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Xu L, Fan YH, Zhang XJ, Bai L. Unraveling the relationship between histone methylation and nonalcoholic fatty liver disease. World J Hepatol 2024; 16:703-715. [PMID: 38818286 PMCID: PMC11135277 DOI: 10.4254/wjh.v16.i5.703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/09/2024] [Accepted: 04/07/2024] [Indexed: 05/22/2024] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) poses a significant health challenge in modern societies due to shifts in lifestyle and dietary habits. Its complexity stems from genetic predisposition, environmental influences, and metabolic factors. Epigenetic processes govern various cellular functions such as transcription, chromatin structure, and cell division. In NAFLD, these epigenetic tendencies, especially the process of histone methylation, are intricately intertwined with fat accumulation in the liver. Histone methylation is regulated by different enzymes like methyltransferases and demethylases and influences the expression of genes related to adipogenesis. While early-stage NAFLD is reversible, its progression to severe stages becomes almost irreversible. Therefore, early detection and intervention in NAFLD are crucial, and understanding the precise role of histone methylation in the early stages of NAFLD could be vital in halting or potentially reversing the progression of this disease.
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Affiliation(s)
- Li Xu
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases; Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China
| | - Yu-Hong Fan
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases; Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China
| | - Xiao-Jing Zhang
- School of Basic Medical Sciences, Wuhan University, Wuhan 430060, China; State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China
| | - Lan Bai
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases; Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China.
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Epidemiologic, Genetic, Pathogenic, Metabolic, Epigenetic Aspects Involved in NASH-HCC: Current Therapeutic Strategies. Cancers (Basel) 2022; 15:cancers15010023. [PMID: PMID: 36612019 PMCID: PMC9818030 DOI: 10.3390/cancers15010023] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver cancer and is the sixth most frequent cancer in the world, being the third cause of cancer-related deaths. Nonalcoholic steatohepatitis (NASH) is characterized by fatty infiltration, oxidative stress and necroinflammation of the liver, with or without fibrosis, which can progress to advanced liver fibrosis, cirrhosis and HCC. Obesity, metabolic syndrome, insulin resistance, and diabetes exacerbates the course of NASH, which elevate the risk of HCC. The growing prevalence of obesity are related with increasing incidence of NASH, which may play a growing role in HCC epidemiology worldwide. In addition, HCC initiation and progression is driven by reprogramming of metabolism, which indicates growing appreciation of metabolism in the pathogenesis of this disease. Although no specific preventive pharmacological treatments have recommended for NASH, dietary restriction and exercise are recommended. This review focuses on the molecular connections between HCC and NASH, including genetic and risk factors, highlighting the metabolic reprogramming and aberrant epigenetic alterations in the development of HCC in NASH. Current therapeutic aspects of NASH/HCC are also reviewed.
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Feng Y, Li W, Wang Z, Zhang R, Li Y, Zang L, Wang P, Li Z, Dong Y. The p-STAT3/ANXA2 axis promotes caspase-1-mediated hepatocyte pyroptosis in non-alcoholic steatohepatitis. J Transl Med 2022; 20:497. [PMID: 36324154 PMCID: PMC9632054 DOI: 10.1186/s12967-022-03692-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/23/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND To explore the roles of Annexin A2 (ANXA2) on hepatocyte pyroptosis and hepatic fibrosis in nonalcoholic steatohepatitis (NASH) and underlying molecular mechanism. METHODS Bioinformatics analyses were performed on transcriptome data of liver tissues from mice and patients with liver fibrosis for screening the hepatocyte pyroptosis-related differential genes. The in vivo NASH mouse model and in vitro NASH cellular model were established. The expression levels of Anxa2/ANXA2 were quantified. Then, the upstream transcription factor of Anxa2 was screened by ChIP-Seq and experimentally verified. The effects of the p-STAT3/ANXA2 axis on Caspase-1 mediated pyroptosis and fibrosis were explored by in vivo and in vitro experiments. RESULTS Bioinformatics analyses suggested that the expression of Anxa2/ANXA2 was significantly up-regulated in liver tissues of both NASH mice and patients scoring with high pyroptotic activity. Experimental data showed that the ANXA2 expression was positively associated with the development of hepatocyte pyroptosis and fibrosis. As a transcription factor of ANXA2, p-STAT3 can bind to the promoter of Anxa2 and promote its transcription. The inhibition of p-STAT3 can significantly suppress hepatocyte pyroptosis and fibrosis, which was significantly reversed after the over-expression of Anxa2. Caspase-1 was verified as the player of the p-STAT3/ANXA2 axis to promote pyroptosis and fibrosis. By specifically inhibiting Caspase-1, the promotion effect of the p-STAT3/ANXA2 axis on pyroptosis and fibrosis can be significantly weakened. CONCLUSION The p-STAT3 promoted Anxa2 expression at the transcription level, thus activating the Caspase-1 mediated hepatocyte pyroptosis and fibrosis in NASH.
