1
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Kumagai M, Tsuchiya A, Yang Y, Takeda N, Natsui K, Natusi Y, Tomiyoshi K, Yamazaki F, Koseki Y, Shinchi H, Imawaka N, Ukekawa R, Nishibu T, Abe H, Sasaki T, Ueda K, Terai S. Fibulin-4 as a potential extracellular vesicle marker of fibrosis in patients with cirrhosis. FEBS Open Bio 2024. [PMID: 38853023 DOI: 10.1002/2211-5463.13842] [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: 03/05/2024] [Revised: 04/19/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024] Open
Abstract
Chronic liver injury leads to decreased liver function and increased fibrosis. Fibrosis is not only associated with the development of portal hypertension and carcinogenesis, but with the occurrence of events and a poor prognosis, highlighting the importance of non-invasive fibrosis assessment in patients. In the present study, we searched for markers related to liver fibrosis via proteomic analysis of small extracellular vesicles (sEVs). In the discovery cohort, proteomic analysis was carried out in the sEVs extracted from the sera of 5 patients with decompensated cirrhosis, 5 patients with compensated cirrhosis, and 5 controls without liver disease. Interestingly, in this cohort, fibulin-4 was significantly associated with cirrhosis while in the validation cohort [formed by 191 patients: 7 patients without disease, 16 patients without liver disease (other diseases), 38 patients with chronic liver disease (CLD), 75 patients with cirrhosis of Child-Pugh class A (36 without hepatocellular carcinoma [HCC], 29 with HCC), and 65 patients with cirrhosis of Child-Pugh class B-C (39 without HCC, 26 with HCC)], fibulin-4/CD9 levels increased with cirrhosis progression. Furthermore, the fibulin-4/CD9 ratio was significantly higher in patients with varices. Immunostaining also revealed strong fibulin-4 expression in cholangiocytes within the fibrous areas and mesothelial cells in liver tissue blood vessels. Taken together, our results suggest that fibulin-4, essential for lysyl oxidase activation, might be a new liver fibrosis marker found in the sEVs of patients with cirrhosis.
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Affiliation(s)
- Masaru Kumagai
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Atsunori Tsuchiya
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
- Future Medical Research Center for Exosome and Designer Cells (F-DEC), Niigata University, Japan
| | - Yuan Yang
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, China
| | - Nobutaka Takeda
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Kazuki Natsui
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Yui Natusi
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Kei Tomiyoshi
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Fusako Yamazaki
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Yohei Koseki
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Hiroki Shinchi
- Project for Realization of Personalized Cancer Medicine, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Naoko Imawaka
- Biotechnology Center, R&D Marketing Operations, FUJIFILM Wako Pure Chemical Corporation, Amagasaki-shi, Japan
| | - Ryo Ukekawa
- Biotechnology Center, R&D Marketing Operations, FUJIFILM Wako Pure Chemical Corporation, Amagasaki-shi, Japan
| | - Takahiro Nishibu
- Biotechnology Center, R&D Marketing Operations, FUJIFILM Wako Pure Chemical Corporation, Amagasaki-shi, Japan
| | - Hiroyuki Abe
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Takako Sasaki
- Department of Pharmacology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Koji Ueda
- Project for Realization of Personalized Cancer Medicine, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Shuji Terai
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
- Future Medical Research Center for Exosome and Designer Cells (F-DEC), Niigata University, Japan
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2
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Gao W, Lin W, Li Q, Chen W, Yin W, Zhu X, Gao S, Liu L, Li W, Wu D, Zhang G, Zhu R, Jiao N. Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder. Nat Protoc 2024:10.1038/s41596-024-00999-9. [PMID: 38745111 DOI: 10.1038/s41596-024-00999-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/05/2024] [Indexed: 05/16/2024]
Abstract
Microbial signatures have emerged as promising biomarkers for disease diagnostics and prognostics, yet their variability across different studies calls for a standardized approach to biomarker research. Therefore, we introduce xMarkerFinder, a four-stage computational framework for microbial biomarker identification with comprehensive validations from cross-cohort datasets, including differential signature identification, model construction, model validation and biomarker interpretation. xMarkerFinder enables the identification and validation of reproducible biomarkers for cross-cohort studies, along with the establishment of classification models and potential microbiome-induced mechanisms. Originally developed for gut microbiome research, xMarkerFinder's adaptable design makes it applicable to various microbial habitats and data types. Distinct from existing biomarker research tools that typically concentrate on a singular aspect, xMarkerFinder uniquely incorporates a sophisticated feature selection process, specifically designed to address the heterogeneity between different cohorts, extensive internal and external validations, and detailed specificity assessments. Execution time varies depending on the sample size, selected algorithm and computational resource. Accessible via GitHub ( https://github.com/tjcadd2020/xMarkerFinder ), xMarkerFinder supports users with diverse expertise levels through different execution options, including step-to-step scripts with detailed tutorials and frequently asked questions, a single-command execution script, a ready-to-use Docker image and a user-friendly web server ( https://www.biosino.org/xmarkerfinder ).
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Affiliation(s)
- Wenxing Gao
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Weili Lin
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Qiang Li
- National Genomics Data Center & Bio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Wanning Chen
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Wenjing Yin
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Xinyue Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Sheng Gao
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Lei Liu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Wenjie Li
- Shanghai Southgene Technology Co., Ltd., Shanghai, P. R. China
| | - Dingfeng Wu
- National Clinical Research Center for Child Health, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Guoqing Zhang
- National Genomics Data Center & Bio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.
| | - Ruixin Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China.
| | - Na Jiao
- National Clinical Research Center for Child Health, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China.
