorphism in the COBLL1 gene, which changes the conserved transcription factor motif of POU domain, class 2, transcription factor 2, and leads to differential COBLL1 gene expression by altering the enhancer activity at the locus in subcutaneous adipocytes. We then establish the cellular programme under the genetic control of the 2q24.3 MONW risk locus and the effector gene COBLL1, which is characterized by impaired actin cytoskeleton remodelling in differentiating subcutaneous adipocytes and subsequent failure of these cells to accumulate lipids and develop into metabolically active and insulin-sensitive adipocytes. Finally, we show that perturbations of the effector gene Cobll1 in a mouse model result in organismal phenotypes matching the MONW association signature, including decreased subcutaneous body fat mass and body weight along with impaired glucose tolerance. Taken together, our results provide a mechanistic link between the genetic risk for insulin resistance and low adiposity, providing a potential therapeutic hypothesis and a framework for future identification of causal relationships between genome associations and cellular programmes in other disorders.
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Affiliation(s)
- Viktoria Glunk
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Samantha Laber
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
| | - Nasa Sinnott-Armstrong
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Herbold Computational Biology Program, Publich Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Debora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Sophie M Strobel
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
| | - Thiago M Batista
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Phil Kubitz
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bahareh Nemati Moud
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Hannah Ebert
- Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Yi Huang
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Beate Brandl
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Garrett Garbo
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
| | - Julius Honecker
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - David R Stirling
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Virtu Calabuig-Navarro
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Thomas Skurk
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Soeren Ocvirk
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Intestinal Microbiology Research Group, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Kerstin Stemmer
- Molecular Cell Biology, Institute for Theoretical Medicine, University of Augsburg, Augsburg, Germany
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Beth A Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Simon N Dankel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Cecilia M Lindgren
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Hans Hauner
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Marcelo A Nobrega
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA.
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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Sakabe NJ, Aneas I, Knoblauch N, Sobreira DR, Clark N, Paz C, Horth C, Ziffra R, Kaur H, Liu X, Anderson R, Morrison J, Cheung VC, Grotegut C, Reddy TE, Jacobsson B, Hallman M, Teramo K, Murtha A, Kessler J, Grobman W, Zhang G, Muglia LJ, Rana S, Lynch VJ, Crawford GE, Ober C, He X, Nóbrega MA. Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth. Sci Adv 2020; 6:eabc8696. [PMID: 33268355 PMCID: PMC7710387 DOI: 10.1126/sciadv.abc8696] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/19/2020] [Indexed: 05/29/2023]
Abstract
While a genetic component of preterm birth (PTB) has long been recognized and recently mapped by genome-wide association studies (GWASs), the molecular determinants underlying PTB remain elusive. This stems in part from an incomplete availability of functional genomic annotations in human cell types relevant to pregnancy and PTB. We generated transcriptome (RNA-seq), epigenome (ChIP-seq of H3K27ac, H3K4me1, and H3K4me3 histone modifications), open chromatin (ATAC-seq), and chromatin interaction (promoter capture Hi-C) annotations of cultured primary decidua-derived mesenchymal stromal/stem cells and in vitro differentiated decidual stromal cells and developed a computational framework to integrate these functional annotations with results from a GWAS of gestational duration in 56,384 women. Using these resources, we uncovered additional loci associated with gestational duration and target genes of associated loci. Our strategy illustrates how functional annotations in pregnancy-relevant cell types aid in the experimental follow-up of GWAS for PTB and, likely, other pregnancy-related conditions.
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Affiliation(s)
- Noboru J Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Ivy Aneas
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas Knoblauch
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Debora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Nicole Clark
- Department of Pediatrics, Center for Genomic and Computational Biology, Duke University, Durham, NC 27705, USA
| | - Cristina Paz
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Horth
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Ryan Ziffra
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Harjot Kaur
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Xiao Liu
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Rebecca Anderson
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Jean Morrison
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Virginia C Cheung
- Department of Neurology and Institute for Stem Cell Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chad Grotegut
- Department of Obstetrics and Gynecology, Duke University Health System, Durham, NC 27713, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, University of Gothenberg, Gothenberg, Sweden
- Department of Genetics and Bioinformatics, Area of Health Data and Digitalization, Institute of Public Health, Oslo, Norway
| | - Mikko Hallman
- Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Kari Teramo
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Amy Murtha
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Duke University School of Medicine, Durham, NC 27713, USA
| | - John Kessler
- Department of Neurology and Institute for Stem Cell Medicine, Northwestern University, Chicago, IL 60611, USA
| | - William Grobman
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ge Zhang
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Louis J Muglia
