1
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Qian S, Wang X, Chen Y, Zai Q, He Y. Inflammation in Steatotic Liver Diseases: Pathogenesis and Therapeutic Targets. Semin Liver Dis 2024. [PMID: 38838739 DOI: 10.1055/a-2338-9261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Alcohol-related liver disease (ALD) and metabolic dysfunction-associated steatotic liver disease (MASLD), two main types of steatotic liver disease (SLDs), are characterized by a wide spectrum of several different liver disorders, including simple steatosis, steatohepatitis, cirrhosis, and hepatocellular carcinoma. Multiple immune cell-mediated inflammatory responses not only orchestrate the killing and removal of infected/damaged cells but also exacerbate the development of SLDs when excessive or persistent inflammation occurs. In recent years, single-cell and spatial transcriptome analyses have revealed the heterogeneity of liver-infiltrated immune cells in ALD and MASLD, revealing a new immunopathological picture of SLDs. In this review, we will emphasize the roles of several key immune cells in the pathogenesis of ALD and MASLD and discuss inflammation-based approaches for effective SLD intervention. In conclusion, the study of immunological mechanisms, especially highly specific immune cell population functions, may provide novel therapeutic opportunities for this life-threatening disease.
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Affiliation(s)
- Shengying Qian
- Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Wang
- Department of Infectious Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai, China
| | - Yingfen Chen
- Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiuhong Zai
- Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong He
- Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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2
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Karin M, Kim JY. MASH as an emerging cause of hepatocellular carcinoma: current knowledge and future perspectives. Mol Oncol 2024. [PMID: 38874196 DOI: 10.1002/1878-0261.13685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 04/15/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
Hepatocellular carcinoma is one of the deadliest and fastest-growing cancers. Among HCC etiologies, metabolic dysfunction-associated fatty liver disease (MAFLD) has served as a major HCC driver due to its great potential for increasing cirrhosis. The obesogenic environment fosters a positive energy balance and results in a continuous rise of obesity and metabolic syndrome. However, it is difficult to understand how metabolic complications lead to the poor prognosis of liver diseases and which molecular mechanisms are underpinning MAFLD-driven HCC development. Thus, suitable preclinical models that recapitulate human etiologies are essentially required. Numerous preclinical models have been created but not many mimicked anthropometric measures and the course of disease progression shown in the patients. Here we review the literature on adipose tissues, liver-related HCC etiologies and recently discovered genetic mutation signatures found in MAFLD-driven HCC patients. We also critically review current rodent models suggested for MAFLD-driven HCC study.
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Affiliation(s)
- Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ju Youn Kim
- Department of Molecular and Life Science, Hanyang University ERICA, Ansan, Korea
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3
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Wang H, Liu J, Zhu P, Shi L, Liu Y, Yang X, Yang X. Single-nucleus transcriptome reveals cell dynamic response of liver during the late chick embryonic development. Poult Sci 2024; 103:103979. [PMID: 38941785 DOI: 10.1016/j.psj.2024.103979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/29/2024] [Accepted: 06/10/2024] [Indexed: 06/30/2024] Open
Abstract
The late embryonic development of the liver, a major metabolic organ, remains poorly characterized at single cell resolution. Here, we used single-nucleus RNA-sequencing (snRNA-seq) to characterize the chicken liver cells at 2 embryonic development time points (E14 and D1). We uncovered 8 cell types including hepatocytes, endothelial cells, hepatic stellate cells, erythrocytes, cholangiocytes, kupffer cells, mesothelial cells, and lymphocytes. And we discovered significant differences in the abundance of different cell types between E14 and D1. Moreover, we characterized the heterogeneity of hepatocytes, endothelial cells, and mesenchymal cells based on the gene regulatory networks of each clusters. Trajectory analyses revealed 128 genes associated with hepatocyte development and function, including apolipoprotein genes involved hepatic lipid metabolism and NADH dehydrogenase subunits involved hepatic oxidative phosphorylation. Furthermore, we identified the differentially expressed genes (DEGs) between E14 and D1 at the cellular levels, which contribute to changes in liver development and function. These DEGs were significantly enriched in PPAR signaling pathways and lipid metabolism related pathways. Our results presented the single-cell mapping of chick embryonic liver at late stages of development and demonstrated the metabolic changes across the 2 age stages at the cellular level, which can help to further study the molecular development mechanism of embryonic liver.
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Affiliation(s)
- Huimei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Jiongyan Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Pinhui Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Lin Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
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4
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Xia J, Chen H, Wang X, Chen W, Lin J, Xu F, Nie Q, Ye C, Zhong B, Zhao M, Yun C, Zeng G, Mao Y, Wen Y, Zhang X, Yan S, Wang X, Sun L, Liu F, Zhong C, Xia P, Jiang C, Rao H, Pang Y. Sphingosine d18:1 promotes nonalcoholic steatohepatitis by inhibiting macrophage HIF-2α. Nat Commun 2024; 15:4755. [PMID: 38834568 PMCID: PMC11150497 DOI: 10.1038/s41467-024-48954-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 05/17/2024] [Indexed: 06/06/2024] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a severe type of the non-alcoholic fatty liver disease (NAFLD). NASH is a growing global health concern due to its increasing morbidity, lack of well-defined biomarkers and lack of clinically effective treatments. Using metabolomic analysis, the most significantly changed active lipid sphingosine d18:1 [So(d18:1)] is selected from NASH patients. So(d18:1) inhibits macrophage HIF-2α as a direct inhibitor and promotes the inflammatory factors secretion. Male macrophage-specific HIF-2α knockout and overexpression mice verified the protective effect of HIF-2α on NASH progression. Importantly, the HIF-2α stabilizer FG-4592 alleviates liver inflammation and fibrosis in NASH, which indicated that macrophage HIF-2α is a potential drug target for NASH treatment. Overall, this study confirms that So(d18:1) promotes NASH and clarifies that So(d18:1) inhibits the transcriptional activity of HIF-2α in liver macrophages by suppressing the interaction of HIF-2α with ARNT, suggesting that macrophage HIF-2α may be a potential target for the treatment of NASH.
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Affiliation(s)
- Jialin Xia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Hong Chen
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Xiaoxiao Wang
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Weixuan Chen
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Jun Lin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Feng Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Qixing Nie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Chuan Ye
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Bitao Zhong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
| | - Min Zhao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Chuyu Yun
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Guangyi Zeng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Yuejian Mao
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Yongping Wen
- Mengniu Institute of Nutrition Science, Shanghai, China
| | - Xuguang Zhang
- Mengniu Institute of Nutrition Science, Shanghai, China
- Shanghai Institute of Nutrition and Health, The Chinese Academy of Sciences, Shanghai, China
| | - Sen Yan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Xuemei Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Lulu Sun
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
- Department of Endocrinology and Metabolism, Peking University Third Hospital, Beijing, China
| | - Feng Liu
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Chao Zhong
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Medicine Innovation Center for Fundamental Research on Major Immunology-related Diseases, Peking University, Beijing, China
| | - Pengyan Xia
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Medicine Innovation Center for Fundamental Research on Major Immunology-related Diseases, Peking University, Beijing, China
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Medicine Innovation Center for Fundamental Research on Major Immunology-related Diseases, Peking University, Beijing, China
| | - Huiying Rao
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China.
| | - Yanli Pang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China.
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China.
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5
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Wang W, Cen Y, Lu Z, Xu Y, Sun T, Xiao Y, Liu W, Li JJ, Wang C. scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data. Genome Biol 2024; 25:136. [PMID: 38783325 PMCID: PMC11112958 DOI: 10.1186/s13059-024-03284-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination for all genes globally. However, there lacks specific evaluation of correction efficacy for varying contamination levels. Here, we show that DecontX and CellBender under-correct highly contaminating genes, while SoupX and scAR over-correct lowly/non-contaminating genes. Here, we develop scCDC as the first method to detect the contamination-causing genes and only correct expression levels of these genes, some of which are cell-type markers. Compared with existing decontamination methods, scCDC excels in decontaminating highly contaminating genes while avoiding over-correction of other genes.
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Affiliation(s)
- Weijian Wang
- Centre of Biomedical Systems and Informatics, International Campus, ZJU-UoE Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, 314400, China
| | - Yihui Cen
- Centre of Biomedical Systems and Informatics, International Campus, ZJU-UoE Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, 314400, China
| | - Zezhen Lu
- Centre of Biomedical Systems and Informatics, International Campus, ZJU-UoE Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, 314400, China
| | - Yueqing Xu
- Centre of Biomedical Systems and Informatics, International Campus, ZJU-UoE Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, 314400, China
| | - Tianyi Sun
- Department of Statistics and Data Science, University of California, Los Angeles, CA, 90095, USA
| | - Ying Xiao
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310020, China
| | - Wanlu Liu
- Centre of Biomedical Systems and Informatics, International Campus, ZJU-UoE Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, 314400, China
| | - Jingyi Jessica Li
- Department of Statistics and Data Science, University of California, Los Angeles, CA, 90095, USA.
| | - Chaochen Wang
- Centre of Biomedical Systems and Informatics, International Campus, ZJU-UoE Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, 314400, China.
- Department of Gynecology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310020, China.
- Biomedical and Health Translational Research Centre, Zhejiang University, Haining, Zhejiang, 314400, China.
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6
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Zhou Y, Zhao Y, Carbonaro M, Chen H, Germino M, Adler C, Ni M, Zhu YO, Kim SY, Altarejos J, Li Z, Burczynski ME, Glass DJ, Sleeman MW, Lee AH, Halasz G, Cheng X. Perturbed liver gene zonation in a mouse model of non-alcoholic steatohepatitis. Metabolism 2024; 154:155830. [PMID: 38428673 DOI: 10.1016/j.metabol.2024.155830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/03/2024]
Abstract
Liver zonation characterizes the separation of metabolic pathways along the lobules and is required for optimal hepatic function. Wnt signaling is a master regulator of spatial liver zonation. A perivenous-periportal Wnt activity gradient orchestrates metabolic zonation by activating gene expression in perivenous hepatocytes, while suppressing gene expression in their periportal counterparts. However, the understanding as to the liver gene zonation and zonation regulators in diseases is limited. Non-alcoholic steatohepatitis (NASH) is a chronic liver disease characterized by fat accumulation, inflammation, and fibrosis. Here, we investigated the perturbation of liver gene zonation in a mouse NASH model by combining spatial transcriptomics, bulk RNAseq and in situ hybridization. Wnt-target genes represented a major subset of genes showing altered spatial expression in the NASH liver. The altered Wnt-target gene expression levels and zonation spatial patterns were in line with the up regulation of Wnt regulators and the augmentation of Wnt signaling. Particularly, we found that the Wnt activator Rspo3 expression was restricted to the perivenous zone in control liver but expanded to the periportal zone in NASH liver. AAV8-mediated RSPO3 overexpression in controls resulted in zonation changes, and further amplified the disturbed zonation of Wnt-target genes in NASH, similarly Rspo3 knockdown in Rspo3+/- mice resulted in zonation changes of Wnt-target genes in both chow and HFD mouse. Interestingly, there were no impacts on steatosis, inflammation, or fibrosis NASH pathology from RSPO3 overexpression nor Rspo3 knockdown. In summary, our study demonstrated the alteration of Wnt signaling in a mouse NASH model, leading to perturbed liver zonation.
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Affiliation(s)
- Ye Zhou
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Yuanqi Zhao
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Marisa Carbonaro
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Helen Chen
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Mary Germino
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Christina Adler
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Min Ni
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Yuan O Zhu
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Sun Y Kim
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Judith Altarejos
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Zhe Li
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | | | - David J Glass
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Mark W Sleeman
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Ann-Hwee Lee
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Gabor Halasz
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Xiping Cheng
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America.