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, Fudan University, Shanghai, P. R. China.
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3
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Sauer J, Steixner-Kumar AA, Gabler S, Motyka M, Rippmann JF, Brosa S, Boettner D, Schönberger T, Lempp C, Frodermann V, Simon E, Krenkel O, Bahrami E. Diverse potential of secretome from natural killer cells and monocyte-derived macrophages in activating stellate cells. Front Immunol 2024; 15:1232070. [PMID: 38638443 PMCID: PMC11025356 DOI: 10.3389/fimmu.2024.1232070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 03/04/2024] [Indexed: 04/20/2024] Open
Abstract
Chronic liver diseases, such as non-alcoholic steatohepatitis (NASH)-induced cirrhosis, are characterized by an increasing accumulation of stressed, damaged, or dying hepatocytes. Hepatocyte damage triggers the activation of resident immune cells, such as Kupffer cells (KC), as well as the recruitment of immune cells from the circulation toward areas of inflammation. After infiltration, monocytes differentiate into monocyte-derived macrophages (MoMF) which are functionally distinct from resident KC. We herein aim to compare the in vitro signatures of polarized macrophages and activated hepatic stellate cells (HSC) with ex vivo-derived disease signatures from human NASH. Furthermore, to shed more light on HSC activation and liver fibrosis progression, we investigate the effects of the secretome from primary human monocytes, macrophages, and NK cells on HSC activation. Interleukin (IL)-4 and IL-13 treatment induced transforming growth factor beta 1 (TGF-β1) secretion by macrophages. However, the supernatant transfer did not induce HSC activation. Interestingly, PMA-activated macrophages showed strong induction of the fibrosis response genes COL10A1 and CTGF, while the supernatant of IL-4/IL-13-treated monocytes induced the upregulation of COL3A1 in HSC. The supernatant of PMA-activated NK cells had the strongest effect on COL10A1 induction in HSC, while IL-15-stimulated NK cells reduced the expression of COL1A1 and CTGF. These data indicate that other factors, aside from the well-known cytokines and chemokines, might potentially be stronger contributors to the activation of HSCs and induction of a fibrotic response, indicating a more diverse and complex role of monocytes, macrophages, and NK cells in liver fibrosis progression.
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Affiliation(s)
- Julia Sauer
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | - Svenja Gabler
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | | | - Stefan Brosa
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Dennis Boettner
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | - Charlotte Lempp
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | - Eric Simon
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Oliver Krenkel
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Ehsan Bahrami
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
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4
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Fuster-Martínez I, Català-Senent JF, Hidalgo MR, Roig FJ, Esplugues JV, Apostolova N, García-García F, Blas-García A. Integrated transcriptomic landscape of the effect of anti-steatotic treatments in high-fat diet mouse models of non-alcoholic fatty liver disease. J Pathol 2024; 262:377-389. [PMID: 38180387 DOI: 10.1002/path.6242] [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: 06/18/2023] [Revised: 10/20/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
High-fat diet (HFD) mouse models are widely used in research to develop medications to treat non-alcoholic fatty liver disease (NAFLD), as they mimic the steatosis, inflammation, and hepatic fibrosis typically found in this complex human disease. The aims of this study were to identify a complete transcriptomic signature of these mouse models and to characterize the transcriptional impact exerted by different experimental anti-steatotic treatments. For this reason, we conducted a systematic review and meta-analysis of liver transcriptomic studies performed in HFD-fed C57BL/6J mice, comparing them with control mice and HFD-fed mice receiving potential anti-steatotic treatments. Analyzing 21 studies broaching 24 different treatments, we obtained a robust HFD transcriptomic signature that included 2,670 differentially expressed genes and 2,567 modified gene ontology biological processes. Treated HFD mice generally showed a reversion of this HFD signature, although the extent varied depending on the treatment. The biological processes most frequently reversed were those related to lipid metabolism, response to stress, and immune system, whereas processes related to nitrogen compound metabolism were generally not reversed. When comparing this HFD signature with a signature of human NAFLD progression, we identified 62 genes that were common to both; 10 belonged to the group that were reversed by treatments. Altered expression of most of these 10 genes was confirmed in vitro in hepatocytes and hepatic stellate cells exposed to a lipotoxic or a profibrogenic stimulus, respectively. In conclusion, this study provides a vast amount of information about transcriptomic changes induced during the progression and regression of NAFLD and identifies some relevant targets. Our results may help in the assessment of treatment efficacy, the discovery of unmet therapeutic targets, and the search for novel biomarkers. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Isabel Fuster-Martínez
- Departamento de Farmacología, Universitat de València, Valencia, Spain
- FISABIO (Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana), Valencia, Spain
| | - José F Català-Senent
- Computational Biomedicine Laboratory, Principe Felipe Research Center, Valencia, Spain
| | - Marta R Hidalgo
- Computational Biomedicine Laboratory, Principe Felipe Research Center, Valencia, Spain
| | - Francisco J Roig
- Computational Biomedicine Laboratory, Principe Felipe Research Center, Valencia, Spain
- Facultad de Ciencias de la Salud, Universidad San Jorge, Campus Universitario Villanueva de Gállego, Zaragoza, Spain
| | - Juan V Esplugues
- Departamento de Farmacología, Universitat de València, Valencia, Spain
- FISABIO (Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana), Valencia, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas), Madrid, Spain
| | - Nadezda Apostolova
- Departamento de Farmacología, Universitat de València, Valencia, Spain
- FISABIO (Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana), Valencia, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas), Madrid, Spain
| | | | - Ana Blas-García
- FISABIO (Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana), Valencia, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas), Madrid, Spain
- Departamento de Fisiología, Universitat de València, Valencia, Spain
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5
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Zhang N, Wu X, Zhang W, Sun Y, Yan X, Xu A, Han Q, Yang A, You H, Chen W. Targeting thrombospondin-2 retards liver fibrosis by inhibiting TLR4-FAK/TGF-β signaling. JHEP Rep 2024; 6:101014. [PMID: 38379585 PMCID: PMC10877131 DOI: 10.1016/j.jhepr.2024.101014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 12/13/2023] [Accepted: 01/08/2024] [Indexed: 02/22/2024] Open