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Affiliation(s)
- Yun Feng
- grid.16821.3c0000 0004 0368 8293Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.100 Haining Road, Hongkou District, 200080 Shanghai, China
| | - Wenhua Li
- grid.16821.3c0000 0004 0368 8293Department of Gastroenterology, Jiading Branch of Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, 800 Huangjiahuayuan Road, 201803 Shanghai, China
| | - Zhuoya Wang
- grid.488482.a0000 0004 1765 5169Department of Endoscopy Center, The First Hospital of Hunan University of Chinese Medicine, 95 middle Shaoshan Road, Yuhua District, Changsha City, Hunan Province China
| | - Ruling Zhang
- grid.16821.3c0000 0004 0368 8293Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.100 Haining Road, Hongkou District, 200080 Shanghai, China
| | - Yan Li
- grid.16821.3c0000 0004 0368 8293Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.100 Haining Road, Hongkou District, 200080 Shanghai, China
| | - Lijuan Zang
- grid.16821.3c0000 0004 0368 8293Department of Pathology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Hongkou District, 200080 Shanghai, China
| | - Peiwen Wang
- grid.16821.3c0000 0004 0368 8293Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.100 Haining Road, Hongkou District, 200080 Shanghai, China
| | - Zhenghong Li
- grid.16821.3c0000 0004 0368 8293Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Konngjiang Road, Hongkou District, 200092 Shanghai, China
| | - Yuwei Dong
- grid.16821.3c0000 0004 0368 8293Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.100 Haining Road, Hongkou District, 200080 Shanghai, China
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Tryndyak VP, Willett RA, Avigan MI, Sanyal AJ, Beland FA, Rusyn I, Pogribny IP. Non-alcoholic fatty liver disease-associated DNA methylation and gene expression alterations in the livers of Collaborative Cross mice fed an obesogenic high-fat and high-sucrose diet. Epigenetics 2022; 17:1462-1476. [PMID: 35324388 PMCID: PMC9586642 DOI: 10.1080/15592294.2022.2043590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a highly prevalent chronic liver disease, and patient susceptibility to its onset and progression is influenced by several factors. In this study, we investigated whether altered hepatic DNA methylation in liver tissue correlates with the degree of severity of NAFLD-like liver injury induced by a high-fat and high-sucrose (HF/HS) diet in Collaborative Cross (CC) mice. Using genome-wide targeted bisulphite DNA methylation next-generation sequencing, we found that mice with different non-alcoholic fatty liver (NAFL) phenotypes could be distinguished by changes in hepatic DNA methylation profiles. Specifically, NAFL-prone male CC042 mice exhibited more prominent DNA methylation changes compared with male CC011 mice and female CC011 and CC042 mice that developed only a mild NAFL phenotype. Moreover, these mouse strains demonstrated different patterns of DNA methylation. While the HF/HS diet induced both DNA hypomethylation and DNA hypermethylation changes in all the mouse strains, the NAFL-prone male CC042 mice demonstrated a global predominance of DNA hypermethylation, whereas a more pronounced DNA hypomethylation pattern developed in the mild-NAFL phenotypic mice. In a targeted analysis of selected genes that contain differentially methylated regions (DMRs), we identified NAFL phenotype-associated differences in DNA methylation and gene expression of the Apoa4, Gls2, and Apom genes in severe NAFL-prone mice but not in mice with mild NAFL phenotypes. These changes in the expression of Apoa4 and Gls2 coincided with similar findings in a human in vitro cell model of diet-induced steatosis and in patients with NAFL. These results suggest that changes in the expression and DNA methylation status of these three genes may serve as a set of predictive markers for the development of NAFLD.