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7
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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] [Abstract] [Key Words] [MESH Headings] [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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8
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Yang C, Xie W, Fu H, Zhi M, Zhang H, Guo Y, Wang J. Single-cell RNA sequencing reveals the heterogeneity of hepatic non-parenchymal cell responses to chronic PFO5DoDA exposure in male mice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123721. [PMID: 38462192 DOI: 10.1016/j.envpol.2024.123721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Perfluoroalkyl ether carboxylic acids (PFECA) have emerged as novel alternatives to legacy per- and polyfluoroalkyl substances (PFAS). Existing research has revealed hepatoxicity induced by various PFAS, including PFECA. However, these studies have primarily focused on overall changes in whole liver tissue, particularly in hepatocytes, with the impact of PFAS on diverse liver non-parenchymal cells (NPCs) still inadequately understood. In the present study, we examined the heterogeneous responses of hepatic NPCs following exposure to perfluoro-3,5,7,9,11-pentaoxadodecanoic acid (PFO5DoDA), a type of PFECA, by administering PFO5DoDA (5 μg/L)-contaminated water to male mice for one year. Single-cell RNA sequencing (scRNA-seq) of 15 008 cells from the liver identified 10 distinct NPC populations. Notably, although relative liver weight remained largely unchanged following exposure to 5 μg/L PFO5DoDA, there was an observed increase in proliferating cells, indicating that proliferating NPCs may contribute to the hepatomegaly frequently noted in PFAS-exposed livers. There was also a considerable alteration in the composition of hepatic NPCs. Specifically, the total number of B cells decreased substantially, while many other cells, such as monocytes and macrophages, increased after PFO5DoDA exposure. In addition, interactions among the hepatic NPC populations changed variously after PFO5DoDA exposure. The findings emphasize the heterogeneity in the responses of hepatic NPCs to PFO5DoDA exposure. Taken together, the changes in immune cell populations and their intercellular interactions suggest that PFO5DoDA disrupts immune homeostasis in the liver. These findings offer new insights into the cellular mechanisms of PFAS-induced liver damage.
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Affiliation(s)
- Chunyu Yang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Yantai University, Yantai, 264005, China
| | - Wei Xie
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Yantai University, Yantai, 264005, China
| | - Huayu Fu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Yantai University, Yantai, 264005, China
| | - Mengxue Zhi
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Yantai University, Yantai, 264005, China
| | - Hongxia Zhang
- Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Guo
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianshe Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Yantai University, Yantai, 264005, China.
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9
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Pinto AT, Lukacs-Kornek V. The role of dendritic cells in MASH: friends or foes? Front Immunol 2024; 15:1379225. [PMID: 38650949 PMCID: PMC11033439 DOI: 10.3389/fimmu.2024.1379225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024] Open
Abstract
Dendritic cells (DCs) are major antigen-presenting cells that connect innate and adaptive immunity. Hepatic DCs are less activated and contribute to maintain the tolerogenic environment of the liver under steady state. Several studies indicated DCs in metabolic dysfunction-associated steatohepatitis (MASH), representing a substantial burden on healthcare systems due to its association with liver-related morbidity and mortality. Studies highlighted the potential disease-promoting role of liver DCs in the development of MASH while other experimental systems suggested their protective role. This review discusses this controversy and the current understanding of how DCs affect the pathogenesis of MASH.
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Affiliation(s)
| | - Veronika Lukacs-Kornek
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn of the Rheinische Friedrich-Wilhelms-University, Bonn, Germany
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10
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Liebold I, Al Jawazneh A, Casar C, Lanzloth C, Leyk S, Hamley M, Wong MN, Kylies D, Gräfe SK, Edenhofer I, Aranda-Pardos I, Kriwet M, Haas H, Krause J, Hadjilaou A, Schromm AB, Richardt U, Eggert P, Tappe D, Weidemann SA, Ghosh S, Krebs CF, A-Gonzalez N, Worthmann A, Lohse AW, Huber S, Rothlin CV, Puelles VG, Jacobs T, Gagliani N, Bosurgi L. Apoptotic cell identity induces distinct functional responses to IL-4 in efferocytic macrophages. Science 2024; 384:eabo7027. [PMID: 38574142 DOI: 10.1126/science.abo7027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 02/26/2024] [Indexed: 04/06/2024]
Abstract
Macrophages are functionally heterogeneous cells essential for apoptotic cell clearance. Apoptotic cells are defined by homogeneous characteristics, ignoring their original cell lineage identity. We found that in an interleukin-4 (IL-4)-enriched environment, the sensing of apoptotic neutrophils by macrophages triggered their tissue remodeling signature. Engulfment of apoptotic hepatocytes promoted a tolerogenic phenotype, whereas phagocytosis of T cells had little effect on IL-4-induced gene expression. In a mouse model of parasite-induced pathology, the transfer of macrophages conditioned with IL-4 and apoptotic neutrophils promoted parasitic egg clearance. Knockout of phagocytic receptors required for the uptake of apoptotic neutrophils and partially T cells, but not hepatocytes, exacerbated helminth infection. These findings suggest that the identity of apoptotic cells may contribute to the development of distinct IL-4-driven immune programs in macrophages.
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Affiliation(s)
- Imke Liebold
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Amirah Al Jawazneh
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Christian Casar
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Bioinformatics Core, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Clarissa Lanzloth
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Stephanie Leyk
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Madeleine Hamley
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Milagros N Wong
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Dominik Kylies
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefanie K Gräfe
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ilka Edenhofer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Marie Kriwet
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Jenny Krause
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexandros Hadjilaou
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andra B Schromm
- Division of Immunobiophysics, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Ulricke Richardt
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Petra Eggert
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Dennis Tappe
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sören A Weidemann
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sourav Ghosh
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Christian F Krebs
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Anna Worthmann
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ansgar W Lohse
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- European Reference Network on Hepatological Diseases (ERN-RARE LIVER), Hamburg, Germany
| | - Samuel Huber
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carla V Rothlin
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Victor G Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Thomas Jacobs
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Nicola Gagliani
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lidia Bosurgi
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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11
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Piell KM, Petri BJ, Xu J, Cai L, Rai SN, Li M, Wilkey DW, Merchant ML, Cave MC, Klinge CM. Chronic Aroclor 1260 exposure alters the mouse liver proteome, selenoproteins, and metals in steatotic liver disease. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 107:104430. [PMID: 38552755 DOI: 10.1016/j.etap.2024.104430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/09/2024]
Abstract
The prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) continues to increase due in part to the obesity epidemic and to environmental exposures to metabolism disrupting chemicals. A single gavage exposure of male mice to Aroclor 1260 (Ar1260), an environmentally relevant mixture of non-dioxin-like polychlorinated biphenyls (PCBs), resulted in steatohepatitis and altered RNA modifications in selenocysteine tRNA 34 weeks post-exposure. Unbiased approaches identified the liver proteome, selenoproteins, and levels of 25 metals. Ar1260 altered the abundance of 128 proteins. Enrichment analysis of the liver Ar1260 proteome included glutathione metabolism and translation of selenoproteins. Hepatic glutathione peroxidase 4 (GPX4) and Selenoprotein O (SELENOO) were increased and Selenoprotein F (SELENOF), Selenoprotein S (SELENOS), Selenium binding protein 2 (SELENBP2) were decreased with Ar1260 exposure. Increased copper, selenium (Se), and zinc and reduced iron levels were detected. These data demonstrate that Ar1260 exposure alters the (seleno)proteome, Se, and metals in MASLD-associated pathways.
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Affiliation(s)
- Kellianne M Piell
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Belinda J Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA
| | - Jason Xu
- Pediatric Research Institute, Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Lu Cai
- Pediatric Research Institute, Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY 40292, USA; Departments of Radiation Oncology, Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, USA
| | - Shesh N Rai
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Ming Li
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Daniel W Wilkey
- University of Louisville Hepatobiology and Toxicology Center; University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Michael L Merchant
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, USA; Division of Nephrology & Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; University of Louisville Hepatobiology and Toxicology Center; University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Matthew C Cave
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, USA; University of Louisville Hepatobiology and Toxicology Center; University of Louisville School of Medicine, Louisville, KY 40202, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA; The University of Louisville Superfund Research Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, USA.
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12
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Yashaswini CN, Qin T, Bhattacharya D, Amor C, Lowe S, Lujambio A, Wang S, Friedman SL. Phenotypes and ontogeny of senescent hepatic stellate cells in metabolic dysfunction-associated steatohepatitis. J Hepatol 2024:S0168-8278(24)00197-1. [PMID: 38508241 DOI: 10.1016/j.jhep.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND & AIMS Hepatic stellate cells (HSCs) are the key drivers of fibrosis in metabolic dysfunction-associated steatohepatitis (MASH), the fastest growing cause of hepatocellular carcinoma (HCC) worldwide. HSCs are heterogenous, and a senescent subset of HSCs is implicated in hepatic fibrosis and HCC. Administration of anti-uPAR (urokinase-type plasminogen activator receptor) CAR T cells has been shown to deplete senescent HSCs and attenuate fibrosis in murine models. However, the comprehensive features of senescent HSCs in MASH, as well as their cellular ontogeny have not been characterized; hence, we aimed to comprehensively characterize and define the origin of HSCs in human and murine MASH. METHODS To comprehensively characterize the phenotype and ontogeny of senescent HSCs in human and murine MASH, we integrated senescence-associated beta galactosidase activity with immunostaining, flow cytometry and single-nucleus RNA sequencing (snRNAseq). We integrated the immunohistochemical profile with a senescence score applied to snRNAseq data to characterize senescent HSCs and mapped the evolution of uPAR expression in MASH. RESULTS Using pseudotime trajectory analysis, we establish that senescent HSCs arise from activated HSCs. While uPAR is expressed in MASH, the magnitude and cell-specificity of its expression evolve with disease stage. In early disease, uPAR is more specific to activated and senescent HSCs, while it is also expressed by myeloid-lineage cells, including Trem2+ macrophages and myeloid-derived suppressor cells, in late disease. Furthermore, we identify novel surface proteins expressed on senescent HSCs in human and murine MASH that could be exploited as therapeutic targets. CONCLUSIONS These data define features of HSC senescence in human and murine MASH, establishing an important blueprint to target these cells as part of future antifibrotic therapies. IMPACT AND IMPLICATIONS Hepatic stellate cells (HSCs) are the primary drivers of scarring in chronic liver diseases. As injury develops, a subset of HSCs become senescent; these cells are non-proliferative and pro-inflammatory, thereby contributing to worsening liver injury. Here we show that senescent HSCs are expanded in MASH (metabolic dysfunction-associated steatohepatitis) in humans and mice, and we trace their cellular origin from the activated HSC subset. We further characterize expression of uPAR (urokinase plasminogen activated receptor), a protein that marks senescent HSCs, and report that uPAR is also expressed by activated HSCs in early injury, and in immune cells as liver injury advances. We have integrated high-resolution single-nucleus RNA sequencing with immunostaining and flow cytometry to identify five other novel proteins expressed by senescent HSCs, including mannose receptor CD206, which will facilitate future therapeutic development.