Abstract
Background & Aims Thrombospondin-2 (THBS2) expression is associated with liver fibrosis regardless of etiology. However, the role of THBS2 in the pathogenesis of liver fibrosis has yet to be elucidated. Methods The in vivo effects of silencing Thbs2 in hepatic stellate cells (HSCs) were examined using an adeno-associated virus vector (serotype 6, AAV6) containing short-hairpin RNAs targeting Thbs2, under the regulatory control of cytomegalovirus, U6 or the α-smooth muscle promoter, in mouse models of carbon tetrachloride or methionine-choline deficient (MCD) diet-induced liver fibrosis. Crosstalk between THBS2 and toll-like receptor 4 (TLR4), as well as the cascaded signaling, was systematically investigated using mouse models, primary HSCs, and human HSC cell lines. Results THBS2 was predominantly expressed in activated HSCs and dynamically increased with liver fibrosis progression and decreased with regression. Selective interference of Thbs2 in HSCs retarded intrahepatic inflammatory infiltration, steatosis accumulation, and fibrosis progression following carbon tetrachloride challenge or in a dietary model of metabolic dysfunction-associated steatohepatitis. Mechanically, extracellular THBS2, as a dimer, specifically recognized and directly bound to TLR4, activating HSCs by stimulating downstream profibrotic focal adhesion kinase (FAK)/transforming growth factor beta (TGF-β) pathways. Disruption of the THBS2-TLR4-FAK/TGF-β signaling axis notably alleviated HSC activation and liver fibrosis aggravation. Conclusions THBS2 plays a crucial role in HSC activation and liver fibrosis progression through TLR4-FAK/TGF-β signaling in an autocrine manner, representing an attractive potential therapeutic target for liver fibrosis. Impact and implications Thrombospondin-2 (THBS2) is emerging as a factor closely associated with liver fibrosis regardless of etiology. However, the mechanisms by which THBS2 is involved in liver fibrosis remain unclear. Here, we showed that THBS2 plays a prominent role in the pathogenesis of liver fibrosis by activating the TLR4-TGF-β/FAK signaling axis and hepatic stellate cells in an autocrine manner, providing a potential therapeutic target for the treatment of liver fibrosis.
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Affiliation(s)
- Ning Zhang
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- State Key Lab of Digestive Health, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- National Clinical Research Center of Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
| | - Xiaoning Wu
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- State Key Lab of Digestive Health, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- National Clinical Research Center of Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
| | - Wen Zhang
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- State Key Lab of Digestive Health, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- National Clinical Research Center of Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
| | - Yameng Sun
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- State Key Lab of Digestive Health, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- National Clinical Research Center of Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
| | - Xuzhen Yan
- State Key Lab of Digestive Health, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- National Clinical Research Center of Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- Beijing Clinical Research Institute, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
| | - Anjian Xu
- State Key Lab of Digestive Health, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- National Clinical Research Center of Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- Beijing Clinical Research Institute, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
| | - Qi Han
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- State Key Lab of Digestive Health, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- National Clinical Research Center of Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
| | - Aiting Yang
- State Key Lab of Digestive Health, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- National Clinical Research Center of Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- Beijing Clinical Research Institute, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
| | - Hong You
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- State Key Lab of Digestive Health, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- National Clinical Research Center of Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
| | - Wei Chen
- State Key Lab of Digestive Health, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- National Clinical Research Center of Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- Beijing Clinical Research Institute, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, No. 95 Yong’an Road, Xicheng District, Beijing 100050, China
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6
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Rocque B, Guion K, Singh P, Bangerth S, Pickard L, Bhattacharjee J, Eguizabal S, Weaver C, Chopra S, Zhou S, Kohli R, Sher L, Akbari O, Ekser B, Emamaullee JA. Technical optimization of spatially resolved single-cell transcriptomic datasets to study clinical liver disease. Sci Rep 2024; 14:3612. [PMID: 38351241 PMCID: PMC10864257 DOI: 10.1038/s41598-024-53993-2] [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: 08/29/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
Single cell and spatially resolved 'omic' techniques have enabled deep characterization of clinical pathologies that remain poorly understood, providing unprecedented insights into molecular mechanisms of disease. However, transcriptomic platforms are costly, limiting sample size, which increases the possibility of pre-analytical variables such as tissue processing and storage procedures impacting RNA quality and downstream analyses. Furthermore, spatial transcriptomics have not yet reached single cell resolution, leading to the development of multiple deconvolution methods to predict individual cell types within each transcriptome 'spot' on tissue sections. In this study, we performed spatial transcriptomics and single nucleus RNA sequencing (snRNAseq) on matched specimens from patients with either histologically normal or advanced fibrosis to establish important aspects of tissue handling, data processing, and downstream analyses of biobanked liver samples. We observed that tissue preservation technique impacts transcriptomic data, especially in fibrotic liver. Single cell mapping of the spatial transcriptome using paired snRNAseq data generated a spatially resolved, single cell dataset with 24 unique liver cell phenotypes. We determined that cell-cell interactions predicted using ligand-receptor analysis of snRNAseq data poorly correlated with cellular relationships identified using spatial transcriptomics. Our study provides a framework for generating spatially resolved, single cell datasets to study gene expression and cell-cell interactions in biobanked clinical samples with advanced liver disease.