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Affiliation(s)
- Volodymyr P. Tryndyak
- Division of Biochemical Toxicology, FDA-National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Rose A. Willett
- Division of Biochemical Toxicology, FDA-National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Mark I. Avigan
- Office of Pharmacovigilance and Epidemiology, FDA-Center for Drug Evaluation and Research, Silver Spring, Maryland, USA
| | - Arun J. Sanyal
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Frederick A. Beland
- Division of Biochemical Toxicology, FDA-National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&m University, College Station, Texas, USA
| | - Igor P. Pogribny
- Division of Biochemical Toxicology, FDA-National Center for Toxicological Research, Jefferson, Arkansas, USA
- CONTACT Igor P. Pogribny Division of Biochemical Toxicology , FDA-National Center for Toxicological Research, Jefferson, Arkansas, USA
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Chen SH, Wang X. A high preoperative serum IL-25 level is a negative prognosis predictor after liver resection for HBV-HCC. Front Oncol 2022; 12:858151. [PMID: 36119529 PMCID: PMC9478489 DOI: 10.3389/fonc.2022.858151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022] Open
Abstract
Objective The aim of this study was to evaluate the association between preoperative IL-25 levels and HBV-HCC patient outcomes following liver surgery. Methods This study enrolled consecutive HCC patients that had undergone liver surgery from 2008 to 2015. Baseline patient clinical properties were assessed to establish predictors of postoperative overall survival and recurrence-free survival (OS and RFS, respectively) following liver resection. In addition, serum IL-25 levels were assessed via ELISA. Results Cox regression analyses revealed IL-25 levels to be independently related to the OS and RFS of 896 HBV-associated HCC patients. An optimal IL-25 cutoff level of 14.9 μg/ml was identified, with 206 patients in this cohort having IL-25 levels above this threshold. Both the OS and RFS of patients with an IL-25 level <14.9 μg/ml were significantly better after liver resection as compared to those of patients with higher preoperative levels of this cytokine (p < 0.05). Cox multivariate regression analyses revealed an IL-25 level ≥ 14.9 μg/L to be an independent predictor of poorer RFS and OS. A combination of IL-25 levels and tumor diameter may be an even more reliable predictor of OS. Conclusions IL-25 levels are independent predictors of postoperative survival within HCC patients undergoing liver resection.
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Affiliation(s)
- Shao-hua Chen
- Department of Hepatobiliary Surgery, 900TH Hospital of Logistics Support Force, Fuzhou, China
| | - Xu Wang
- Outpatient Department, Meng chao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- *Correspondence: Xu Wang,
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Deficiency of WTAP in hepatocytes induces lipoatrophy and non-alcoholic steatohepatitis (NASH). Nat Commun 2022; 13:4549. [PMID: 35927268 PMCID: PMC9352699 DOI: 10.1038/s41467-022-32163-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/18/2022] [Indexed: 01/18/2023] Open
Abstract
Ectopic lipid accumulation and inflammation are the essential signs of NASH. However, the molecular mechanisms of ectopic lipid accumulation and inflammation during NASH progression are not fully understood. Here we reported that hepatic Wilms' tumor 1-associating protein (WTAP) is a key integrative regulator of ectopic lipid accumulation and inflammation during NASH progression. Hepatic deletion of Wtap leads to NASH due to the increased lipolysis in white adipose tissue, enhanced hepatic free fatty acids uptake and induced inflammation, all of which are mediated by IGFBP1, CD36 and cytochemokines such as CCL2, respectively. WTAP binds to specific DNA motifs which are enriched in the promoters and suppresses gene expression (e.g., Igfbp1, Cd36 and Ccl2) with the involvement of HDAC1. In NASH, WTAP is tranlocated from nucleus to cytosol, which is related to CDK9-mediated phosphorylation. These data uncover a mechanism by which hepatic WTAP regulates ectopic lipid accumulation and inflammation during NASH progression. Ectopic lipid accumulation and inflammation are the essential signs of NASH. Here, the authors show that hepatic WTAP is a key integrative repressor of ectopic lipid accumulation and inflammation during NASH progression, and hepatic deletion of Wtap promotes both of them, leading to NASH
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Lindholm C, Batakis P, Altimiras J, Lees J. Intermittent fasting induces chronic changes in the hepatic gene expression of Red Jungle Fowl (Gallus gallus). BMC Genomics 2022; 23:304. [PMID: 35421924 PMCID: PMC9009039 DOI: 10.1186/s12864-022-08533-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/06/2022] [Indexed: 11/23/2022] Open
Abstract
Background Intermittent fasting (IF), the implementation of fasting periods of at least 12 consecutive hours on a daily to weekly basis, has received a lot of attention in recent years for imparting the life-prolonging and health-promoting effects of caloric restriction with no or only moderate actual restriction of caloric intake. IF is also widely practiced in the rearing of broiler breeders, the parent stock of meat-type chickens, who require strict feed restriction regimens to prevent the serious health problems associated with their intense appetites. Although intermittent fasting has been extensively used in this context to reduce feed competition and its resulting stress, the potential of IF in chickens as an alternative and complementary model to rodents has received less investigation. In both mammals and birds, the liver is a key component of the metabolic response to IF, responding to variations in energy balance. Here we use a microarray analysis to examine the liver transcriptomics of wild-type Red Jungle Fowl chickens fed either ad libitum, chronically restricted to around 70% of ad libitum daily or intermittently fasted (IF) on a 2:1 (2 days fed, 1 day fasted) schedule without actual caloric restriction. As red junglefowl are ancestral to domestic chicken breeds, these data serve as a baseline to which existing and future transcriptomic results from farmed birds such as broiler breeders can be compared. Results We find large effects of feeding regimen on liver transcriptomics, with most of the affected genes relating to energy metabolism. A cluster analysis shows that IF is associated with large and reciprocal changes in genes related to lipid and carbohydrate metabolism, but also chronic changes in genes related to amino acid metabolism (generally down-regulated) and cell cycle progression (generally up-regulated). The overall transcription pattern appears to be one of promoting high proliferative plasticity in response to fluctuations in available energy substrates. A small number of inflammation-related genes also show chronically changed expression profiles, as does one circadian rhythm gene. Conclusions The increase in proliferative potential suggested by the gene expression changes reported here indicates that birds and mammals respond similarly to intermittent fasting practices. Our findings therefore suggest that the health benefits of periodic caloric restriction are ubiquitous and not restricted to mammals alone. Whether a common fundamental mechanism, for example involving leptin, underpins these benefits remains to be elucidated. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08533-5.