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Affiliation(s)
- Chittampalli N Yashaswini
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tianyue Qin
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Dipankar Bhattacharya
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Corina Amor
- Cold Spring Harbor Laboratory. Cold Spring Harbor, NY, United States
| | - Scott Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Amaia Lujambio
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Shuang Wang
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Scott L Friedman
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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13
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Li HY, Gao YX, Wu JC, Li JZ, Fu SW, Xu MY. Single-cell transcriptome reveals a novel mechanism of C-Kit +-liver sinusoidal endothelial cells in NASH. Cell Biosci 2024; 14:31. [PMID: 38461242 PMCID: PMC10925010 DOI: 10.1186/s13578-024-01215-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/04/2024] [Indexed: 03/11/2024] Open
Abstract
AIM To understand how liver sinusoidal endothelial cells (LSECs) respond to nonalcoholic steatohepatitis (NASH). METHODS We profiled single-LSEC from livers of control and MCD-fed mice. The functions of C-Kit+-LSECs were determined using coculture and bone marrow transplantation (BMT) methods. RESULTS Three special clusters of single-LSEC were differentiated. C-Kit+-LSECs of cluster 0, Msr1+-LSECs of cluster 1 and Bmp4+Selp+-VECs of cluster 2 were revealed, and these cells with diverse ectopic expressions of genes participated in regulation of endothelial, fibrosis and lipid metabolism in NASH. The number of C-Kit+-primary LSECs isolated from MCD mice was lower than control mice. Immunofluorescence co-staining of CD31 and C-KIT showed C-Kit+-LSECs located in hepatic sinusoid were also reduced in NASH patients and MCD mice, compared to AIH patients and control mice respectively. Interestingly, lipotoxic hepatocytes/HSCs cocultured with C-Kit+-LSECs or the livers of MCD mice receipting of C-Kit+-BMCs (bone marrow cells) showed less steatosis, inflammation and fibrosis, higher expression of prolipolytic FXR and PPAR-α, lower expression of TNF-α and α-SMA. Furthermore, coculturing or BMT of C-Kit+-endothelial derived cells could increase the levels of hepatic mitochondrial LC3B, decrease the degree of mitochondrial damage and ROS production through activating Pink1-mediated mitophagy pathway in NASH. CONCLUSIONS Hence, a novel transcriptomic view of LSECs was revealed to have heterogeneity and complexity in NASH. Importantly, a cluster of C-Kit+-LSECs was confirmed to recovery Pink1-related mitophagy and NASH progression.
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Affiliation(s)
- Hui-Yi Li
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, No. 551, Pudong-South Road, Shanghai, 200120, China
| | - Yu-Xuan Gao
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, No. 551, Pudong-South Road, Shanghai, 200120, China
| | - Jun-Cheng Wu
- Departments of Gastroenterology, The Third Affiliated Hospital of Soochow University, Changzhou, 213000, Jiangsu, China
| | - Jing-Ze Li
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Seng-Wang Fu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100, Haining Rd, Shanghai, 200080, China.
| | - Ming-Yi Xu
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, No. 551, Pudong-South Road, Shanghai, 200120, China.
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14
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Parsons BD, Medina-Luna D, Scur M, Pinelli M, Gamage GS, Chilvers RA, Hamon Y, Ahmed IHI, Savary S, Makrigiannis AP, Braverman NE, Rodriguez-Alcazar JF, Latz E, Karakach TK, Di Cara F. Peroxisome deficiency underlies failures in hepatic immune cell development and antigen presentation in a severe Zellweger disease model. Cell Rep 2024; 43:113744. [PMID: 38329874 DOI: 10.1016/j.celrep.2024.113744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/21/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Peroxisome biogenesis disorders (PBDs) represent a group of metabolic conditions that cause severe developmental defects. Peroxisomes are essential metabolic organelles, present in virtually every eukaryotic cell and mediating key processes in immunometabolism. To date, the full spectrum of PBDs remains to be identified, and the impact PBDs have on immune function is unexplored. This study presents a characterization of the hepatic immune compartment of a neonatal PBD mouse model at single-cell resolution to establish the importance and function of peroxisomes in developmental hematopoiesis. We report that hematopoietic defects are a feature in a severe PBD murine model. Finally, we identify a role for peroxisomes in the regulation of the major histocompatibility class II expression and antigen presentation to CD4+ T cells in dendritic cells. This study adds to our understanding of the mechanisms of PBDs and expands our knowledge of the role of peroxisomes in immunometabolism.
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Affiliation(s)
- Brendon D Parsons
- University of Alberta, Department of Laboratory Medicine and Pathology, Edmonton, AB T6G 1C9, Canada
| | - Daniel Medina-Luna
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Michal Scur
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Marinella Pinelli
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Gayani S Gamage
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Rebecca A Chilvers
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Yannick Hamon
- Aix Marseille University, CNRS, INSERM au Centre d'Immunologie de Marseille Luminy, 13288 Marseille, France
| | - Ibrahim H I Ahmed
- Dalhousie University, Department of Pharmacology, Halifax, NS B3H 4R2, Canada; Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Stéphane Savary
- University of Bourgogne, Laboratoire Bio-PeroxIL EA7270, Dijon, France
| | - Andrew P Makrigiannis
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada; Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Nancy E Braverman
- Research Institute of the McGill University Children's Hospital, Montreal, QC H4A 3J1, Canada
| | | | - Eicke Latz
- University of Bonn, Institute of Innate Immunity, Medical Faculty, 53127 Bonn, Germany
| | - Tobias K Karakach
- Dalhousie University, Department of Pharmacology, Halifax, NS B3H 4R2, Canada; Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Francesca Di Cara
- University of Alberta, Department of Laboratory Medicine and Pathology, Edmonton, AB T6G 1C9, Canada; Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada.
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15
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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16
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Zhang C, Sui Y, Liu S, Yang M. The Roles of Myeloid-Derived Suppressor Cells in Liver Disease. Biomedicines 2024; 12:299. [PMID: 38397901 PMCID: PMC10886773 DOI: 10.3390/biomedicines12020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Liver disease-related mortality is a major cause of death worldwide. Hepatic innate and adaptive immune cells play diverse roles in liver homeostasis and disease. Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of immature myeloid cells. MDSCs can be broadly divided into monocytic MDSCs and polymorphonuclear or granulocytic MDSCs, and they functionally interact with both liver parenchymal and nonparenchymal cells, such as hepatocytes and regulatory T cells, to impact liver disease progression. The infiltration and activation of MDSCs in liver disease can be regulated by inflammatory chemokines and cytokines, tumor-associated fibroblasts, epigenetic regulation factors, and gut microbiota during liver injury and cancer. Given the pivotal roles of MDSCs in advanced liver diseases, they can be targeted to treat primary and metastatic liver cancer, liver generation, alcoholic and nonalcoholic liver disease, and autoimmune hepatitis. Currently, several treatments such as the antioxidant and anti-inflammatory agent berberine are under preclinical and clinical investigation to evaluate their therapeutic efficacy on liver disease and their effect on MDSC infiltration and function. Phenotypic alteration of MDSCs in different liver diseases that are in a model-dependent manner and lack special markers for distinct MDSCs are challenges for targeting MDSCs to treat liver disease. Multi-omics study is an option to uncover the features of disease-specific MDSCs and potential gene or protein targets for liver disease treatment. In summary, MDSCs play important roles in the pathogenesis and progression of liver disease by regulating both intrahepatic innate and adaptive immune responses.
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Affiliation(s)
- Chunye Zhang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA;
| | - Yuxiang Sui
- School of Life Science, Shanxi Normal University, Linfen 041004, China
| | - Shuai Liu
- The First Affiliated Hospital, Zhejiang University, Hangzhou 310006, China
| | - Ming Yang
- Department of Surgery, University of Missouri, Columbia, MO 65212, USA
- NextGen Precision Health Institute, University of Missouri, Columbia, MO 65212, USA
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17
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Lambertucci F, Motiño O, Pérez-Lanzón M, Li S, Plantureux C, Pol J, Maiuri MC, Kroemer G, Martins I. Isolation of Primary Mouse Hepatocytes and Non-Parenchymal Cells from a Liver with Precancerous Lesions. Methods Mol Biol 2024; 2769:109-128. [PMID: 38315393 DOI: 10.1007/978-1-0716-3694-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
In the early stages of liver carcinogenesis, rare hepatocytes and cholangiocytes are transformed into preneoplastic cells, which can progressively acquire a neoplastic phenotype, favored by the failure of natural antitumor immunosurveillance. The detailed study of both hepatic parenchymal (e.g., hepatocytes) and non-parenchymal cells (NPCs), such as immune cells, could help understand the cellular microenvironment surrounding these pre-cancerous and neoplastic lesions.Cultures of primary hepatocytes are of interest in various biomedical research disciplines, serving as an ex vivo model for liver physiology. Obtaining high viability and yield of primary mouse hepatocytes and other liver cell populations is technically challenging, thus limiting their use. In the first section of the current chapter, we introduce a protocol based on the two-step collagenase perfusion technique (by inferior vena cava) to isolate hepatocytes and, to a lower extent, NPCs and detailed the different considerations to take into account for a successful perfusion. The liver is washed by perfusion, hepatocytes are dissociated with collagenase, and different cell populations are separated by centrifugation. Various techniques have been described for the isolation of healthy and malignant hepatocytes; however, the viability and purity of the isolated cells is frequently not satisfactory. Here, we significantly optimized this protocol to reach improved yield and viability of the hepatocytes and concomitantly obtain preserved NPC populations of the liver.Within NPCs, tissue-resident or recruited immune cells are essential actors regulating hepatocarcinogenesis. However, simultaneous isolation of hepatic leukocytes together with other cell types generally yields low immune cell numbers hindering downstream application with these cells. In the second section of this chapter, as opposed to the first section primarily aiming to isolate hepatocytes, we present a tissue dissociation protocol adapted to efficiently recover leukocytes from non-perfused bulk (pre-)cancerous livers. This protocol has been optimized to be operator-friendly and fast compared to other liver processing methods, allowing easy simultaneous sample processing to retrieve hepatic (tumor-infiltrating) immune cells.
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Affiliation(s)
- Flavia Lambertucci
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, UMS AMMICa, Gustave Roussy, Villejuif, France
| | - Omar Motiño
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, UMS AMMICa, Gustave Roussy, Villejuif, France
| | - Maria Pérez-Lanzón
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, UMS AMMICa, Gustave Roussy, Villejuif, France
| | - Sijing Li
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, UMS AMMICa, Gustave Roussy, Villejuif, France
- Faculté de Médecine, Université de Paris Saclay, Kremlin Bicêtre, France
| | - Céleste Plantureux
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, UMS AMMICa, Gustave Roussy, Villejuif, France
- Faculté de Médecine, Université de Paris Saclay, Kremlin Bicêtre, France
| | - Jonathan Pol
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, UMS AMMICa, Gustave Roussy, Villejuif, France
| | - Maria Chiara Maiuri
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, UMS AMMICa, Gustave Roussy, Villejuif, France
- Department of Molecular Medicine and Medical Biotechnologies, University of Napoli Federico II, Naples, Italy
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, UMS AMMICa, Gustave Roussy, Villejuif, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Isabelle Martins
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France.
- Metabolomics and Cell Biology Platforms, UMS AMMICa, Gustave Roussy, Villejuif, France.