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Affiliation(s)
- Brittany Rocque
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Kate Guion
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Pranay Singh
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Sarah Bangerth
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Lauren Pickard
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Jashdeep Bhattacharjee
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Sofia Eguizabal
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Carly Weaver
- Division of Abdominal Organ Transplantation, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Shefali Chopra
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shengmei Zhou
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California Los Angeles, Los Angeles, CA, USA
| | - Rohit Kohli
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Linda Sher
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Omid Akbari
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Burcin Ekser
- Division of Transplant Surgery, Department of Surgery, Indiana University School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Juliet A Emamaullee
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA.
- Division of Abdominal Organ Transplantation, Children's Hospital Los Angeles, Los Angeles, CA, USA.
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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Ahmadi Badi S, Bereimipour A, Rohani P, Khatami S, Siadat SD. Interplay between gut microbiota and the master iron regulator, hepcidin, in the pathogenesis of liver fibrosis. Pathog Dis 2024; 82:ftae005. [PMID: 38555503 PMCID: PMC10990161 DOI: 10.1093/femspd/ftae005] [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: 10/23/2023] [Revised: 02/12/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
INTRODUCTION There is a proven role for hepcidin and the composition of gut microbiota and its derivatives in the pathophysiology of liver fibrosis. AREA COVERED This review focuses on the literature search regarding the effect of hepcidin and gut microbiota on regulating liver physiology. We presented the regulating mechanisms of hepcidin expression and discussed the possible interaction between gut microbiota and hepcidin regulation. Furthermore, we investigated the importance of the hepcidin gene in biological processes and bacterial interactions using bioinformatics analysis. EXPERT OPINION One of the main features of liver fibrosis is iron accumulation in hepatic cells, including hepatocytes. This accumulation can induce an oxidative stress response, inflammation, and activation of hepatic stellate cells. Hepcidin is a crucial regulator of iron by targeting ferroportin expressed on hepatocytes, macrophages, and enterocytes. Various stimuli, such as iron load and inflammatory signals, control hepcidin regulation. Furthermore, a bidirectional relationship exists between iron and the composition and metabolic activity of gut microbiota. We explored the potential of gut microbiota to influence hepcidin expression and potentially manage liver fibrosis, as the regulation of iron metabolism plays a crucial role in this context.
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Affiliation(s)
- Sara Ahmadi Badi
- Biochemistry Department, Pasteur Institute of Iran, Tehran, 1963737611, Iran
- Pediatric Gastroenterology and Hepatology Research Center, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, 1416753955, Iran
| | - Ahmad Bereimipour
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA
| | - Pejman Rohani
- Pediatric Gastroenterology and Hepatology Research Center, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, 1416753955, Iran
| | - Shohreh Khatami
- Biochemistry Department, Pasteur Institute of Iran, Tehran, 1963737611, Iran
| | - Seyed Davar Siadat
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, 1963737611, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran,1963737611, Iran
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8
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Zhang R, Li Y, Zhang J. Molecular mechanisms of pelvic organ prolapse influenced by FBLN5 via FOSL1/miR-222/MEIS1/COL3A1 axis. Cell Signal 2024; 114:111000. [PMID: 38056607 DOI: 10.1016/j.cellsig.2023.111000] [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: 07/11/2023] [Revised: 10/27/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
This study delves into the role of FBLN5 in pelvic organ prolapse (POP) and its molecular mechanisms, focusing on the FOSL1/miR-222/MEIS1/COL3A1 axis. Gene relationships linked to POP were confirmed using bioinformatics databases like GEO and StarBase. Primary human uterosacral ligament fibroblasts (hUSLF) were extracted and subjected to mechanical stretching. Cellular cytoskeletal changes were examined via phalloidin staining, intracellular ROS levels with a ROS kit, cell apoptosis through flow cytometry, and cell senescence using β-galactosidase staining. FBLN5's downstream targets were identified, and the interaction between FOSL1 and miR-222 and miR-222 and MEIS1 were validated using assays. In rat models, the role of FBLN5 in POP was assessed using bladder pressure tests. Results indicated diminished FBLN5 expression in uterine prolapse. Enhanced FBLN5 countered mechanical damage in hUSLF cells by downregulating FOSL1. FOSL1 augmented miR-222, inhibiting MEIS1, which subsequently fostered COL3A1 transcription. In rat models, the absence of FBLN5 exacerbated POP by influencing the FOSL1/miR-222/MEIS1/COL3A1 pathway. FBLN5's protective role likely involves regulating the above axis and boosting COL3A1 expression. Further research is needed to validate the effectiveness and safety of this mechanism in human patients and to propose potential new treatment options.