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Berthou F, Sobolewski C, Abegg D, Fournier M, Maeder C, Dolicka D, Correia de Sousa M, Adibekian A, Foti M. Hepatic PTEN Signaling Regulates Systemic Metabolic Homeostasis through Hepatokines-Mediated Liver-to-Peripheral Organs Crosstalk. Int J Mol Sci 2022; 23:ijms23073959. [PMID: 35409319 PMCID: PMC8999584 DOI: 10.3390/ijms23073959] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/25/2022] [Accepted: 03/31/2022] [Indexed: 11/16/2022] Open
Abstract
Liver-derived circulating factors deeply affect the metabolism of distal organs. Herein, we took advantage of the hepatocyte-specific PTEN knockout mice (LPTENKO), a model of hepatic steatosis associated with increased muscle insulin sensitivity and decreased adiposity, to identify potential secreted hepatic factors improving metabolic homeostasis. Our results indicated that protein factors, rather than specific metabolites, released by PTEN-deficient hepatocytes trigger an improved muscle insulin sensitivity and a decreased adiposity in LPTENKO. In this regard, a proteomic analysis of conditioned media from PTEN-deficient primary hepatocytes identified seven hepatokines whose expression/secretion was deregulated. Distinct expression patterns of these hepatokines were observed in hepatic tissues from human/mouse with NAFLD. The expression of specific factors was regulated by the PTEN/PI3K, PPAR or AMPK signaling pathways and/or modulated by classical antidiabetic drugs. Finally, loss-of-function studies identified FGF21 and the triad AHSG, ANGPTL4 and LECT2 as key regulators of insulin sensitivity in muscle cells and in adipocytes biogenesis, respectively. These data indicate that hepatic PTEN deficiency and steatosis alter the expression/secretion of hepatokines regulating insulin sensitivity in muscles and the lipid metabolism in adipose tissue. These hepatokines could represent potential therapeutic targets to treat obesity and insulin resistance.
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Affiliation(s)
- Flavien Berthou
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (F.B.); (C.S.); (M.F.); (C.M.); (D.D.); (M.C.d.S.)
| | - Cyril Sobolewski
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (F.B.); (C.S.); (M.F.); (C.M.); (D.D.); (M.C.d.S.)
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; (D.A.); (A.A.)
| | - Margot Fournier
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (F.B.); (C.S.); (M.F.); (C.M.); (D.D.); (M.C.d.S.)
| | - Christine Maeder
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (F.B.); (C.S.); (M.F.); (C.M.); (D.D.); (M.C.d.S.)
| | - Dobrochna Dolicka
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (F.B.); (C.S.); (M.F.); (C.M.); (D.D.); (M.C.d.S.)
| | - Marta Correia de Sousa
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (F.B.); (C.S.); (M.F.); (C.M.); (D.D.); (M.C.d.S.)
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; (D.A.); (A.A.)
| | - Michelangelo Foti
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (F.B.); (C.S.); (M.F.); (C.M.); (D.D.); (M.C.d.S.)
- Diabetes Center, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
- Correspondence: ; Tel.: +41-(22)-379-52-04
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Pan J, Cen L, Zhou T, Yu M, Chen X, Jiang W, Li Y, Yu C, Shen Z. Insulin-like growth factor binding protein 1 ameliorates lipid accumulation and inflammation in nonalcoholic fatty liver disease. J Gastroenterol Hepatol 2021; 36:3438-3447. [PMID: 34273192 DOI: 10.1111/jgh.15627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Insulin-like growth factor binding protein 1 (IGFBP1) is recently proved to be associated with glucose regulation and insulin resistance. However, little is known about its direct impact on nonalcoholic fatty liver disease (NAFLD). This study aims to investigate the effect and potential mechanism of IGFBP1 in NAFLD. METHODS We first measured the expression level of IGFBP1 in NAFLD patients, mice, and cells. Then in in vivo study, C57BL/6 mice were fed with a methionine/choline-deficient (MCD) diet for 4 weeks to establish the model of NAFLD. And for the last 2 weeks, the mice were injected intraperitoneally with vehicle or recombinant mouse IGFBP1 0.015 mg/kg/d. The L02 cells were treated with free fatty acids (FFA) or palmitate acids (PA) and recombinant IGFBP1 for 48 h. Integrin-linked kinase (ILK) inhibitor and small interfering RNA were used to explore the potential interactions between IGFBP1 and integrin β1 (ITGB1). RESULTS The expression of IGFBP1 was increased in NAFLD patients, mice, and cells. IGFBP1 treatment significantly ameliorated lipid accumulation and hepatic injury in MCD-fed mice. IGFBP1 downregulated hepatic lipogenesis and upregulated lipid β-oxidation. In addition, IGFBP1 attenuated the nuclear factor-kappa B (NF-κB) and extracellular regulated protein kinases (ERK) signaling pathways. In vitro, we proved that IGFBP1 relieved FFA-induced lipid accumulation via interacting with ITGB1 and alleviated inflammation by inhibiting NF-κB and ERK signaling pathways. CONCLUSIONS IGFBP1 treatment significantly ameliorated hepatic steatosis by interacting with ITGB1 and suppressed inflammation by inhibiting NF-κB and ERK signaling pathways. Therefore, IGFBP1 might be a potential therapeutic target for NAFLD.