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18
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Casari M, Siegl D, Deppermann C, Schuppan D. Macrophages and platelets in liver fibrosis and hepatocellular carcinoma. Front Immunol 2023; 14:1277808. [PMID: 38116017 PMCID: PMC10728659 DOI: 10.3389/fimmu.2023.1277808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
During fibrosis, (myo)fibroblasts deposit large amounts of extracellular matrix proteins, thereby replacing healthy functional tissue. In liver fibrosis, this leads to the loss of hepatocyte function, portal hypertension, variceal bleeding, and increased susceptibility to infection. At an early stage, liver fibrosis is a dynamic and reversible process, however, from the cirrhotic stage, there is significant progression to hepatocellular carcinoma. Both liver-resident macrophages (Kupffer cells) and monocyte-derived macrophages are important drivers of fibrosis progression, but can also induce its regression once triggers of chronic inflammation are eliminated. In liver cancer, they are attracted to the tumor site to become tumor-associated macrophages (TAMs) polarized towards a M2- anti-inflammatory/tumor-promoting phenotype. Besides their role in thrombosis and hemostasis, platelets can also stimulate fibrosis and tumor development by secreting profibrogenic factors and regulating the innate immune response, e.g., by interacting with monocytes and macrophages. Here, we review recent literature on the role of macrophages and platelets and their interplay in liver fibrosis and hepatocellular carcinoma.
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Affiliation(s)
- Martina Casari
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Dominik Siegl
- Institute for Translational Immunology, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Carsten Deppermann
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
- Research Center for Immune Therapy Forschungszentrum für Immuntherapie (FZI), University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Detlef Schuppan
- Institute for Translational Immunology, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
- Research Center for Immune Therapy Forschungszentrum für Immuntherapie (FZI), University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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19
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Hsu WL, Hsieh YT, Chen WM, Chien MH, Luo WJ, Chang JH, Devlin K, Su KY. High-fat diet induces C-reactive protein secretion, promoting lung adenocarcinoma via immune microenvironment modulation. Dis Model Mech 2023; 16:dmm050360. [PMID: 37929799 PMCID: PMC10651111 DOI: 10.1242/dmm.050360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023] Open
Abstract
To understand the effects of a high-fat diet (HFD) on lung cancer progression and biomarkers, we here used an inducible mutant epidermal growth factor receptor (EGFR)-driven lung cancer transgenic mouse model fed a regular diet (RD) or HFD. The HFD lung cancer (LC-HFD) group exhibited significant tumor formation and deterioration, such as higher EGFR activity and proliferation marker expression, compared with the RD lung cancer (LC-RD) group. Transcriptomic analysis of the lung tissues revealed that the significantly changed genes in the LC-HFD group were highly enriched in immune-related signaling pathways, suggesting that an HFD alters the immune microenvironment to promote tumor growth. Cytokine and adipokine arrays combined with a comprehensive analysis using meta-database software indicated upregulation of C-reactive protein (CRP) in the LC-HFD group, which presented with increased lung cancer proliferation and metastasis; this was confirmed experimentally. Our results imply that an HFD can turn the tumor growth environment into an immune-related pro-tumorigenic microenvironment and demonstrate that CRP has a role in promoting lung cancer development in this microenvironment.
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Affiliation(s)
- Wei-Lun Hsu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Yun-Ting Hsieh
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Wei-Ming Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Min-Hui Chien
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Wei-Jia Luo
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Jung-Hsuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Kevin Devlin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10055, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 10055, Taiwan
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20
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He W, Wang X, Chen M, Li C, Chen W, Pan L, Cui Y, Yu Z, Wu G, Yang Y, Xu M, Dong Z, Ma K, Wang J, He Z. Metformin reduces hepatocarcinogenesis by inducing downregulation of Cyp26a1 and CD8 + T cells. Clin Transl Med 2023; 13:e1465. [PMID: 37997519 PMCID: PMC10668005 DOI: 10.1002/ctm2.1465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer with major challenges in both prevention and therapy. Metformin, adenosine monophosphate-activated protein kinase (AMPK) activator, has been suggested to reduce the incidence of HCC when used for patients with diabetes in preclinical and clinical studies. However, the possible effects of metformin and their mechanisms of action in non-diabetic HCC have not been adequately investigated. METHODS Fah-/- mice were used to construct a liver-injury-induced non-diabetic HCC model for exploring hepatocarcinogenesis and therapeutic potential of metformin. Changes in relevant tumour and biochemical indicators were measured. Bulk and single-cell RNA-sequencing analyses were performed to validate the crucial role of proinflammatory/pro-tumour CD8+ T cells. In vitro and in vivo experiments were performed to confirm Cyp26a1-related antitumour mechanisms of metformin. RESULTS RNA-sequencing analysis showed that chronic liver injury led to significant changes in AMPK-, glucose- and retinol metabolism-related pathways in Fah-/- mice. Metformin prevented the formation of non-diabetic HCC in Fah-/- mice with chronic liver injury. Cyp26a1 ddexpression in hepatocytes was significantly suppressed after metformin treatment. Moreover, downregulation of Cyp26a1 occurred in conjunction with increased levels of all-trans-retinoic acid (atRA), which is involved in the activation of metformin-suppressed hepatocarcinogenesis in Fah-/- mice. In contrast, both CD8+ T-cell infiltration and proinflammatory/pro-tumour cytokines in the liver were significantly upregulated in Fah-/- mice during chronic liver injury, which was notably reversed by either metformin or atRA treatment. Regarding mechanisms, metformin regulated the decrease in Cyp26a1 enzyme expression and increased atRA expression via the AMPK/STAT3/Gadd45β/JNK/c-Jun pathway. CONCLUSIONS Metformin inhibits non-diabetic HCC by upregulating atRA levels and downregulating CD8+ T cells. This is the first reporting that the traditional drug metformin regulates the metabolite atRA via the Cyp26a1-involved pathway. The present study provides a potential application of metformin and atRA in non-diabetic HCC.
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Affiliation(s)
- Weizhi He
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
- Fudan University Shanghai Cancer Center, International Co‐Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Institutes of Biomedical SciencesShanghai Key Laboratory of Medical EpigeneticsShanghaiChina
| | - Xicheng Wang
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
| | - Miaomiao Chen
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
| | - Chong Li
- Zhoupu Community Health Service Center of Pudong New AreaShanghaiChina
| | - Wenjian Chen
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
| | - Lili Pan
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
| | - Yangyang Cui
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Postgraduate Training Base of Shanghai East HospitalJinzhou Medical UniversityJinzhouLiaoningChina
| | - Zhao Yu
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
| | - Guoxiu Wu
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
| | - Yang Yang
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
| | - Mingyang Xu
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
| | - Zhaoxuan Dong
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
| | - Keming Ma
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
| | - Jinghan Wang
- Department of Hepatobiliary and Pancreatic SurgeryShanghai East Hospital, Tongji UniversityShanghaiChina
| | - Zhiying He
- Institute for Regenerative Medicine, Ji'an Hospital, Shanghai East HospitalSchool of Life Sciences and TechnologyTongji University School of MedicineShanghaiChina
- Shanghai Engineering Research Center of Stem Cells Translational MedicineShanghaiChina
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21
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Harvest CK, Abele TJ, Yu C, Beatty CJ, Amason ME, Billman ZP, DePrizio MA, Souza FW, Lacey CA, Maltez VI, Larson HN, McGlaughon BD, Saban DR, Montgomery SA, Miao EA. An innate granuloma eradicates an environmental pathogen using Gsdmd and Nos2. Nat Commun 2023; 14:6686. [PMID: 37865673 PMCID: PMC10590453 DOI: 10.1038/s41467-023-42218-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023] Open
Abstract
Granulomas often form around pathogens that cause chronic infections. Here, we discover an innate granuloma model in mice with an environmental bacterium called Chromobacterium violaceum. Granuloma formation not only successfully walls off, but also clears, the infection. The infected lesion can arise from a single bacterium that replicates despite the presence of a neutrophil swarm. Bacterial replication ceases when macrophages organize around the infection and form a granuloma. This granuloma response is accomplished independently of adaptive immunity that is typically required to organize granulomas. The C. violaceum-induced granuloma requires at least two separate defense pathways, gasdermin D and iNOS, to maintain the integrity of the granuloma architecture. This innate granuloma successfully eradicates C. violaceum infection. Therefore, this C. violaceum-induced granuloma model demonstrates that innate immune cells successfully organize a granuloma and thereby resolve infection by an environmental pathogen.
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Affiliation(s)
- Carissa K Harvest
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Taylor J Abele
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Chen Yu
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA
| | - Cole J Beatty
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA
| | - Megan E Amason
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zachary P Billman
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Morgan A DePrizio
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Fernando W Souza
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Carolyn A Lacey
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Vivien I Maltez
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heather N Larson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Benjamin D McGlaughon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel R Saban
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA
| | - Stephanie A Montgomery
- Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Edward A Miao
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
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22
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Sanchez-Quant E, Richter ML, Colomé-Tatché M, Martinez-Jimenez CP. Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug challenge. Genome Biol 2023; 24:234. [PMID: 37848949 PMCID: PMC10583437 DOI: 10.1186/s13059-023-03075-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Xenobiotics are primarily metabolized by hepatocytes in the liver, and primary human hepatocytes are the gold standard model for the assessment of drug efficacy, safety, and toxicity in the early phases of drug development. Recent advances in single-cell genomics demonstrate liver zonation and ploidy as main drivers of cellular heterogeneity. However, little is known about the impact of hepatocyte specialization on liver function upon metabolic challenge, including hepatic metabolism, detoxification, and protein synthesis. RESULTS Here, we investigate the metabolic capacity of individual human hepatocytes in vitro. We assess how chronic accumulation of lipids enhances cellular heterogeneity and impairs the metabolisms of drugs. Using a phenotyping five-probe cocktail, we identify four functional subgroups of hepatocytes responding differently to drug challenge and fatty acid accumulation. These four subgroups display differential gene expression profiles upon cocktail treatment and xenobiotic metabolism-related specialization. Notably, intracellular fat accumulation leads to increased transcriptional variability and diminishes the drug-related metabolic capacity of hepatocytes. CONCLUSIONS Our results demonstrate that, upon a metabolic challenge such as exposure to drugs or intracellular fat accumulation, hepatocyte subgroups display different and heterogeneous transcriptional responses.
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Affiliation(s)
- Eva Sanchez-Quant
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Maria Lucia Richter
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), 85354, Freising, Germany.
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 82152, Munich, Germany.
| | - Celia Pilar Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany.
- TUM School of Medicine, Technical University of Munich, Munich (TUM), 80333, Munich, Germany.
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23
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Beil J, Perner J, Pfaller L, Gérard MA, Piaia A, Doelemeyer A, Wasserkrug Naor A, Martin L, Piequet A, Dubost V, Chibout SD, Moggs J, Terranova R. Unaltered hepatic wound healing response in male rats with ancestral liver injury. Nat Commun 2023; 14:6353. [PMID: 37816736 PMCID: PMC10564731 DOI: 10.1038/s41467-023-41998-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/26/2023] [Indexed: 10/12/2023] Open
Abstract
The possibility that ancestral environmental exposure could result in adaptive inherited effects in mammals has been long debated. Numerous rodent models of transgenerational responses to various environmental factors have been published but due to technical, operational and resource burden, most still await independent confirmation. A previous study reported multigenerational epigenetic adaptation of the hepatic wound healing response upon exposure to the hepatotoxicant carbon tetrachloride (CCl4) in male rats. Here, we comprehensively investigate the transgenerational effects by repeating the original CCl4 multigenerational study with increased power, pedigree tracing, F2 dose-response and suitable randomization schemes. Detailed pathology evaluations do not support adaptive phenotypic suppression of the hepatic wound healing response or a greater fitness of F2 animals with ancestral liver injury exposure. However, transcriptomic analyses identified genes whose expression correlates with ancestral liver injury, although the biological relevance of this apparent transgenerational transmission at the molecular level remains to be determined. This work overall highlights the need for independent evaluation of transgenerational epigenetic inheritance paradigms in mammals.