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Affiliation(s)
- Rui Zhang
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, PR China
| | - Ya Li
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, PR China
| | - Jin Zhang
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, PR China.
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Monfeuga T, Norlin J, Bugge A, Gaalsgaard ED, Prada-Medina CA, Latta M, Veidal SS, Petersen PS, Feigh M, Holst D. Evaluation of long acting GLP1R/GCGR agonist in a DIO and biopsy-confirmed mouse model of NASH suggest a beneficial role of GLP-1/glucagon agonism in NASH patients. Mol Metab 2024; 79:101850. [PMID: 38065435 PMCID: PMC10772820 DOI: 10.1016/j.molmet.2023.101850] [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: 10/04/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
OBJECTIVE The metabolic benefits of GLP-1 receptor (GLP-1R) agonists on glycemic and weight control are well established as therapy for type 2 diabetes and obesity. Glucagon's ability to increase energy expenditure is well described, and the combination of these mechanisms-of-actions has the potential to further lower hepatic steatosis in metabolic disorders and could therefore be attractive for the treatment for non-alcoholic steatohepatitis (NASH). Here, we have investigated the effects of a dual GLP-1/glucagon receptor agonist NN1177 on hepatic steatosis, fibrosis, and inflammation in a preclinical mouse model of NASH. Having observed strong effects on body weight loss in a pilot study with NN1177, we hypothesized that direct engagement of the hepatic glucagon receptor (GCGR) would result in a superior effect on steatosis and other liver related parameters as compared to the GLP-1R agonist semaglutide at equal body weight. METHODS Male C57Bl/6 mice were fed a diet high in trans-fat, fructose, and cholesterol (Diet-Induced Obese (DIO)-NASH) for 36 weeks. Following randomization based on the degree of fibrosis at baseline, mice were treated once daily with subcutaneous administration of a vehicle or three different doses of NN1177 or semaglutide for 8 weeks. Hepatic steatosis, inflammation and fibrosis were assessed by immunohistochemistry and morphometric analyses. Plasma levels of lipids and liver enzymes were determined, and hepatic gene expression was analyzed by RNA sequencing. RESULTS NN1177 dose-dependently reduced body weight up to 22% compared to vehicle treatment. Plasma levels of ALT, a measure of liver injury, were reduced in all treatment groups with body weight loss. The dual agonist reduced hepatic steatosis to a greater extent than semaglutide at equal body weight loss, as demonstrated by three independent methods. Both the co-agonist and semaglutide significantly decreased histological markers of inflammation such as CD11b and Galectin-3, in addition to markers of hepatic stellate activation (αSMA) and fibrosis (Collagen I). Interestingly, the maximal beneficial effects on above mentioned clinically relevant endpoints of NN1177 treatment on hepatic health appear to be achieved with the middle dose tested. Administering the highest dose resulted in a further reduction of liver fat and accompanied by a massive induction in genes involved in oxidative phosphorylation and resulted in exaggerated body weight loss and a downregulation of a module of co-expressed genes involved in steroid hormone biology, bile secretion, and retinol and linoleic acid metabolism that are also downregulated due to NASH itself. CONCLUSIONS These results indicate that, in a setting of overnutrition, the liver health benefits of activating the fasting-related metabolic pathways controlled by the glucagon receptor displays a bell-shaped curve. This observation is of interest to the scientific community, due to the high number of ongoing clinical trials attempting to leverage the positive effects of glucagon biology to improve metabolic health.
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Affiliation(s)
- Thomas Monfeuga
- AI & Digital Research, Research & Early Development, Novo Nordisk Research Centre Oxford, UK
| | - Jenny Norlin
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark
| | - Anne Bugge
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark
| | | | - Cesar A Prada-Medina
- AI & Digital Research, Research & Early Development, Novo Nordisk Research Centre Oxford, UK
| | - Markus Latta
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark
| | - Sanne S Veidal
- Gubra A/S, Hørsholm Kongevej 11, B, DK-2970 Hørsholm, Denmark
| | - Pia S Petersen
- Gubra A/S, Hørsholm Kongevej 11, B, DK-2970 Hørsholm, Denmark
| | - Michael Feigh
- Gubra A/S, Hørsholm Kongevej 11, B, DK-2970 Hørsholm, Denmark
| | - Dorte Holst
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark.
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Hess A, Gentile SD, Ben Saad A, Rahman R, Habboub T, Pratt DS, Mullen AC. Single-cell transcriptomics stratifies organoid models of metabolic dysfunction-associated steatotic liver disease. EMBO J 2023; 42:e113898. [PMID: 37962490 PMCID: PMC10711666 DOI: 10.15252/embj.2023113898] [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: 02/28/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 11/15/2023] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing cause of morbidity with limited treatment options. Thus, accurate in vitro systems to test new therapies are indispensable. While recently, human liver organoid models have emerged to assess steatotic liver disease, a systematic evaluation of their translational potential is still missing. Here, we evaluated human liver organoid models of MASLD, comparatively testing disease induction in three conditions: oleic acid, palmitic acid, and TGF-β1. Through single-cell analyses, we find that all three models induce inflammatory signatures, but only TGF-β1 promotes collagen production, fibrosis, and hepatic stellate cell expansion. In striking contrast, oleic acid ameliorates fibrotic signatures and reduces the hepatic stellate cell population. Linking data from each model to gene expression signatures associated with MASLD disease progression further demonstrates that palmitic acid and TGF-β1 more robustly model inflammation and fibrosis. Our findings highlight the importance of stratifying MASLD organoid models by signatures of clinical disease progression, provide a single-cell reference to benchmark future organoid injury models, and allow us to study evolving steatohepatitis, fibrosis, and HSC susceptibility to injury in a dynamic, multi-lineage human in vitro system.