- Department of Obstetrics and Gynecology, University of Chicago, Chicago IL 60637, USA
| | - Sarosh Rana
- Department of Obstetrics and Gynecology, University of Chicago, Chicago IL 60637, USA
| | - Vincent J Lynch
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Gregory E Crawford
- Department of Pediatrics, Center for Genomic and Computational Biology, Duke University, Durham, NC 27705, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
- Department of Obstetrics and Gynecology, University of Chicago, Chicago IL 60637, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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Boogerd CJ, Zhu X, Aneas I, Sakabe N, Zhang L, Sobreira DR, Montefiori L, Bogomolovas J, Joslin AC, Zhou B, Chen J, Nobrega MA, Evans SM. Tbx20 Is Required in Mid-Gestation Cardiomyocytes and Plays a Central Role in Atrial Development. Circ Res 2019; 123:428-442. [PMID: 29903739 PMCID: PMC6092109 DOI: 10.1161/circresaha.118.311339] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Supplemental Digital Content is available in the text. Rationale: Mutations in the transcription factor TBX20 (T-box 20) are associated with congenital heart disease. Germline ablation of Tbx20 results in abnormal heart development and embryonic lethality by embryonic day 9.5. Because Tbx20 is expressed in multiple cell lineages required for myocardial development, including pharyngeal endoderm, cardiogenic mesoderm, endocardium, and myocardium, the cell type–specific requirement for TBX20 in early myocardial development remains to be explored. Objective: Here, we investigated roles of TBX20 in midgestation cardiomyocytes for heart development. Methods and Results: Ablation of Tbx20 from developing cardiomyocytes using a doxycycline inducible cTnTCre transgene led to embryonic lethality. The circumference of developing ventricular and atrial chambers, and in particular that of prospective left atrium, was significantly reduced in Tbx20 conditional knockout mutants. Cell cycle analysis demonstrated reduced proliferation of Tbx20 mutant cardiomyocytes and their arrest at the G1-S phase transition. Genome-wide transcriptome analysis of mutant cardiomyocytes revealed differential expression of multiple genes critical for cell cycle regulation. Moreover, atrial and ventricular gene programs seemed to be aberrantly regulated. Putative direct TBX20 targets were identified using TBX20 ChIP-Seq (chromatin immunoprecipitation with high throughput sequencing) from embryonic heart and included key cell cycle genes and atrial and ventricular specific genes. Notably, TBX20 bound a conserved enhancer for a gene key to atrial development and identity, COUP-TFII/Nr2f2 (chicken ovalbumin upstream promoter transcription factor 2/nuclear receptor subfamily 2, group F, member 2). This enhancer interacted with the NR2F2 promoter in human cardiomyocytes and conferred atrial specific gene expression in a transgenic mouse in a TBX20-dependent manner. Conclusions: Myocardial TBX20 directly regulates a subset of genes required for fetal cardiomyocyte proliferation, including those required for the G1-S transition. TBX20 also directly downregulates progenitor-specific genes and, in addition to regulating genes that specify chamber versus nonchamber myocardium, directly activates genes required for establishment or maintenance of atrial and ventricular identity. TBX20 plays a previously unappreciated key role in atrial development through direct regulation of an evolutionarily conserved COUPT-FII enhancer.
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Affiliation(s)
- Cornelis J. Boogerd
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
| | - Xiaoming Zhu
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
| | - Ivy Aneas
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Noboru Sakabe
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Lunfeng Zhang
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
| | - Debora R. Sobreira
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Lindsey Montefiori
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Julius Bogomolovas
- Department of Medicine (J.B., J.C., S.M.E.)
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (J.B.)
| | - Amelia C. Joslin
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Bin Zhou
- Department of Genetics, Medicine and Pediatrics, Albert Einstein College of Medicine of Yeshiva University, New York, NY (B.Z.)
| | - Ju Chen
- Department of Medicine (J.B., J.C., S.M.E.)
| | - Marcelo A. Nobrega
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Sylvia M. Evans
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
- Department of Medicine (J.B., J.C., S.M.E.)
- Department of Pharmacology (S.M.E.)
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Nicodemus-Johnson J, Myers RA, Sakabe NJ, Sobreira DR, Hogarth DK, Naureckas ET, Sperling AI, Solway J, White SR, Nobrega MA, Nicolae DL, Gilad Y, Ober C. DNA methylation in lung cells is associated with asthma endotypes and genetic risk. JCI Insight 2016; 1:e90151. [PMID: 27942592 DOI: 10.1172/jci.insight.90151] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The epigenome provides a substrate through which environmental exposures can exert their effects on gene expression and disease risk, but the relative importance of epigenetic variation on human disease onset and progression is poorly characterized. Asthma is a heterogeneous disease of the airways, for which both onset and clinical course result from interactions between host genotype and environmental exposures, yet little is known about the molecular mechanisms for these interactions. We assessed genome-wide DNA methylation using the Infinium Human Methylation 450K Bead Chip and characterized the transcriptome by RNA sequencing in primary airway epithelial cells from 74 asthmatic and 41 nonasthmatic adults. Asthma status was based on doctor's diagnosis and current medication use. Genotyping was performed using various Illumina platforms. Our study revealed a regulatory locus on chromosome 17q12-21 associated with asthma risk and epigenetic signatures of specific asthma endotypes and molecular networks. Overall, these data support a central role for DNA methylation in lung cells, which promotes distinct molecular pathways of asthma pathogenesis and modulates the effects of genetic variation on disease risk and clinical heterogeneity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Dan L Nicolae
- Department of Human Genetics.,Department of Medicine, and.,Department of Statistics, University of Chicago, Chicago, Illinois, USA
| | - Yoav Gilad
- Department of Human Genetics.,Department of Medicine, and
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