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Affiliation(s)
- Johanna Beil
- Novartis, Biomedical Research, Basel, Switzerland
| | | | - Lena Pfaller
- Novartis, Biomedical Research, Basel, Switzerland
| | | | | | | | | | - Lori Martin
- Novartis, Biomedical Research, East-Hanover, NJ, USA
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24
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Cogliati B, Yashaswini CN, Wang S, Sia D, Friedman SL. Friend or foe? The elusive role of hepatic stellate cells in liver cancer. Nat Rev Gastroenterol Hepatol 2023; 20:647-661. [PMID: 37550577 PMCID: PMC10671228 DOI: 10.1038/s41575-023-00821-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/06/2023] [Indexed: 08/09/2023]
Abstract
Liver fibrosis is a substantial risk factor for the development and progression of liver cancer, which includes hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). Studies utilizing cell fate mapping and single-cell transcriptomics techniques have identified quiescent perisinusoidal hepatic stellate cells (HSCs) as the primary source of activated collagen-producing HSCs and liver cancer-associated fibroblasts (CAFs) in HCC and liver metastasis, complemented in iCCA by contributions from portal fibroblasts. At the same time, integrative computational analysis of single-cell, single-nucleus and spatial RNA sequencing data have revealed marked heterogeneity among HSCs and CAFs, with distinct subpopulations displaying unique gene expression signatures and functions. Some of these subpopulations have divergent roles in promoting or inhibiting liver fibrogenesis and carcinogenesis. In this Review, we discuss the dual roles of HSC subpopulations in liver fibrogenesis and their contribution to liver cancer promotion, progression and metastasis. We review the transcriptomic and functional similarities between HSC and CAF subpopulations, highlighting the pathways that either promote or prevent fibrosis and cancer, and the immunological landscape from which these pathways emerge. Insights from ongoing studies will yield novel strategies for developing biomarkers, assessing prognosis and generating new therapies for both HCC and iCCA prevention and treatment.
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Affiliation(s)
- Bruno Cogliati
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil
| | | | - Shuang Wang
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniela Sia
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott L Friedman
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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25
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Zheng L, Wu J, Hu H, Cao H, Xu N, Chen K, Wen B, Wang H, Yuan H, Xie L, Jiang Y, Li Z, Liang C, Yuan J, Li Z, Yuan X, Xiao W, Wang J. Single-cell RNA transcriptome landscape of murine liver following systemic administration of mesoporous silica nanoparticles. J Control Release 2023; 361:427-442. [PMID: 37487929 DOI: 10.1016/j.jconrel.2023.07.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/28/2023] [Accepted: 07/22/2023] [Indexed: 07/26/2023]
Abstract
Due to the unique physicochemical properties, mesoporous silica nanoparticles (MONs) have been widely utilized in biomedical fields for drug delivery, gene therapy, disease diagnosis and imaging. With the extensive applications and large-scale production of MONs, the potential effects of MONs on human health are gaining increased attention. To better understand the cellular and molecular mechanisms underlying the effects of MONs on the mouse liver, we profiled the transcriptome of 63,783 single cells from mouse livers following weekly intravenous administration of MONs for 2 weeks. The results showed that the proportion of endothelial cells and CD4+ T cells was increased, whereas that of Kupffer cells was decreased, in a dose-dependent manner after MONs treatment in the mouse liver. We also observed that the proportion of inflammation-related Kupffer cell subtype and wound healing-related hepatocyte subtype were elevated, but the number of hepatocytes with detoxification characteristics was reduced after MONs treatment. The cell-cell communication network revealed that there was more crosstalk between cholangiocytes and Kupffer cells, liver capsular macrophages, hepatic stellate cells, and endothelial cells following MONs treatment. Furthermore, we identified key ligand-receptor pairs between crucial subtypes after MONs treatment that are known to promote liver fibrosis. Collectively, our study explored the effects of MONs on mouse liver at a single-cell level and provides comprehensive information on the potential hepatotoxicity of MONs.
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Affiliation(s)
- Liuhai Zheng
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong 510632, China
| | - Jiangpeng Wu
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China
| | - Hong Hu
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China
| | - Hua Cao
- Department of Oncology, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China
| | - Nan Xu
- Division of Thyroid surgery, Department of General Surgery, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China
| | - Kun Chen
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China
| | - Bowen Wen
- College of Natural Resources and Environment, South China Agricultural University, 483 Wushan Road, Guangzhou, Guangdong 510642, China
| | - Huifang Wang
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong 510632, China
| | - Haitao Yuan
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong 510632, China
| | - Lulin Xie
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China
| | - Yuke Jiang
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China
| | - Zhifen Li
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Xing Yun Street, Pingcheng District, Datong, Shanxi Province 037009, PR China
| | - Cailing Liang
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China
| | - Jimin Yuan
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China
| | - Zhijie Li
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China.
| | - Xiaopeng Yuan
- Department of Laboratory Medicine, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Wei Xiao
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, China.
| | - Jigang Wang
- Department of Breast Surgery, Department of General Surgery, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, China.
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Park HJ, Choi J, Kim H, Yang DY, An TH, Lee EW, Han BS, Lee SC, Kim WK, Bae KH, Oh KJ. Cellular heterogeneity and plasticity during NAFLD progression. Front Mol Biosci 2023; 10:1221669. [PMID: 37635938 PMCID: PMC10450943 DOI: 10.3389/fmolb.2023.1221669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a progressive liver disease that can progress to nonalcoholic steatohepatitis (NASH), NASH-related cirrhosis, and hepatocellular carcinoma (HCC). NAFLD ranges from simple steatosis (or nonalcoholic fatty liver [NAFL]) to NASH as a progressive form of NAFL, which is characterized by steatosis, lobular inflammation, and hepatocellular ballooning with or without fibrosis. Because of the complex pathophysiological mechanism and the heterogeneity of NAFLD, including its wide spectrum of clinical and histological characteristics, no specific therapeutic drugs have been approved for NAFLD. The heterogeneity of NAFLD is closely associated with cellular plasticity, which describes the ability of cells to acquire new identities or change their phenotypes in response to environmental stimuli. The liver consists of parenchymal cells including hepatocytes and cholangiocytes and nonparenchymal cells including Kupffer cells, hepatic stellate cells, and endothelial cells, all of which have specialized functions. This heterogeneous cell population has cellular plasticity to adapt to environmental changes. During NAFLD progression, these cells can exert diverse and complex responses at multiple levels following exposure to a variety of stimuli, including fatty acids, inflammation, and oxidative stress. Therefore, this review provides insights into NAFLD heterogeneity by addressing the cellular plasticity and metabolic adaptation of hepatocytes, cholangiocytes, hepatic stellate cells, and Kupffer cells during NAFLD progression.
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Affiliation(s)
- Hyun-Ju Park
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Juyoung Choi
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Hyunmi Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Da-Yeon Yang
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Tae Hyeon An
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Eun-Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Baek-Soo Han
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
- Biodefense Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Sang Chul Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Won Kon Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Kwang-Hee Bae
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
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27
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Guo Q, Wu J, Wang Q, Huang Y, Chen L, Gong J, Du M, Cheng G, Lu T, Zhao M, Zhao Y, Qiu C, Xia F, Zhang J, Chen J, Qiu F, Wang J. Single-cell transcriptome analysis uncovers underlying mechanisms of acute liver injury induced by tripterygium glycosides tablet in mice. J Pharm Anal 2023; 13:908-925. [PMID: 37719192 PMCID: PMC10499593 DOI: 10.1016/j.jpha.2023.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/17/2023] [Accepted: 03/14/2023] [Indexed: 09/19/2023] Open
Abstract
Tripterygium glycosides tablet (TGT), the classical commercial drug of Tripterygium wilfordii Hook. F. has been effectively used in the treatment of rheumatoid arthritis, nephrotic syndrome, leprosy, Behcet's syndrome, leprosy reaction and autoimmune hepatitis. However, due to its narrow and limited treatment window, TGT-induced organ toxicity (among which liver injury accounts for about 40% of clinical reports) has gained increasing attention. The present study aimed to clarify the cellular and molecular events underlying TGT-induced acute liver injury using single-cell RNA sequencing (scRNA-seq) technology. The TGT-induced acute liver injury mouse model was constructed through short-term TGT exposure and further verified by hematoxylin-eosin staining and liver function-related serum indicators, including alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase and total bilirubin. Using the mouse model, we identified 15 specific subtypes of cells in the liver tissue, including endothelial cells, hepatocytes, cholangiocytes, and hepatic stellate cells. Further analysis indicated that TGT caused a significant inflammatory response in liver endothelial cells at different spatial locations; led to marked inflammatory response, apoptosis and fatty acid metabolism dysfunction in hepatocytes; activated hepatic stellate cells; brought about the activation, inflammation, and phagocytosis of liver capsular macrophages cells; resulted in immune dysfunction of liver lymphocytes; disturbed the intercellular crosstalk in liver microenvironment by regulating various signaling pathways. Thus, these findings elaborate the mechanism underlying TGT-induced acute liver injury, provide new insights into the safe and rational applications in the clinic, and complement the identification of new biomarkers and therapeutic targets for liver protection.
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Affiliation(s)
- Qiuyan Guo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jiangpeng Wu
- School of Chinese Materia Medica, and State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518020, China
| | - Qixin Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yuwen Huang
- College of Food Science and Engineering, Institute of Ocean, Bohai University, Jinzhou, Liaoning, 121013, China
| | - Lin Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jie Gong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Maobo Du
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Guangqing Cheng
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Tianming Lu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Minghong Zhao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yuan Zhao
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518033, China
| | - Chong Qiu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Fei Xia
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Junzhe Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jiayun Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Feng Qiu
- School of Chinese Materia Medica, and State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Jigang Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- School of Chinese Materia Medica, and State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518020, China
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Karri K, Waxman DJ. TCDD dysregulation of lncRNA expression, liver zonation and intercellular communication across the liver lobule. Toxicol Appl Pharmacol 2023; 471:116550. [PMID: 37172768 PMCID: PMC10330769 DOI: 10.1016/j.taap.2023.116550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/21/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
The persistent environmental aryl hydrocarbon receptor agonist and hepatotoxin TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) induces hepatic lipid accumulation (steatosis), inflammation (steatohepatitis) and fibrosis. Thousands of liver-expressed, nuclear-localized lncRNAs with regulatory potential have been identified; however, their roles in TCDD-induced hepatoxicity and liver disease are unknown. We analyzed single nucleus (sn)RNA-seq data from control and subchronic (4 wk) TCDD-exposed mouse liver to determine liver cell-type specificity, zonation and differential expression profiles for thousands of lncRNAs. TCDD dysregulated >4000 of these lncRNAs in one or more liver cell types, including 684 lncRNAs specifically dysregulated in liver non-parenchymal cells. Trajectory inference analysis revealed major disruption by TCDD of hepatocyte zonation, affecting >800 genes, including 121 lncRNAs, with strong enrichment for lipid metabolism genes. TCDD also dysregulated expression of >200 transcription factors, including 19 Nuclear Receptors, most notably in hepatocytes and Kupffer cells. TCDD-induced changes in cell-cell communication patterns included marked decreases in EGF signaling from hepatocytes to non-parenchymal cells and increases in extracellular matrix-receptor interactions central to liver fibrosis. Gene regulatory networks constructed from the snRNA-seq data identified TCDD-exposed liver network-essential lncRNA regulators linked to functions such as fatty acid metabolic process, peroxisome and xenobiotic metabolism. Networks were validated by the striking enrichments that predicted regulatory lncRNAs showed for specific biological pathways. These findings highlight the power of snRNA-seq to discover functional roles for many xenobiotic-responsive lncRNAs in both hepatocytes and liver non-parenchymal cells and to elucidate novel aspects of foreign chemical-induced hepatotoxicity and liver disease, including dysregulation of intercellular communication within the liver lobule.