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Affiliation(s)
- Anja Hess
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Present address:
Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
| | - Stefan D Gentile
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Klarman Cell ObservatoryBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Amel Ben Saad
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Raza‐Ur Rahman
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Tim Habboub
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Daniel S Pratt
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Autoimmune and Cholestatic Liver CenterMassachusetts General HospitalBostonMAUSA
| | - Alan C Mullen
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Klarman Cell ObservatoryBroad Institute of MIT and HarvardCambridgeMAUSA
- Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonMAUSA
- Harvard Stem Cell InstituteCambridgeMAUSA
- Present address:
University of Massachusetts Chan Medical SchoolWorcesterMAUSA
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11
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Gunes A, Schmitt C, Bilodeau L, Huet C, Belblidia A, Baldwin C, Giard JM, Biertho L, Lafortune A, Couture CY, Cheung A, Nguyen BN, Galun E, Bémeur C, Bilodeau M, Laplante M, Tang A, Faraj M, Estall JL. IL-6 Trans-Signaling Is Increased in Diabetes, Impacted by Glucolipotoxicity, and Associated With Liver Stiffness and Fibrosis in Fatty Liver Disease. Diabetes 2023; 72:1820-1834. [PMID: 37757741 PMCID: PMC10658070 DOI: 10.2337/db23-0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
Many people living with diabetes also have nonalcoholic fatty liver disease (NAFLD). Interleukin-6 (IL-6) is involved in both diseases, interacting with both membrane-bound (classical) and circulating (trans-signaling) soluble receptors. We investigated whether secretion of IL-6 trans-signaling coreceptors are altered in NAFLD by diabetes and whether this might associate with the severity of fatty liver disease. Secretion patterns were investigated with use of human hepatocyte, stellate, and monocyte cell lines. Associations with liver pathology were investigated in two patient cohorts: 1) biopsy-confirmed steatohepatitis and 2) class 3 obesity. We found that exposure of stellate cells to high glucose and palmitate increased IL-6 and soluble gp130 (sgp130) secretion. In line with this, plasma sgp130 in both patient cohorts positively correlated with HbA1c, and subjects with diabetes had higher circulating levels of IL-6 and trans-signaling coreceptors. Plasma sgp130 strongly correlated with liver stiffness and was significantly increased in subjects with F4 fibrosis stage. Monocyte activation was associated with reduced sIL-6R secretion. These data suggest that hyperglycemia and hyperlipidemia can directly impact IL-6 trans-signaling and that this may be linked to enhanced severity of NAFLD in patients with concomitant diabetes. ARTICLE HIGHLIGHTS IL-6 and its circulating coreceptor sgp130 are increased in people with fatty liver disease and steatohepatitis. High glucose and lipids stimulated IL-6 and sgp130 secretion from hepatic stellate cells. sgp130 levels correlated with HbA1c, and diabetes concurrent with steatohepatitis further increased circulating levels of all IL-6 trans-signaling mediators. Circulating sgp130 positively correlated with liver stiffness and hepatic fibrosis. Metabolic stress to liver associated with fatty liver disease might shift the balance of IL-6 classical versus trans-signaling, promoting liver fibrosis that is accelerated by diabetes.
