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Divoux A, Sandor K, Bojcsuk D, Yi F, Hopf ME, Smith JS, Balint BL, Osborne TF, Smith SR. Fat Distribution in Women Is Associated With Depot-Specific Transcriptomic Signatures and Chromatin Structure. J Endocr Soc 2020; 4:bvaa042. [PMID: 32500109 PMCID: PMC7261146 DOI: 10.1210/jendso/bvaa042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Preferential accumulation of fat in the upper body (apple shape) is associated with higher risk of developing metabolic syndrome relative to lower body fat (pear shape). We previously discovered that chromatin openness partially defined the transcriptome of preadipocytes isolated from abdominal and gluteofemoral fat. However, the molecular mechanisms underlying interindividual variation in body shape are unknown. METHODS Adipocyte fraction was isolated from abdominal and gluteofemoral fat biopsies of premenopausal women (age and body mass index matched) segregated initially only by their waist-to-hip ratio. We evaluated transcriptomic and chromatin accessibility using RNA sequencing and assay for transposase-accessible chromatin using sequencing (ATAC-seq) along with key clinical parameters. RESULTS Our data showed that higher lower body fat mass was associated with better lipid profile and free fatty acid decrease after glucose administration. Lipid and glucose metabolic pathways genes were expressed at higher levels in gluteofemoral adipocyte fraction in pears, whereas genes associated with inflammation were higher both in abdominal and gluteofemoral apple adipocyte fraction. Gluteofemoral adipocyte chromatin from pear-shaped women contained a significantly higher number of differentially open ATAC-seq peaks relative to chromatin from the apple-shaped gluteofemoral adipocytes. In contrast, abdominal adipocyte chromatin openness showed few differences between apple- and pear-shaped women. We revealed a correlation between gene transcription and open chromatin at the proximity of the transcriptional start site of some of the differentially expressed genes. CONCLUSIONS Integration of data from all 3 approaches suggests that chromatin openness partially governs the transcriptome of gluteofemoral adipocytes and may be involved in the early metabolic syndrome predisposition associated with body shape.
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Affiliation(s)
- Adeline Divoux
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, USA
| | - Katalin Sandor
- Department of Medicine, Johns Hopkins University School of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
| | - Dora Bojcsuk
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Fanchao Yi
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, USA
| | - Meghan E Hopf
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, USA
| | - Joshua S Smith
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, USA
| | - Balint L Balint
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Timothy F Osborne
- Department of Medicine, Johns Hopkins University School of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
| | - Steven R Smith
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, USA
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Divoux A, Sandor K, Bojcsuk D, Talukder A, Li X, Balint BL, Osborne TF, Smith SR. Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes. Clin Epigenetics 2018; 10:148. [PMID: 30477572 PMCID: PMC6258289 DOI: 10.1186/s13148-018-0582-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022] Open
Abstract
Background Increased lower body fat is associated with reduced cardiometabolic risk. The molecular basis for depot-specific differences in gluteofemoral (GF) compared with abdominal (A) subcutaneous adipocyte function is poorly understood. In the current report, we used a combination of Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq), RNA-seq, and chromatin immunoprecipitation (ChIP)-qPCR analyses that provide evidence that depot-specific gene expression patterns are associated with differential epigenetic chromatin signatures. Methods Preadipocytes cultured from A and GF adipose tissue obtained from premenopausal apple-shaped women were used to perform transcriptome analysis by RNA-seq and assess accessible chromatin regions by ATAC-seq. We measured mRNA expression and performed ChIP-qPCR experiments for histone modifications of active (H3K4me3) and repressed chromatin (H3K27me3) regions respectively on the promoter regions of differentially expressed genes. Results RNA-seq experiments revealed an A-fat and GF-fat selective gene expression signature, with 126 genes upregulated in abdominal preadipocytes and 90 genes upregulated in GF cells. ATAC-seq identified almost 10-times more A-specific chromatin-accessible regions. Using a combined analysis of ATAC-seq and global gene expression data, we identified 74 of the 126 abdominal-specific genes (59%) with A-specific accessible chromatin sites within 200 kb of the transcription start site (TSS), including HOXA3, HOXA5, IL8, IL1b, and IL6. Interestingly, only 14 of the 90 GF-specific genes (15%) had GF-specific accessible chromatin sites within 200 kb of the corresponding TSS, including HOXC13 and HOTAIR, whereas 25 of them (28%) had abdominal-specific accessible chromatin sites. ChIP-qPCR experiments confirmed that the active H3K4me3 chromatin mark was significantly enriched at the promoter regions of HOXA5 and HOXA3 genes in abdominal preadipocytes, while H3K27me3 was less abundant relative to chromatin from GF. This is consistent with their A-fat specific gene expression pattern. Conversely, analysis of the promoter regions of the GF specific HOTAIR and HOXC13 genes exhibited high H3K4me3 and low H3K27me3 levels in GF chromatin compared to A chromatin. Conclusions Global transcriptome and open chromatin analyses of depot-specific preadipocytes identified their gene expression signature and differential open chromatin profile. Interestingly, A-fat-specific open chromatin regions can be observed in the proximity of GF-fat genes, but not vice versa. Trial registration Clinicaltrials.gov, NCT01745471. Registered 5 December 2012. Electronic supplementary material The online version of this article (10.1186/s13148-018-0582-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adeline Divoux
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, 301 E. Princeton Street, Orlando, FL, 32804, USA. .,Diabetes and Obesity Research Center, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA.