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Affiliation(s)
- Jiaqi Pan
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Li Cen
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Tianyu Zhou
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Mengli Yu
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xueyang Chen
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Wenxi Jiang
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Youming Li
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Chaohui Yu
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhe Shen
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Li J, Yu N, Li X, Cui M, Guo Q. The Single-Cell Sequencing: A Dazzling Light Shining on the Dark Corner of Cancer. Front Oncol 2021; 11:759894. [PMID: 34745998 PMCID: PMC8566994 DOI: 10.3389/fonc.2021.759894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/30/2021] [Indexed: 11/30/2022] Open
Abstract
Tumorigenesis refers to the process of clonal dysplasia that occurs due to the collapse of normal growth regulation in cells caused by the action of various carcinogenic factors. These “successful” tumor cells pass on the genetic templates to their generations in evolutionary terms, but they also constantly adapt to ever-changing host environments. A unique peculiarity known as intratumor heterogeneity (ITH) is extensively involved in tumor development, metastasis, chemoresistance, and immune escape. An understanding of ITH is urgently required to identify the diversity and complexity of the tumor microenvironment (TME), but achieving this understanding has been a challenge. Single-cell sequencing (SCS) is a powerful tool that can gauge the distribution of genomic sequences in a single cell and the genetic variability among tumor cells, which can improve the understanding of ITH. SCS provides fundamental ideas about existing diversity in specific TMEs, thus improving cancer diagnosis and prognosis prediction, as well as improving the monitoring of therapeutic response. Herein, we will discuss advances in SCS and review SCS application in tumors based on current evidence.
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Affiliation(s)
- Jing Li
- Department of Clinical Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Nan Yu
- Department of Pharmacy, Qingdao Eighth People's Hospital, Qingdao, China
| | - Xin Li
- Department of Clinical Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Mengna Cui
- Department of Clinical Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qie Guo
- Department of Clinical Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
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11
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The immune niche of the liver. Clin Sci (Lond) 2021; 135:2445-2466. [PMID: 34709406 DOI: 10.1042/cs20190654] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/17/2021] [Accepted: 10/08/2021] [Indexed: 12/19/2022]
Abstract
The liver is an essential organ that is critical for the removal of toxins, the production of proteins, and the maintenance of metabolic homeostasis. Behind each liver functional unit, termed lobules, hides a heterogeneous, complex, and well-orchestrated system. Despite parenchymal cells being most commonly associated with the liver's primary functionality, it has become clear that it is the immune niche of the liver that plays a central role in maintaining both local and systemic homeostasis by propagating hepatic inflammation and orchestrating its resolution. As such, the immunological processes that are at play in healthy and diseased livers are being investigated thoroughly in order to understand the underpinnings of inflammation and the potential avenues for restoring homeostasis. This review highlights recent advances in our understanding of the immune niche of the liver and provides perspectives for how the implementation of new transcriptomic, multimodal, and spatial technologies can uncover the heterogeneity, plasticity, and location of hepatic immune populations. Findings from these technologies will further our understanding of liver biology and create a new framework for the identification of therapeutic targets.