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Affiliation(s)
- Aysim Gunes
- Institut de recherches cliniques de Montréal (IRCM), Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- Montreal Diabetes Research Centre, Montreal, Quebec, Canada
| | - Clémence Schmitt
- Institut de recherches cliniques de Montréal (IRCM), Montreal, Quebec, Canada
- Programmes de biologie moléculaire, Faculté de médecine, Université de Montréal, Montreal, Quebec, Canada
| | - Laurent Bilodeau
- Département de radiologie, Centre hospitalier de l’Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - Catherine Huet
- Département de radiologie, Centre hospitalier de l’Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - Assia Belblidia
- Département de radiologie, Centre hospitalier de l’Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - Cindy Baldwin
- Institut de recherches cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Jeanne-Marie Giard
- Liver Unit, Centre hospitalier de l’Université de Montréal (CHUM), Département de médecine, Université de Montréal, Montreal, Quebec, Canada
| | - Laurent Biertho
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
- Département de chirurgie, Faculté de médecine, Université Laval, Quebec City, Quebec, Canada
| | - Annie Lafortune
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
- Département de chirurgie, Faculté de médecine, Université Laval, Quebec City, Quebec, Canada
| | - Christian Yves Couture
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
- Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Quebec City, Quebec, Canada
| | - Angela Cheung
- Gastroenterology and Hepatology, Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Bich N. Nguyen
- Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, Quebec, Canada
| | - Eithan Galun
- Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Chantal Bémeur
- Département de nutrition, Université de Montréal, Montreal, Quebec, Canada
- Labo HépatoNeuro, Centre de recherche du CHUM, Montreal, Quebec, Canada
| | - Marc Bilodeau
- Liver Unit, Centre hospitalier de l’Université de Montréal (CHUM), Département de médecine, Université de Montréal, Montreal, Quebec, Canada
| | - Mathieu Laplante
- Montreal Diabetes Research Centre, Montreal, Quebec, Canada
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
| | - An Tang
- Département de radiologie, Centre hospitalier de l’Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - May Faraj
- Institut de recherches cliniques de Montréal (IRCM), Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- Montreal Diabetes Research Centre, Montreal, Quebec, Canada
- Département de nutrition, Université de Montréal, Montreal, Quebec, Canada
| | - Jennifer L. Estall
- Institut de recherches cliniques de Montréal (IRCM), Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- Montreal Diabetes Research Centre, Montreal, Quebec, Canada
- Programmes de biologie moléculaire, Faculté de médecine, Université de Montréal, Montreal, Quebec, Canada
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12
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Tzouanas CN, Sherman MS, Shay JE, Rubin AJ, Mead BE, Dao TT, Butzlaff T, Mana MD, Kolb KE, Walesky C, Pepe-Mooney BJ, Smith CJ, Prakadan SM, Ramseier ML, Tong EY, Joung J, Chi F, McMahon-Skates T, Winston CL, Jeong WJ, Aney KJ, Chen E, Nissim S, Zhang F, Deshpande V, Lauer GM, Yilmaz ÖH, Goessling W, Shalek AK. Chronic metabolic stress drives developmental programs and loss of tissue functions in non-transformed liver that mirror tumor states and stratify survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569407. [PMID: 38077056 PMCID: PMC10705501 DOI: 10.1101/2023.11.30.569407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Under chronic stress, cells must balance competing demands between cellular survival and tissue function. In metabolic dysfunction-associated steatotic liver disease (MASLD, formerly NAFLD/NASH), hepatocytes cooperate with structural and immune cells to perform crucial metabolic, synthetic, and detoxification functions despite nutrient imbalances. While prior work has emphasized stress-induced drivers of cell death, the dynamic adaptations of surviving cells and their functional repercussions remain unclear. Namely, we do not know which pathways and programs define cellular responses, what regulatory factors mediate (mal)adaptations, and how this aberrant activity connects to tissue-scale dysfunction and long-term disease outcomes. Here, by applying longitudinal single-cell multi -omics to a mouse model of chronic metabolic stress and extending to human cohorts, we show that stress drives survival-linked tradeoffs and metabolic rewiring, manifesting as shifts towards development-associated states in non-transformed hepatocytes with accompanying decreases in their professional functionality. Diet-induced adaptations occur significantly prior to tumorigenesis but parallel tumorigenesis-induced phenotypes and predict worsened human cancer survival. Through the development of a multi -omic computational gene regulatory inference framework and human in vitro and mouse in vivo genetic perturbations, we validate transcriptional (RELB, SOX4) and metabolic (HMGCS2) mediators that co-regulate and couple the balance between developmental state and hepatocyte functional identity programming. Our work defines cellular features of liver adaptation to chronic stress as well as their links to long-term disease outcomes and cancer hallmarks, unifying diverse axes of cellular dysfunction around core causal mechanisms.
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Affiliation(s)
- Constantine N. Tzouanas
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- These authors contributed equally
| | - Marc S. Sherman
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
- These authors contributed equally
| | - Jessica E.S. Shay
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Alcohol Liver Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Adam J. Rubin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin E. Mead
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler T. Dao
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Titus Butzlaff
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Miyeko D. Mana
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Kellie E. Kolb
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chad Walesky
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian J. Pepe-Mooney
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Colton J. Smith
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sanjay M. Prakadan
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michelle L. Ramseier
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Evelyn Y. Tong
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julia Joung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Science, MA, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Fangtao Chi
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Thomas McMahon-Skates
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Carolyn L. Winston
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Woo-Jeong Jeong
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine J. Aney
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ethan Chen
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sahar Nissim
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Gastroenterology Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Science, MA, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Georg M. Lauer
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ömer H. Yilmaz
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
- These senior authors contributed equally
| | - Wolfram Goessling
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA, USA
- These senior authors contributed equally
| | - Alex K. Shalek
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- These senior authors contributed equally
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Duan W, Shi R, Yang F, Zhou Z, Wang L, Huang Z, Zang S. FSTL3 partially mediates the association of increased nonalcoholic fatty liver disease fibrosis risk with acute myocardial infarction in patients with type 2 diabetes mellitus. Cardiovasc Diabetol 2023; 22:297. [PMID: 37904173 PMCID: PMC10617048 DOI: 10.1186/s12933-023-02024-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/11/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND The study aimed to investigate an association of increased liver fibrosis with acute myocardial infarction (AMI), and to investigate the mediating effect of serum follistatin-like protein 3 (FSTL3) on the association in patients with type 2 diabetes mellitus (T2DM). METHOD A total of 1424 participants were included in this study, and were firstly divided into two groups: 429 T2DM patients and 995 T2DM patients with NAFLD to assess the association of NAFLD and AMI. Then 995 T2DM co-existent NAFLD patients were categorized by NAFLD fibrosis risk to explore the association between NAFLD fibrosis risk and AMI. Immunohistochemistry staining and semi-quantitative analysis of liver FSTL3 were performed in 60 patients with NAFLD. There were 323 individuals (191 without AMI and 132 with AMI) in T2DM co-existent NAFLD patients who had serum samples, and serum FSTL3 was tested and mediation effect of FSTL3 in association of NAFLD fibrosis and AMI was performed. RESULTS First, increased NAFLD fibrosis risk was an independent risk factor for AMI in patients with T2DM and co-existent NAFLD. In addition, analysis of Gene Expression Omnibus (GEO) database and immunohistochemical staining confirmed the increased expression of FSTL3 in the liver of NAFLD patients with fibrosis. Serum FSTL3 significantly increased in patients with high NAFLD fibrosis risk and AMI, and closely associated with NAFLD fibrosis and AMI severity in T2DM patients with co-existent NAFLD. Most importantly, analysis of the level of mediation revealed that increased serum FSTL3 partially mediated the association of increased NAFLD fibrosis risk with AMI in T2DM patients with co-existent NAFLD. CONCLUSIONS NAFLD fibrosis was closely associated with AMI in T2DM patients. FSTL3 expression was enriched in the liver of NAFLD patients with significant and advanced fibrosis, and serum FSTL3 partially mediated the association of increased liver fibrosis risk with AMI in T2DM patients.