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Affiliation(s)
- Kritika Karri
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215, USA.
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Lee J, Kim H, Kang YW, Kim Y, Park MY, Song JH, Jo Y, Dao T, Ryu D, Lee J, Oh CM, Park S. LY6D is crucial for lipid accumulation and inflammation in nonalcoholic fatty liver disease. Exp Mol Med 2023:10.1038/s12276-023-01033-w. [PMID: 37394588 PMCID: PMC10394021 DOI: 10.1038/s12276-023-01033-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/07/2023] [Accepted: 04/17/2023] [Indexed: 07/04/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a serious metabolic disorder characterized by excess fat accumulation in the liver. Over the past decade, NAFLD prevalence and incidence have risen globally. There are currently no effective licensed drugs for its treatment. Thus, further study is required to identify new targets for NAFLD prevention and treatment. In this study, we fed C57BL6/J mice one of three diets, a standard chow diet, high-sucrose diet, or high-fat diet, and then characterized them. The mice fed a high-sucrose diet had more severely compacted macrovesicular and microvesicular lipid droplets than those in the other groups. Mouse liver transcriptome analysis identified lymphocyte antigen 6 family member D (Ly6d) as a key regulator of hepatic steatosis and the inflammatory response. Data from the Genotype-Tissue Expression project database showed that individuals with high liver Ly6d expression had more severe NAFLD histology than those with low liver Ly6d expression. In AML12 mouse hepatocytes, Ly6d overexpression increased lipid accumulation, while Ly6d knockdown decreased lipid accumulation. Inhibition of Ly6d ameliorated hepatic steatosis in a diet-induced NAFLD mouse model. Western blot analysis showed that Ly6d phosphorylated and activated ATP citrate lyase, which is a key enzyme in de novo lipogenesis. In addition, RNA- and ATAC-sequencing analyses revealed that Ly6d drives NAFLD progression by causing genetic and epigenetic changes. In conclusion, Ly6d is responsible for the regulation of lipid metabolism, and inhibiting Ly6d can prevent diet-induced steatosis in the liver. These findings highlight Ly6d as a novel therapeutic target for NAFLD.
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Affiliation(s)
- Jibeom Lee
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Hyeonhui Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Yun-Won Kang
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Yumin Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Moon-Young Park
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Ji-Hong Song
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Yunju Jo
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, Korea
| | - Tam Dao
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, Korea
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, Korea
| | - Junguee Lee
- Department of Pathology, St Mary's Hospital, the Catholic University of Korea, Daejeon, Korea
| | - Chang-Myung Oh
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea.
| | - Sangkyu Park
- Department of Precision Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea.
- Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju, Gangwon-do, Korea.
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Xie B, Gao D, Zhou B, Chen S, Wang L. New discoveries in the field of metabolism by applying single-cell and spatial omics. J Pharm Anal 2023; 13:711-725. [PMID: 37577385 PMCID: PMC10422156 DOI: 10.1016/j.jpha.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 08/15/2023] Open
Abstract
Single-cell multi-Omics (SCM-Omics) and spatial multi-Omics (SM-Omics) technologies provide state-of-the-art methods for exploring the composition and function of cell types in tissues/organs. Since its emergence in 2009, single-cell RNA sequencing (scRNA-seq) has yielded many groundbreaking new discoveries. The combination of this method with the emergence and development of SM-Omics techniques has been a pioneering strategy in neuroscience, developmental biology, and cancer research, especially for assessing tumor heterogeneity and T-cell infiltration. In recent years, the application of these methods in the study of metabolic diseases has also increased. The emerging SCM-Omics and SM-Omics approaches allow the molecular and spatial analysis of cells to explore regulatory states and determine cell fate, and thus provide promising tools for unraveling heterogeneous metabolic processes and making them amenable to intervention. Here, we review the evolution of SCM-Omics and SM-Omics technologies, and describe the progress in the application of SCM-Omics and SM-Omics in metabolism-related diseases, including obesity, diabetes, nonalcoholic fatty liver disease (NAFLD) and cardiovascular disease (CVD). We also conclude that the application of SCM-Omics and SM-Omics approaches can help resolve the molecular mechanisms underlying the pathogenesis of metabolic diseases in the body and facilitate therapeutic measures for metabolism-related diseases. This review concludes with an overview of the current status of this emerging field and the outlook for its future.
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Affiliation(s)
- Baocai Xie
- Department of Critical Care Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, 518060, China
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450014, China
| | - Dengfeng Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Biqiang Zhou
- Department of Geriatric & Spinal Pain Multi-Department Treatment, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, Guangdong, 518035, China
| | - Shi Chen
- Department of Critical Care Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, 518060, China
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lianrong Wang
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450014, China
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
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31
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Karri K, Waxman DJ. Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis. RNA (NEW YORK, N.Y.) 2023; 29:977-1006. [PMID: 37015806 DOI: 10.1261/rna.079580.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
LncRNAs comprise a heterogeneous class of RNA-encoding genes typified by low expression, nuclear enrichment, high tissue-specificity, and functional diversity, but the vast majority remain uncharacterized. Here, we assembled the mouse liver noncoding transcriptome from >2000 bulk RNA-seq samples and discovered 48,261 liver-expressed lncRNAs, a majority novel. Using these lncRNAs as a single-cell transcriptomic reference set, we elucidated lncRNA dysregulation in mouse models of high fat diet-induced nonalcoholic steatohepatitis and carbon tetrachloride-induced liver fibrosis. Trajectory inference analysis revealed lncRNA zonation patterns across the liver lobule in each major liver cell population. Perturbations in lncRNA expression and zonation were common in several disease-associated liver cell types, including nonalcoholic steatohepatitis-associated macrophages, a hallmark of fatty liver disease progression, and collagen-producing myofibroblasts, a central feature of liver fibrosis. Single-cell-based gene regulatory network analysis using bigSCale2 linked individual lncRNAs to specific biological pathways, and network-essential regulatory lncRNAs with disease-associated functions were identified by their high network centrality metrics. For a subset of these lncRNAs, promoter sequences of the network-defined lncRNA target genes were significantly enriched for lncRNA triplex formation, providing independent mechanistic support for the lncRNA-target gene linkages predicted by the gene regulatory networks. These findings elucidate liver lncRNA cell-type specificities, spatial zonation patterns, associated regulatory networks, and temporal patterns of dysregulation during hepatic disease progression. A subset of the liver disease-associated regulatory lncRNAs identified have human orthologs and are promising candidates for biomarkers and therapeutic targets.
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Affiliation(s)
- Kritika Karri
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
| | - David J Waxman
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
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Clemente-Suárez VJ, Martín-Rodríguez A, Redondo-Flórez L, López-Mora C, Yáñez-Sepúlveda R, Tornero-Aguilera JF. New Insights and Potential Therapeutic Interventions in Metabolic Diseases. Int J Mol Sci 2023; 24:10672. [PMID: 37445852 DOI: 10.3390/ijms241310672] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Endocrine homeostasis and metabolic diseases have been the subject of extensive research in recent years. The development of new techniques and insights has led to a deeper understanding of the mechanisms underlying these conditions and opened up new avenues for diagnosis and treatment. In this review, we discussed the rise of metabolic diseases, especially in Western countries, the genetical, psychological, and behavioral basis of metabolic diseases, the role of nutrition and physical activity in the development of metabolic diseases, the role of single-cell transcriptomics, gut microbiota, epigenetics, advanced imaging techniques, and cell-based therapies in metabolic diseases. Finally, practical applications derived from this information are made.
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Affiliation(s)
- Vicente Javier Clemente-Suárez
- Faculty of Sports Sciences, Universidad Europea de Madrid, Tajo Street, s/n, 28670 Madrid, Spain
- Grupo de Investigación en Cultura, Educación y Sociedad, Universidad de la Costa, Barranquilla 080002, Colombia
| | | | - Laura Redondo-Flórez
- Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Tajo Street s/n, 28670 Villaviciosa de Odon, Spain
| | - Clara López-Mora
- Facultad de Ciencias Biomédicas y de la Salud, Universidad Europea de Valencia, Pg. de l'Albereda, 7, 46010 València, Spain
| | - Rodrigo Yáñez-Sepúlveda
- Faculty of Education and Social Sciences, Universidad Andres Bello, Viña del Mar 2520000, Chile
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Guan D, Bae H, Zhou D, Chen Y, Jiang C, La CM, Xiao Y, Zhu K, Hu W, Trinh TM, Liu P, Xiong Y, Cai B, Jang C, Lazar MA. Hepatocyte SREBP signaling mediates clock communication within the liver. J Clin Invest 2023; 133:e163018. [PMID: 37066875 PMCID: PMC10104893 DOI: 10.1172/jci163018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/23/2023] [Indexed: 04/18/2023] Open
Abstract
Rhythmic intraorgan communication coordinates environmental signals and the cell-intrinsic clock to maintain organ homeostasis. Hepatocyte-specific KO of core components of the molecular clock Rev-erbα and -β (Reverb-hDKO) alters cholesterol and lipid metabolism in hepatocytes as well as rhythmic gene expression in nonparenchymal cells (NPCs) of the liver. Here, we report that in fatty liver caused by diet-induced obesity (DIO), hepatocyte SREBP cleavage-activating protein (SCAP) was required for Reverb-hDKO-induced diurnal rhythmic remodeling and epigenomic reprogramming in liver macrophages (LMs). Integrative analyses of isolated hepatocytes and LMs revealed that SCAP-dependent lipidomic changes in REV-ERB-depleted hepatocytes led to the enhancement of LM metabolic rhythms. Hepatocytic loss of REV-ERBα and β (REV-ERBs) also attenuated LM rhythms via SCAP-independent polypeptide secretion. These results shed light on the signaling mechanisms by which hepatocytes regulate diurnal rhythms in NPCs in fatty liver disease caused by DIO.
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Affiliation(s)
- Dongyin Guan
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Hosung Bae
- Department of Biological Chemistry, University of California Irvine, Irvine, California, USA
| | - Dishu Zhou
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Ying Chen
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Chunjie Jiang
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Cam Mong La
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Yang Xiao
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kun Zhu
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wenxiang Hu
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Basic Research, Guangzhou Laboratory, Guangdong, China
| | - Trang Minh Trinh
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Panpan Liu
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Ying Xiong
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bishuang Cai
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, University of California Irvine, Irvine, California, USA
| | - Mitchell A. Lazar
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine and
- Department of Genetics, the University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Huang H, Guo S, Chen Y, Liu Y, Jin J, Liang Y, Fan L, Xiang R. Increased RTN3 phenocopies nonalcoholic fatty liver disease by inhibiting the AMPK-IDH2 pathway. MedComm (Beijing) 2023; 4:e226. [PMID: 36925557 PMCID: PMC10013133 DOI: 10.1002/mco2.226] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 03/16/2023] Open
Abstract
Reticulon 3 (RTN3), an endoplasmic reticulum protein, is crucial in neurodegenerative and kidney diseases. However, the role of RTN3 in liver tissues has not been described. Here, we employed public datasets, patients, and several animal models to explore the role of RTN3 in nonalcoholic fatty liver disease (NAFLD). The underlying mechanisms were studied in primary hepatocytes and L02 cells in vitro. We found an increased expression of RTN3 in NAFLD patients, high-fat diet mice, and oxidized low-density lipoprotein-treated L02 cells. The RTN3 transgenic mice exhibited the phenotypes of fatty liver and lipid accumulation. Single-cell RNA sequencing analysis indicated that increased RTN3 might induce mitochondrial dysfunction. We further showed this in primary hepatocytes, the L02 cell line, and the Caenorhabditis elegans strain. Mechanistically, RTN3 regulated these events through its interactions with glucose-regulated protein 78 (GRP78), which further inhibited the adenosine 5 monophosphate-activated protein kinase (AMPK)-isocitrate dehydrogenase 2 (IDH2) pathway. In the end, knockout of RTN3 relieved fatty liver and mitochondrial dysfunction. Our study indicated that RTN3 was important in NAFLD and lipid catabolism and that an increase in RTN3 in the liver might be a risk factor for nonalcoholic steatohepatitis and NAFLD.