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Zhang Z, Liu L, Shen Y, Meng Z, Chen M, Lu Z, Zhang X. Characterization of chromatin accessibility in psoriasis. Front Med 2021; 16:483-495. [PMID: 34669155 DOI: 10.1007/s11684-021-0872-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/29/2021] [Indexed: 12/13/2022]
Abstract
The pathological hallmarks of psoriasis involve alterations in T cell genes associated with transcriptional levels, which are determined by chromatin accessibility. However, to what extent these alterations in T cell transcriptional levels recapitulate the epigenetic features of psoriasis remains unknown. Here, we systematically profiled chromatin accessibility on Th1, Th2, Th1-17, Th17, and Treg cells and found that chromatin remodeling contributes significantly to the pathogenesis of the disease. The chromatin remodeling tendency of different subtypes of Th cells were relatively consistent. Next, we profiled chromatin accessibility and transcriptional dynamics on memory Th/Treg cells. In the memory Th cells, 803 increased and 545 decreased chromatin-accessible regions were identified. In the memory Treg cells, 713 increased and 1206 decreased chromatin-accessible regions were identified. A total of 54 and 53 genes were differentially expressed in the peaks associated with the memory Th and Treg cells. FOSL1, SPI1, ATF3, NFKB1, RUNX, ETV4, ERG, FLI1, and ETC1 were identified as regulators in the development of psoriasis. The transcriptional regulatory network showed that NFKB1 and RELA were highly connected and central to the network. NFKB1 regulated the genes of CCL3, CXCL2, and IL1RN. Our results provided candidate transcription factors and a foundational framework of the regulomes of the disease.
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Affiliation(s)
- Zheng Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Lu Liu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | - Yanyun Shen
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ziyuan Meng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | - Min Chen
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China.,Department of Dermatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215123, China
| | - Zhong Lu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Xuejun Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China. .,Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China. .,Department of Dermatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215123, China.
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13
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Fan H, Ren Z, Xu C, Wang H, Wu Z, Rehman ZU, Wu S, Sun MA, Bao W. Chromatin Accessibility and Transcriptomic Alterations in Murine Ovarian Granulosa Cells upon Deoxynivalenol Exposure. Cells 2021; 10:2818. [PMID: 34831041 PMCID: PMC8616273 DOI: 10.3390/cells10112818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 11/26/2022] Open
Abstract
Deoxynivalenol (DON) is a common environmental toxin that is secreted by fusarium fungi that frequently contaminates feedstuff and food. While the detrimental effects of DON on human and animal reproductive systems have been well recognized, the underlying mechanism remains poorly understood. Ovarian granulosa cells (GCs), which surround oocytes, are crucial for regulating oocyte development, mainly through the secretion of hormones such as estrogen and progesterone. Using an in vitro model of murine GCs, we characterized the cytotoxic effects of DON and profiled genome-wide chromatin accessibility and transcriptomic alterations after DON exposure. Our results suggest that DON can induce decreased viability and growth, increased apoptosis rate, and disrupted hormone secretion. In total, 2533 differentially accessible loci and 2675 differentially expressed genes were identified that were associated with Hippo, Wnt, steroid biosynthesis, sulfur metabolism, and inflammation-related pathways. DON-induced genes usually have a concurrently increased occupancy of active histone modifications H3K4me3 and H3K27ac in their promoters. Integrative analyses identified 35 putative directly affected genes including Adrb2 and Fshr, which are key regulators of follicular growth, and revealed that regions with increased chromatin accessibility are enriched with the binding motifs for NR5A1 and NR5A2, which are important for GCs. Moreover, DON-induced inflammatory response is due to the activation of the NF-κB and MAPK signaling pathways. Overall, our results provide novel insights into the regulatory elements, genes, and key pathways underlying the response of ovarian GCs to DON cytotoxicity.
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Affiliation(s)
- Hairui Fan
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Zhanshi Ren
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Chao Xu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Haifei Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Zhengchang Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Zia ur Rehman
- Faculty of Animal Husbandry and Veterinary Sciences, College of Veterinary Sciences, The University of Agriculture Peshawar, Peshawar 25000, Pakistan;
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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14
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Yue J, Hou X, Liu X, Wang L, Gao H, Zhao F, Shi L, Shi L, Yan H, Deng T, Gong J, Wang L, Zhang L. The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs. J Anim Sci Biotechnol 2021; 12:56. [PMID: 33934724 PMCID: PMC8091695 DOI: 10.1186/s40104-021-00577-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/01/2021] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms, which depend on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45, 70 and 100 days post coitus (dpc). RESULTS In total, 21,638, 35,447 and 60,181 unique regions (or peaks) were found across the embryos at 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100), respectively. More than 91% of the peaks were annotated within - 1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes. Moreover, the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle development-related genes, such as MyoG, Mef2c, and Mef2d. Several potential transcriptional repressors, including E2F6, OTX2 and CTCF, were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data. CONCLUSIONS This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.