| | - Katalin Sandor
- Diabetes and Obesity Research Center, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA.,Present address: Department of Medicine, Johns Hopkins All Children's Hospital, Johns Hopkins University School of Medicine, St. Petersburg, FL, 33701, USA
| | - Dora Bojcsuk
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Nagyerdei krt 98, Debrecen, 4032, Hungary
| | - Amlan Talukder
- Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, 32816, USA
| | - Xiaoman Li
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Boulevard, Orlando, FL, USA
| | - Balint L Balint
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Nagyerdei krt 98, Debrecen, 4032, Hungary
| | - Timothy F Osborne
- Diabetes and Obesity Research Center, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA.,Present address: Department of Medicine, Johns Hopkins All Children's Hospital, Johns Hopkins University School of Medicine, St. Petersburg, FL, 33701, USA
| | - Steven R Smith
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, 301 E. Princeton Street, Orlando, FL, 32804, USA.,Diabetes and Obesity Research Center, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA
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Márton J, Péter M, Balogh G, Bódi B, Vida A, Szántó M, Bojcsuk D, Jankó L, Bhattoa HP, Gombos I, Uray K, Horváth I, Török Z, Balint BL, Papp Z, Vígh L, Bai P. Poly(ADP-ribose) polymerase-2 is a lipid-modulated modulator of muscular lipid homeostasis. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:1399-1412. [PMID: 30077797 DOI: 10.1016/j.bbalip.2018.07.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/22/2018] [Accepted: 07/29/2018] [Indexed: 01/11/2023]
Abstract
There is a growing body of evidence that poly(ADP-ribose) polymerase-2 (PARP2), although originally described as a DNA repair protein, has a widespread role as a metabolic regulator. We show that the ablation of PARP2 induced characteristic changes in the lipidome. The silencing of PARP2 induced the expression of sterol regulatory element-binding protein-1 and -2 and initiated de novo cholesterol biosynthesis in skeletal muscle. Increased muscular cholesterol was shunted to muscular biosynthesis of dihydrotestosterone, an anabolic steroid. Thus, skeletal muscle fibers in PARP2-/- mice were stronger compared to those of their wild-type littermates. In addition, we detected changes in the dynamics of the cell membrane, suggesting that lipidome changes also affect the biophysical characteristics of the cell membrane. In in silico and wet chemistry studies, we identified lipid species that can decrease the expression of PARP2 and potentially phenocopy the genetic abruption of PARP2, including artificial steroids. In view of these observations, we propose a new role for PARP2 as a lipid-modulated regulator of lipid metabolism.
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Affiliation(s)
- Judit Márton
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032, Hungary
| | - Mária Péter
- Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Gábor Balogh
- Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Beáta Bódi
- Divison of Clinical Physiology, Faculty of Medicine, University of Debrecen, 4032, Hungary
| | - Andras Vida
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032, Hungary; MTA-DE Lendület Laboratory of Cellular Metabolism Research Group, Debrecen 4032, Hungary
| | - Magdolna Szántó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032, Hungary
| | - Dora Bojcsuk
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032, Hungary
| | - Laura Jankó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032, Hungary
| | - Harjit Pal Bhattoa
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032, Hungary
| | - Imre Gombos
- Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Karen Uray
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032, Hungary
| | - Ibolya Horváth
- Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Zsolt Török
- Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Balint L Balint
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032, Hungary
| | - Zoltán Papp
- Divison of Clinical Physiology, Faculty of Medicine, University of Debrecen, 4032, Hungary; HAS-UD Vascular Biology and Myocardial Pathophysiology Research Group, Hungarian Academy of Sciences, Debrecen 4012, Hungary
| | - László Vígh
- Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Péter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032, Hungary; MTA-DE Lendület Laboratory of Cellular Metabolism Research Group, Debrecen 4032, Hungary; Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, 4032, Hungary.
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