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Affiliation(s)
- Hao Huang
- Department of NephrologyXiangya HospitalCentral South UniversityChangshaChina
- Department of Cell BiologySchool of Life SciencesCentral South UniversityChangshaChina
- Hunan Key Laboratory of Animal Models for Human DiseasesSchool of Life SciencesCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaChina
| | - Shuai Guo
- Department of Cell BiologySchool of Life SciencesCentral South UniversityChangshaChina
| | - Ya‐Qin Chen
- Department of CardiologySecond Xiangya HospitalCentral South UniversityChangshaChina
| | - Yu‐Xing Liu
- Department of Cell BiologySchool of Life SciencesCentral South UniversityChangshaChina
| | - Jie‐Yuan Jin
- Department of Cell BiologySchool of Life SciencesCentral South UniversityChangshaChina
| | - Yun Liang
- Department of Cell BiologySchool of Life SciencesCentral South UniversityChangshaChina
| | - Liang‐Liang Fan
- Department of NephrologyXiangya HospitalCentral South UniversityChangshaChina
- Department of Cell BiologySchool of Life SciencesCentral South UniversityChangshaChina
- Hunan Key Laboratory of Animal Models for Human DiseasesSchool of Life SciencesCentral South UniversityChangshaChina
| | - Rong Xiang
- Department of NephrologyXiangya HospitalCentral South UniversityChangshaChina
- Department of Cell BiologySchool of Life SciencesCentral South UniversityChangshaChina
- Hunan Key Laboratory of Animal Models for Human DiseasesSchool of Life SciencesCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaChina
- Department of CardiologySecond Xiangya HospitalCentral South UniversityChangshaChina
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Wang X, Jin X, Li H, Zhang X, Chen X, Lu K, Chu C. Effects of various interventions on non-alcoholic fatty liver disease (NAFLD): A systematic review and network meta-analysis. Front Pharmacol 2023; 14:1180016. [PMID: 37063273 PMCID: PMC10090390 DOI: 10.3389/fphar.2023.1180016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Background: With the increasing prevalence of obesity and metabolic syndrome, the incidence of non-alcoholic fatty liver disease (NAFLD) is also increasing. In the next decade, NAFLD may become the main cause of liver transplantation. Therefore, the choice of treatment plan is particularly important. The purpose of this study was to compare several interventions in the treatment of NAFLD to provide some reference for clinicians in selecting treatment methods.Methods: We searched Public Medicine (PubMed), Medline, Excerpta Medica Database (Embase), and Cochrane Library from January 2013 to January 2023 to identify randomized controlled trials (RCTs) published in English. The network meta-analysis was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Forty-three studies accounting for a total of 2,969 patients were included, and alanine aminotransferase (ALT), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL) were selected as outcome measures for analysis and comparison.Results: We evaluated the results of drug, diet, and lifestyle interventions between the intervention and control groups. Curcumin (CUN) and probiotics (PTC) were selected for medication, the Mediterranean diet (MDED) was selected for special diet (SPD), and various kinds of exercise and lifestyle advice were selected for lifestyle interventions (LFT). The SUCRA was used to rank interventions according to the effect on ALT indicators (SUCRA: PTC 80.3%, SPD 65.2%, LFT 61.4%, PLB 32.8%, CUN 10.2%), TC indicators (SUCRA: PTC 89.4%, SPD 64%, CUN 34%, LFT 36.6%, PLB 17%), and LDL indicators (SUCRA: PTC 84.2%, CUN 69.5%, LFT 51.7%, PLB 30.1%, SPD 14.5%). The pairwise meta-analysis results showed that MDED was significantly better than NT in improving ALT [SMD 1.99, 95% CI (0.38, 3.60)]. In terms of improving TC and LDL, ATS was significantly better than NT [SMD 0.19, 95% CI (0.03, 0.36)] [SMD 0.18, 95% CI (0.01, 0.35)].Conclusion: Our study showed that PTC is most likely to be the most effective treatment for improving NAFLD indicators. Professional advice on diet or exercise was more effective in treating NAFLD than no intervention.
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Affiliation(s)
- Xinchen Wang
- Department of Pharmaceutical Engineering, College of Food and Pharmaceutical Engineering, Zhaoqing University, Zhaoqing, Guangdong, China
| | - Xiaoqian Jin
- Rehabilitation Medicine Department, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Hancheng Li
- Department of Pharmaceutical Engineering, College of Food and Pharmaceutical Engineering, Zhaoqing University, Zhaoqing, Guangdong, China
| | - Xianyu Zhang
- Department of Pharmaceutical Engineering, College of Food and Pharmaceutical Engineering, Zhaoqing University, Zhaoqing, Guangdong, China
| | - Xi Chen
- Department of Epidemiology and Statistics, School of Public Health, Medical College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kuan Lu
- Department of Pharmaceutical Engineering, College of Food and Pharmaceutical Engineering, Zhaoqing University, Zhaoqing, Guangdong, China
| | - Chenliang Chu
- Department of Pharmaceutical Engineering, College of Food and Pharmaceutical Engineering, Zhaoqing University, Zhaoqing, Guangdong, China
- *Correspondence: Chenliang Chu,
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Harvest CK, Abele TJ, Yu C, Beatty CJ, Amason ME, Billman ZP, DePrizio MA, Lacey CA, Maltez VI, Larson HN, McGlaughon BD, Saban DR, Montgomery SA, Miao EA. An innate granuloma eradicates an environmental pathogen using Gsdmd and Nos2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531568. [PMID: 36945446 PMCID: PMC10028874 DOI: 10.1101/2023.03.07.531568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Granulomas often form around pathogens that cause chronic infections. Here, we discover a novel granuloma model in mice. Chromobacterium violaceum is an environmental bacterium that stimulates granuloma formation that not only successfully walls off but also clears the infection. The infected lesion can arise from a single bacterium that replicates in the presence of a neutrophil swarm. Bacterial replication ceases when macrophages organize around the infection and form a granuloma. This granuloma response is accomplished independently of adaptive immunity that is typically required to organize granulomas. The C. violaceum -induced granuloma requires at least two separate defense pathways, gasdermin D and iNOS, to maintain the integrity of the granuloma architecture. These innate granulomas successfully eradicate C. violaceum infection. Therefore, this new C. violaceum -induced granuloma model demonstrates that innate immune cells successfully organize a granuloma and thereby eradicate infection by an environmental pathogen.
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Blériot C, Dalmas É, Ginhoux F, Venteclef N. Inflammatory and immune etiology of type 2 diabetes. Trends Immunol 2023; 44:101-109. [PMID: 36604203 DOI: 10.1016/j.it.2022.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 01/04/2023]
Abstract
Type 2 diabetes (T2D) represents a global threat affecting millions of patients worldwide. However, its causes remain incompletely dissected and we lack the tools to predict which individuals will develop T2D. Although there is a clear proven clinical association of T2D with metabolic disorders such as obesity and nonalcoholic fatty liver disease (NAFLD), the existence of a significant number of nondiabetic obese subjects suggests yet-uncovered features of such relationships. Here, we propose that a significant proportion of individuals may harbor an immune profile that renders them susceptible to developing T2D. We note the heterogeneity of circulating monocytes and tissue macrophages in organs that are key to metabolic disorders such as liver, white adipose tissue (WAT), and endocrine pancreas, as well as their contribution to T2D genesis.
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Affiliation(s)
- Camille Blériot
- Institut Necker-Enfants Malades (INEM), Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Paris, France; Gustave Roussy Cancer Campus, Villejuif, France.
| | - Élise Dalmas
- Institut Necker-Enfants Malades (INEM), Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Paris, France.
| | - Florent Ginhoux
- Gustave Roussy Cancer Campus, Villejuif, France; Singapore Immunology Network (SIgN), Agency for Science, Technology, and Research (A∗STAR), Singapore 138648, Singapore; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore; Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nicolas Venteclef
- Institut Necker-Enfants Malades (INEM), Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Paris, France
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Karri K, Waxman DJ. TCDD dysregulation of lncRNA expression, liver zonation and intercellular communication across the liver lobule. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.07.523119. [PMID: 36711947 PMCID: PMC9881922 DOI: 10.1101/2023.01.07.523119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The persistent environmental aryl hydrocarbon receptor agonist and hepatotoxin TCDD (2,3,7,8-tetrachlorodibenzo- p -dioxin) induces hepatic lipid accumulation (steatosis), inflammation (steatohepatitis) and fibrosis. Thousands of liver-expressed, nuclear-localized lncRNAs with regulatory potential have been identified; however, their roles in TCDD-induced hepatoxicity and liver disease are unknown. We analyzed single nucleus (sn)RNA-seq data from control and chronic TCDD-exposed mouse liver to determine liver cell-type specificity, zonation and differential expression profiles for thousands of IncRNAs. TCDD dysregulated >4,000 of these lncRNAs in one or more liver cell types, including 684 lncRNAs specifically dysregulated in liver non-parenchymal cells. Trajectory inference analysis revealed major disruption by TCDD of hepatocyte zonation, affecting >800 genes, including 121 IncRNAs, with strong enrichment for lipid metabolism genes. TCDD also dysregulated expression of >200 transcription factors, including 19 Nuclear Receptors, most notably in hepatocytes and Kupffer cells. TCDD-induced changes in cellâ€"cell communication patterns included marked decreases in EGF signaling from hepatocytes to non-parenchymal cells and increases in extracellular matrix-receptor interactions central to liver fibrosis. Gene regulatory networks constructed from the snRNA-seq data identified TCDD-exposed liver network-essential lncRNA regulators linked to functions such as fatty acid metabolic process, peroxisome and xenobiotic metabolic. Networks were validated by the striking enrichments that predicted regulatory IncRNAs showed for specific biological pathways. These findings highlight the power of snRNA-seq to discover functional roles for many xenobiotic-responsive lncRNAs in both hepatocytes and liver non-parenchymal cells and to elucidate novel aspects of foreign chemical-induced hepatotoxicity and liver disease, including dysregulation of intercellular communication within the liver lobule.
