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Castellano-Castillo D, Ramos-Molina B, Frutos MD, Arranz-Salas I, Reyes-Engel A, Queipo-Ortuño MI, Cardona F. RNA expression changes driven by altered epigenetics status related to NASH etiology. Biomed Pharmacother 2024; 174:116508. [PMID: 38579398 DOI: 10.1016/j.biopha.2024.116508] [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] [Received: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a growing health problem due to the increased obesity rates, among other factors. In its more severe stage (NASH), inflammation, hepatocellular ballooning and fibrosis are present in the liver, which can further evolve to total liver dysfunction or even hepatocarcinoma. As a metabolic disease, is associated to environmental factors such as diet and lifestyle conditions, which in turn can influence the epigenetic landscape of the cells, affecting to the gene expression profile and chromatin organization. In this study we performed ATAC-sequencing and RNA-sequencing to interrogate the chromatin status of liver biopsies in subjects with and without NASH and its effects on RNA transcription and NASH etiology. NASH subjects showed transcriptional downregulation for lipid and glucose metabolic pathways (e.g., ABC transporters, AMPK, FoxO or insulin pathways). A total of 229 genes were differentially enriched (ATAC and mRNA) in NASH, which were mainly related to lipid transport activity, nuclear receptor-binding, dicarboxylic acid transporter, and PPARA lipid regulation. Interpolation of ATAC data with known liver enhancer regions showed differential openness at 8 enhancers, some linked to genes involved in lipid metabolism, (i.e., FASN) and glucose homeostasis (i.e., GCGR). In conclusion, the chromatin landscape is altered in NASH patients compared to patients without this liver condition. This alteration might cause mRNA changes explaining, at least partially, the etiology and pathophysiology of the disease.
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Affiliation(s)
- Daniel Castellano-Castillo
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA)-CIMES-UMA, Málaga 29010, Spain
| | - Bruno Ramos-Molina
- Obesity, Diabetes and Metabolism Laboratory, Biomedical Research Institute of Murcia (IMIB), Murcia 30120, Spain.
| | - María Dolores Frutos
- General and Digestive System Surgery Department, Virgen de la Arrixaca University Hospital, Murcia 31020, Spain
| | - Isabel Arranz-Salas
- Instituto de Investigación Biomédica de Málaga-Plataforma BIONAND (IBIMA), Virgen de la Victoria University Hospital, Malaga University, 2ª Planta, Campus Teatinos S/N, Málaga 29010, Spain; Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, Malaga University, Málaga 29010, Spain; 11 Department of Anatomical Pathology, Virgen de la Victoria Hospital, Málaga, Spain
| | - Armando Reyes-Engel
- Departamento de especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, 29010, Spain
| | - María Isabel Queipo-Ortuño
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA)-CIMES-UMA, Málaga 29010, Spain; Departamento de especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, 29010, Spain.
| | - Fernando Cardona
- Departamento de especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, 29010, Spain
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Luo C, Wang Z, Wang J, Yun F, Lu F, Fu J, Liu Q, Shi D. Individual variation in buffalo somatic cell cloning efficiency is related to glycolytic metabolism. Sci China Life Sci 2022; 65:2076-2092. [PMID: 35366153 DOI: 10.1007/s11427-021-2039-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Mammalian individuals differ in their somatic cell cloning efficiency, but the mechanisms leading to this variation is poorly understood. Here we found that high cloning efficiency buffalo fetal fibroblasts (BFFs) displayed robust energy metabolism, looser chromatin structure, high H3K9 acetylation and low heterochromatin protein 1α (HP1α) expression. High cloning efficiency BFFs had more H3K9ac regions near to the upstream of glycolysis genes by ChIP-seq, and involved more openness loci related to glycolysis genes through ATAC-seq. The expression of these glycolysis genes was also found to be higher in high cloning efficiency BFFs by qRT-PCR. Two key enzymes of glycolysis, PDKs and LDH, were confirmed to be associated with histone acetylation and chromatin openness of BFFs. Treatment of low cloning efficiency BFFs with PS48 (activator of PDK1) resulted in an increase in the intracellular lactate production and H3K9 acetylation, decrease in histone deacetylase activity and HP1α expression, less condensed chromatin structure and more cloning embryos developing to blastocysts. These results indicate that the cloning efficiency of buffalo somatic cells is associated with their glycolytic metabolism and chromatin structure, and can be improved by increasing glycolytic metabolism.
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Affiliation(s)
- Chan Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Zhiqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Jinling Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Feng Yun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Fenghua Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Jiayuan Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China.
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Ren X, She C, Huang S, Yang T, Tong Y, Yuan X, Shi D, Li X. Chromatin openness of donor cells is directly correlated with the in vitro developmental capabilities of cloned buffalo embryos. Reprod Domest Anim 2022; 57:1113-1124. [PMID: 35689464 DOI: 10.1111/rda.14177] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022]
Abstract
The Switch/sucrose nonfermentable (SWI/SNF) chromatin remodelling complex is closely related to chromatin openness and gene transcriptional activity. To understand if the chromatin openness of donor cells was related to the development efficiency of somatic cell cloning embryos, two buffalo fetal fibroblasts (BFF), BFF1 and BFF3, with significantly different cloned blastocyst development rates (18.4% and 30.9% respectively), were selected in this study. The expression of SWI/SNF complex genes, chromatin openness, and transcript level of these two cell lines were analysed, and the effect of ATP on the expression of the SWI/SNF complex genes was further explored. The results showed that compared with BFF1, the expression of SWI/SNF complex family genes was higher in BFF3 at the G0/G1 phase, where SMARCC1, SMARCC2 and SMARCE1 were significantly different (p < .05). Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) results showed that, at the genome-wide level, BFF3 had more open chromatin, especially which having more open chromatin peaks at SMARCA4, SMARCA2, and RBPMS2 (RNA Binding Protein, mRNA Processing Factor 2) sites. In total, 2,712 differentially expressed genes (DEGs) were identified by the RNA-Seq method, with 1380 up- and 1332 down-regulated genes in BFF3. Interestingly, the ATPase-related genes ATP1B1 and ATP11A were extreme significantly up-regulated in BFF3 (p < .01). The ATP content and the expression of SWI/SNF complex genes in both BFF1 and BFF3 decreased when treated with rotenone. The above results demonstrated that the SWI/SNF complex contributed to chromatin opening, and chromatin opening of donor cells was essential for cloned embryo development.
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Affiliation(s)
- Xuan Ren
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Chun She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Shihai Huang
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ting Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Yi Tong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Xi Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Xiangping Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
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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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