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Affiliation(s)
- Jingwei Yue
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xinhua Hou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xin Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ligang Wang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongmei Gao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fuping Zhao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lijun Shi
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Liangyu Shi
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hua Yan
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tianyu Deng
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jianfei Gong
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lixian Wang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Longchao Zhang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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15
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Melia T, Waxman DJ. Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice. PLoS One 2020; 15:e0242665. [PMID: 33264334 PMCID: PMC7710091 DOI: 10.1371/journal.pone.0242665] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Sex-specific transcription characterizes hundreds of genes in mouse liver, many implicated in sex-differential drug and lipid metabolism and disease susceptibility. While the regulation of liver sex differences by growth hormone-activated STAT5 is well established, little is known about autosomal genetic factors regulating the sex-specific liver transcriptome. Here we show, using genotyping and expression data from a large population of Diversity Outbred mice, that genetic factors work in tandem with growth hormone to control the individual variability of hundreds of sex-biased genes, including many long non-coding RNA genes. Significant associations between single nucleotide polymorphisms and sex-specific gene expression were identified as expression quantitative trait loci (eQTLs), many of which showed strong sex-dependent associations. Remarkably, autosomal genetic modifiers of sex-specific genes were found to account for more than 200 instances of gain or loss of sex-specificity across eight Diversity Outbred mouse founder strains. Sex-biased STAT5 binding sites and open chromatin regions with strain-specific variants were significantly enriched at eQTL regions regulating correspondingly sex-specific genes, supporting the proposed functional regulatory nature of the eQTL regions identified. Binding of the male-biased, growth hormone-regulated repressor BCL6 was most highly enriched at trans-eQTL regions controlling female-specific genes. Co-regulated gene clusters defined by overlapping eQTLs included sets of highly correlated genes from different chromosomes, further supporting trans-eQTL action. These findings elucidate how an unexpectedly large number of autosomal factors work in tandem with growth hormone signaling pathways to regulate the individual variability associated with sex differences in liver metabolism and disease.
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Affiliation(s)
- Tisha Melia
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - David J. Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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16
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Lucendo-Villarin B, Nell P, Hellwig B, Filis P, Feuerborn D, O'Shaughnessy PJ, Godoy P, Rahnenführer J, Hengstler JG, Cherianidou A, Sachinidis A, Fowler PA, Hay DC. Genome-wide expression changes induced by bisphenol A, F and S in human stem cell derived hepatocyte-like cells. EXCLI JOURNAL 2020; 19:1459-1476. [PMID: 33312107 PMCID: PMC7726493 DOI: 10.17179/excli2020-2934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022]
Abstract
The debate about possible adverse effects of bisphenol A (BPA) has been ongoing for decades. Bisphenol F (BPF) and S (BPS) have been suggested as “safer” alternatives. In the present study we used hepatocyte-like cells (HLCs) derived from the human embryonic stem cell lines Man12 and H9 to compare the three bisphenol derivatives. Stem cell-derived progenitors were produced using an established system and were exposed to BPA, BPF and BPS for 8 days during their transition to HLCs. Subsequently, we examined cell viability, inhibition of cytochrome P450 (CYP) activity, and genome-wide RNA profiles. Sub-cytotoxic, inhibitory concentrations (IC50) of CYP3A were 20, 9.5 and 25 µM for BPA, BPF and BPS in Man12 derived HLCs, respectively. The corresponding concentrations for H9-derived HLCs were 19, 29 and 31 µM. These IC50 concentrations were used to study global expression changes in this in vitro study and are higher than unconjugated BPA in serum of the general population. A large overlap of up- as well as downregulated genes induced by the three bisphenol derivatives was seen. This is at least 28-fold higher compared to randomly expected gene expression changes. Moreover, highly significant correlations of expression changes induced by the three bisphenol derivatives were obtained in pairwise comparisons. Dysregulated genes were associated with reduced metabolic function, cellular differentiation, embryonic development, cell survival and apoptosis. In conclusion, no major differences in cytochrome inhibitory activities of BPA, BPF and BPS were observed and gene expression changes showed a high degree of similarity.
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Affiliation(s)
- B Lucendo-Villarin
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - P Nell
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - B Hellwig
- Department of Statistics, Technical University Dortmund, Dortmund, Germany
| | - P Filis
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - D Feuerborn
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - P J O'Shaughnessy
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, UK
| | - P Godoy
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - J Rahnenführer
- Department of Statistics, Technical University Dortmund, Dortmund, Germany
| | - J G Hengstler
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - A Cherianidou
- Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Cologne, Germany
| | - A Sachinidis
- Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Cologne, Germany
| | - P A Fowler
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - D C Hay
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
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17
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Zhao Y, Zhang X, Song Z, Wei D, Wang H, Chen W, Sun G, Ma W, Chen K. Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection. Front Med (Lausanne) 2020; 7:584728. [PMID: 33224964 PMCID: PMC7670091 DOI: 10.3389/fmed.2020.584728] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is associated with significant progress in biological research and has attracted increasing attention. However, the impact of ATAC-seq on cancer biology has not been objectively analyzed. We categorized 440 ATAC-seq publications according to the publication date, type, field, and country. R 3.6.2 was used to analyze the distribution of research fields. VOSviewer was used for country co-authorship and author co-authorship analyses, and GraphPad Prism 8 was used for correlation analyses of the factors that may affect the number of articles published in different countries. We found that ATAC-seq plays roles in carcinogenesis, anticancer immunity, targeted therapy, and metastasis risk predictions and is most frequently used in studies of leukemia among all types of cancer. We found a significantly strong correlation between the top 10 countries in terms of the number of publications and the gross expenditure on research and development (R&D), the number of universities, and the number of researchers. At present, ATAC-seq technology is undergoing a period of rapid development, making it inseparable from the emphasis and investment in scientific research by many countries. Collectively, ATAC-seq has advantages in the study of the cancer mechanisms because it can detect nucleic acids and thus has good application prospects in the field of cancer, especially in leukemia studies. As a country's economic strength increases and the emphasis on scientific research deepens, ATAC-seq will definitely play a more significant role in the field of cancer biology.