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Sheng W, Ji G, Zhang L. Role of macrophage scavenger receptor MSR1 in the progression of non-alcoholic steatohepatitis. Front Immunol 2022; 13:1050984. [PMID: 36591228 PMCID: PMC9797536 DOI: 10.3389/fimmu.2022.1050984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is the progressive form of nonalcoholic fatty liver disease (NAFLD), and the dysregulation of lipid metabolism and oxidative stress are the typical features. Subsequent dyslipidemia and oxygen radical production may render the formation of modified lipids. Macrophage scavenger receptor 1 (MSR1) is responsible for the uptake of modified lipoprotein and is one of the key molecules in atherosclerosis. However, the unrestricted uptake of modified lipoproteins by MSR1 and the formation of cholesterol-rich foamy macrophages also can be observed in NASH patients and mouse models. In this review, we highlight the dysregulation of lipid metabolism and oxidative stress in NASH, the alteration of MSR1 expression in physiological and pathological conditions, the formation of modified lipoproteins, and the role of MSR1 on macrophage foaming and NASH development and progression.
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40
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Non-alcoholic fatty liver disease and liver secretome. Arch Pharm Res 2022; 45:938-963. [PMCID: PMC9703441 DOI: 10.1007/s12272-022-01419-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022]
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41
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Zhang C, Chen R, Zhang Y. Accurate inference of genome-wide spatial expression with iSpatial. SCIENCE ADVANCES 2022; 8:eabq0990. [PMID: 36026447 PMCID: PMC9417177 DOI: 10.1126/sciadv.abq0990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Spatially resolved transcriptomic analyses can reveal molecular insights underlying tissue structure and context-dependent cell-cell or cell-environment interaction. Because of the current technical limitation, obtaining genome-wide spatial transcriptome at single-cell resolution is challenging. Here, we developed a new algorithm named iSpatial to derive the spatial pattern of the entire transcriptome by integrating spatial transcriptomic and single-cell RNA-seq datasets. Compared to other existing methods, iSpatial has higher accuracy in predicting gene expression and spatial distribution. Furthermore, it reduces false-positive and false-negative signals in the original datasets. By testing iSpatial with multiple spatial transcriptomic datasets, we demonstrate its wide applicability to datasets from different tissues and by different techniques. Thus, we provide a computational approach to reveal spatial organization of the entire transcriptome at single-cell resolution. With numerous high-quality datasets available in the public domain, iSpatial provides a unique way to understand the structure and function of complex tissues and disease processes.
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Affiliation(s)
- Chao Zhang
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Renchao Chen
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA
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Liu G, Wang L, Wess J, Dean A. Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors. Nucleic Acids Res 2022; 50:9195-9211. [PMID: 36018801 PMCID: PMC9458430 DOI: 10.1093/nar/gkac707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022] Open
Abstract
Enhancers establish proximity with distant target genes to regulate temporospatial gene expression and specify cell identity. Lim domain binding protein 1 (LDB1) is a conserved and widely expressed protein that functions as an enhancer looping factor. Previous studies in erythroid cells and neuronal cells showed that LDB1 forms protein complexes with different transcription factors to regulate cell-specific gene expression. Here, we show that LDB1 regulates expression of liver genes by occupying enhancer elements and cooperating with hepatic transcription factors HNF4A, FOXA1, TCF7 and GATA4. Using the glucose transporter SLC2A2 gene, encoding GLUT2, as an example, we find that LDB1 regulates gene expression by mediating enhancer-promoter interactions. In vivo, we find that LDB1 deficiency in primary mouse hepatocytes dysregulates metabolic gene expression and changes the enhancer landscape. Conditional deletion of LDB1 in adult mouse liver induces glucose intolerance. However, Ldb1 knockout hepatocytes show improved liver pathology under high-fat diet conditions associated with increased expression of genes related to liver fatty acid metabolic processes. Thus, LDB1 is linked to liver metabolic functions under normal and obesogenic conditions.
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Affiliation(s)
- Guoyou Liu
- Correspondence may also be addressed to Guoyou Liu. Tel: +1 301 435 9396;
| | - Lei Wang
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jürgen Wess
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann Dean
- To whom correspondence should be addressed. Tel: +1 301 496 6068;
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Zhang R, Zhong B, He J, Yang X, He M, Zeng W, Pan J, Fang Z, Jia J, Liu H. Single-cell transcriptomes identifies characteristic features of mouse macrophages in liver Mallory-Denk bodies formation. Exp Mol Pathol 2022; 127:104811. [PMID: 35850229 DOI: 10.1016/j.yexmp.2022.104811] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/09/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022]
Abstract
Mallory-Denk bodies (MDBs) consist of intracellular aggregates of misfolded proteins in ballooned hepatocytes and serve as important markers of progression in certain liver diseases. Resident hepatic macrophage-mediated inflammation influences the development of chronic liver diseases and cancer. Here, the first systematic study of macrophages heterogeneity in mice was conducted to illustrate the pathogenesis of MDB formation using single-nucleus RNA sequencing (snRNA-seq). Furthermore, we provided transcriptional profiles of macrophages obtained from the fractionation of mouse liver tissues following chronic injury. We equally identified seven discrete macrophage subpopulations, each involved in specific cellular activated pathways such as basal metabolism, immune regulation, angiogenesis, and cell cycle regulation. Among these, a specific macrophage cluster (Cluster4), a subpopulation specifically expressing genes that regulate cell division and the cell cycle, was identified. Interestingly, we found that CCR2 was significantly induced in Cluster2, thereby inducing monocytes to migrate to macrophages to promote MDB pathogenesis. Thus, our study is the first to demonstrate the heterogeneity of macrophages associated with liver MDB formation in mice through single-cell resolution. This serves as the basis for further insights into the pathogenesis of liver MDB formation and molecular mechanisms of chronic liver disease progression.
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Affiliation(s)
- Rong Zhang
- School of Basic Medical Sciences, Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China; Clinical Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Bei Zhong
- School of Basic Medical Sciences, Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Jiashan He
- School of Basic Medical Sciences, Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Xinyu Yang
- School of Basic Medical Sciences, Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Menghua He
- School of Basic Medical Sciences, Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Wuyi Zeng
- School of Basic Medical Sciences, Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Jiayi Pan
- School of Basic Medical Sciences, Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Zixuan Fang
- School of Basic Medical Sciences, Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Jiangtao Jia
- School of Basic Medical Sciences, Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Hui Liu
- School of Basic Medical Sciences, Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China; The State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
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Iannacone M, Blériot C, Andreata F, Ficht X, Laura C, Garcia-Manteiga JM, Uderhardt S, Ginhoux F. Response to contamination of isolated mouse Kupffer cells with liver sinusoidal endothelial cells. Immunity 2022; 55:1141-1142. [PMID: 35830819 DOI: 10.1016/j.immuni.2022.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy.
| | - Camille Blériot
- Inserm U1015, Institut Gustave Roussy, Villejuif 94800, France
| | - Francesco Andreata
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Xenia Ficht
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Chiara Laura
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Jose M Garcia-Manteiga
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Stefan Uderhardt
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen 91054, Germany, Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen 91054, Germany
| | - Florent Ginhoux
- Inserm U1015, Institut Gustave Roussy, Villejuif 94800, France; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore; Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Goldfarb CN, Karri K, Pyatkov M, Waxman DJ. Interplay Between GH-regulated, Sex-biased Liver Transcriptome and Hepatic Zonation Revealed by Single-Nucleus RNA Sequencing. Endocrinology 2022; 163:6580481. [PMID: 35512247 PMCID: PMC9154260 DOI: 10.1210/endocr/bqac059] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Indexed: 11/19/2022]
Abstract
The zonation of liver metabolic processes is well-characterized; however, little is known about the cell type-specificity and zonation of sexually dimorphic gene expression or its growth hormone (GH)-dependent transcriptional regulators. We address these issues using single-nucleus RNA-sequencing of 32 000 nuclei representing 9 major liver cell types. Nuclei were extracted from livers from adult male and female mice; from males infused with GH continuously, mimicking the female plasma GH pattern; and from mice exposed to TCPOBOP, a xenobiotic agonist ligand of the nuclear receptor CAR that perturbs sex-biased gene expression. Analysis of these rich transcriptomic datasets revealed the following: 1) expression of sex-biased genes and their GH-dependent transcriptional regulators is primarily restricted to hepatocytes and is not a feature of liver nonparenchymal cells; 2) many sex-biased transcripts show sex-dependent zonation within the liver lobule; 3) gene expression is substantially feminized both in periportal and pericentral hepatocytes when male mice are infused with GH continuously; 4) sequencing nuclei increases the sensitivity for detecting thousands of nuclear-enriched long-noncoding RNAs (lncRNAs) and enables determination of their liver cell type-specificity, sex-bias and hepatocyte zonation profiles; 5) the periportal to pericentral hepatocyte cell ratio is significantly higher in male than female liver; and 6) TCPOBOP exposure disrupts both sex-specific gene expression and hepatocyte zonation within the liver lobule. These findings highlight the complex interconnections between hepatic sexual dimorphism and zonation at the single-cell level and reveal how endogenous hormones and foreign chemical exposure can alter these interactions across the liver lobule with large effects both on protein-coding genes and lncRNAs.
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Affiliation(s)
- Christine N Goldfarb
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Kritika Karri
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Bioinformatics Program Boston University, Boston, Massachusetts 02215, USA
| | - Maxim Pyatkov
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | - David J Waxman
- Correspondence: David J. Waxman, PhD, Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA.
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Ansari L, Shahhamzeh A, Seifi Makrani D, Haghighi Borujeini M, Banaei A, Zamani H, Ataei G, Abbaspour S, Mehdizadeh A, Abedi-Firouzjah R. Comparing the two concentrations of Co0.6 Zn0.4 Fe2O4 nanoparticles coated with dimercaptosuccinic acid based on T2-and T2*- weighted MRI: An animal study. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2022. [DOI: 10.1016/j.jrras.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Flessa C, Kyrou I, Nasiri‐Ansari N, Kaltsas G, Kassi E, Randeva HS. Endoplasmic reticulum stress in nonalcoholic (metabolic associated) fatty liver disease (NAFLD/MAFLD). J Cell Biochem 2022; 123:1585-1606. [DOI: 10.1002/jcb.30247] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/09/2022] [Accepted: 03/28/2022] [Indexed: 02/06/2023]
Affiliation(s)
- Christina‐Maria Flessa
- Department of Biological Chemistry, Medical School National and Kapodistrian University of Athens Athens Greece
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM) University Hospitals Coventry and Warwickshire NHS Trust Coventry UK
| | - Ioannis Kyrou
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM) University Hospitals Coventry and Warwickshire NHS Trust Coventry UK
- Division of Translational and Experimental Medicine, Metabolic and Vascular Health, Warwick Medical School University of Warwick Coventry UK
- Centre for Sport, Exercise and Life Sciences, Research Institute for Health & Wellbeing Coventry University Coventry UK
- Aston Medical School, College of Health and Life Sciences Aston University Birmingham UK
- Department of Food Science & Human Nutrition Agricultural University of Athens Athens Greece
| | - Narjes Nasiri‐Ansari
- Department of Biological Chemistry, Medical School National and Kapodistrian University of Athens Athens Greece
| | - Gregory Kaltsas
- Endocrine Unit, 1st Department of Propaedeutic and Internal Medicine, Laiko Hospital National and Kapodistrian University of Athens Athens Greece
| | - Eva Kassi
- Department of Biological Chemistry, Medical School National and Kapodistrian University of Athens Athens Greece
- Endocrine Unit, 1st Department of Propaedeutic and Internal Medicine, Laiko Hospital National and Kapodistrian University of Athens Athens Greece
| | - Harpal S. Randeva
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM) University Hospitals Coventry and Warwickshire NHS Trust Coventry UK
- Division of Translational and Experimental Medicine, Metabolic and Vascular Health, Warwick Medical School University of Warwick Coventry UK
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