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Affiliation(s)
- Yu Zhao
- Department of Hematology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Xianwen Zhang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhenhua Song
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Disease, Department of Treatment Center for Traumatic Injuries, The Third Affiliated Hospital of Southern Medical University (Academy of Orthopedics of Guangdong Province), Guangzhou, China
| | - Danian Wei
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Disease, Department of Treatment Center for Traumatic Injuries, The Third Affiliated Hospital of Southern Medical University (Academy of Orthopedics of Guangdong Province), Guangzhou, China
| | - Hong Wang
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Disease, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,Academy of Orthopedics of Guangdong Province, Guangzhou, China
| | - Wei Chen
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Disease, Department of Musculoskeletal Oncology, The Third Affiliated Hospital of Southern Medical University (Academy of Orthopedics of Guangdong Province), Guangzhou, China
| | - Guodong Sun
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Weiying Ma
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Kebing Chen
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Disease, Department of Spine Surgery, The Third Affiliated Hospital of Southern Medical University (Academy of Orthopedics of Guangdong Province), Guangzhou, China
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18
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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] [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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19
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Wang Y, Zhang X, Song Q, Hou Y, Liu J, Sun Y, Wang P. Characterization of the chromatin accessibility in an Alzheimer's disease (AD) mouse model. ALZHEIMERS RESEARCH & THERAPY 2020; 12:29. [PMID: 32293531 PMCID: PMC7092509 DOI: 10.1186/s13195-020-00598-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
Background The pathological hallmarks of Alzheimer’s disease (AD) involve alterations in the expression of numerous genes associated with transcriptional levels, which are determined by chromatin accessibility. Here, the landscape of chromatin accessibility was studied to understand the outline of the transcription and expression of AD-associated metabolism genes in an AD mouse model. Methods The assay for transposase-accessible chromatin by sequencing (ATAC-seq) was used to investigate the AD-associated chromatin reshaping in the APPswe/PS1dE9 (APP/PS1) mouse model. ATAC-seq data in the hippocampus of 8-month-old APP/PS1 mice were generated, and the relationship between chromatin accessibility and gene expression was analyzed in combination with RNA sequencing. Gene ontology (GO) analysis was applied to elucidate biological processes and signaling pathways altered in APP/PS1 mice. Critical transcription factors were identified; alterations in chromatin accessibility were further confirmed using chromatin immunoprecipitation assays. Results We identified 1690 increased AD-associated chromatin-accessible regions in the hippocampal tissues of APP/PS1 mice. These regions were enriched in genes related to diverse signaling pathways, including the PI3K-Akt, Hippo, TGF-β, and Jak-Stat signaling pathways, which play essential roles in regulating cell proliferation, apoptosis, and inflammatory responses. A total of 1003 decreased chromatin-accessible regions were considered to be related with declined AD-associated biological processes including cellular response to hyperoxia and insulin stimulus, synaptic transmission, and positive regulation of autophagy. In the APP/PS1 hippocampus, 1090 genes were found to be upregulated and 1081 downregulated. Interestingly, enhanced ATAC-seq signal was found in approximately 740 genes, with 43 exhibiting upregulated mRNA levels. Several genes involved in AD development were found to have a significantly increased expression in APP/PS1 mice compared to controls, including Sele, Clec7a, Cst7, and Ccr6. The signatures of numerous transcription factors, including Olig2, NeuroD1, TCF4, and NeuroG2, were found enriched in the AD-associated accessible chromatin regions. The transcription-activating marks of H3K4me3 and H3K27ac were also found increased in the promoters of these genes. These results indicate that the mechanism for the upregulation of genes could be attributed to the enrichment of open chromatin regions with transcription factors motifs and the histone marks H3K4me3 and H3K27ac. Conclusion Our study reveals that alterations in chromatin accessibility may be an initial mechanism in AD pathogenesis. Supplementary information Supplementary information accompanies this paper at 10.1186/s13195-020-00598-2.
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Affiliation(s)
- Yaqi Wang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Xiaomin Zhang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Qiao Song
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Yuli Hou
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Jing Liu
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Yu Sun
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China.
| | - Peichang Wang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China.
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