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Affiliation(s)
- Wenfei Duan
- Department of Endocrinology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, China
| | - Ruixiao Shi
- Department of Traditional Chinese Medicine, Maqiao Community Health Service Center, Minhang District, Shanghai, 20111, China
- Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Fang Yang
- Department of Genetics and Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhoujunhao Zhou
- Department of Endocrinology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, China
| | - Lihong Wang
- Department of Endocrinology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, China
| | - Zhe Huang
- Department of Genetics and Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Shufei Zang
- Department of Endocrinology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, China.
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O'Neill NK, Stein TD, Hu J, Rehman H, Campbell JD, Yajima M, Zhang X, Farrer LA. Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM. BMC Bioinformatics 2023; 24:349. [PMID: 37726653 PMCID: PMC10507917 DOI: 10.1186/s12859-023-05476-w] [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: 12/06/2022] [Accepted: 09/12/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Quantifying cell-type abundance in bulk tissue RNA-sequencing enables researchers to better understand complex systems. Newer deconvolution methodologies, such as MuSiC, use cell-type signatures derived from single-cell RNA-sequencing (scRNA-seq) data to make these calculations. Single-nuclei RNA-sequencing (snRNA-seq) reference data can be used instead of scRNA-seq data for tissues such as human brain where single-cell data are difficult to obtain, but accuracy suffers due to sequencing differences between the technologies. RESULTS We propose a modification to MuSiC entitled 'DeTREM' which compensates for sequencing differences between the cell-type signature and bulk RNA-seq datasets in order to better predict cell-type fractions. We show DeTREM to be more accurate than MuSiC in simulated and real human brain bulk RNA-sequencing datasets with various cell-type abundance estimates. We also compare DeTREM to SCDC and CIBERSORTx, two recent deconvolution methods that use scRNA-seq cell-type signatures. We find that they perform well in simulated data but produce less accurate results than DeTREM when used to deconvolute human brain data. CONCLUSION DeTREM improves the deconvolution accuracy of MuSiC and outperforms other deconvolution methods when applied to snRNA-seq data. DeTREM enables accurate cell-type deconvolution in situations where scRNA-seq data are not available. This modification improves characterization cell-type specific effects in brain tissue and identification of cell-type abundance differences under various conditions.
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Affiliation(s)
- Nicholas K O'Neill
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Thor D Stein
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Veterans Administration Medical Center, Bedford, MA, USA
| | - Junming Hu
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Habbiburr Rehman
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Joshua D Campbell
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Medicine (Computational Biomedicine), Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Masanao Yajima
- Department of Mathematics and Statistics, Boston University, Boston, MA, USA
| | - Xiaoling Zhang
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
| | - Lindsay A Farrer
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.
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15
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Rocque B, Guion K, Singh P, Bangerth S, Pickard L, Bhattacharjee J, Eguizabal S, Weaver C, Chopra S, Zhou S, Kohli R, Sher L, Ekser B, Emamaullee JA. Technical optimization of spatially resolved single-cell transcriptomic datasets to study clinical liver disease. RESEARCH SQUARE 2023:rs.3.rs-3307940. [PMID: 37720049 PMCID: PMC10503835 DOI: 10.21203/rs.3.rs-3307940/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Single cell and spatially resolved 'omic' techniques have enabled deep characterization of clinical pathologies that remain poorly understood, providing unprecedented insights into molecular mechanisms of disease. However, transcriptomic platforms are costly, limiting sample size, which increases the possibility of pre-analytical variables such as tissue processing and storage procedures impacting RNA quality and downstream analyses. Furthermore, spatial transcriptomics have not yet reached single cell resolution, leading to the development of multiple deconvolution methods to predict individual cell types within each transcriptome 'spot' on tissue sections. In this study, we performed spatial transcriptomics and single nucleus RNA sequencing (snRNASeq) on matched specimens from patients with either histologically normal or advanced fibrosis to establish important aspects of tissue handling, data processing, and downstream analyses of biobanked liver samples. We observed that tissue preservation technique impacts transcriptomic data, especially in fibrotic liver. Deconvolution of the spatial transcriptome using paired snRNASeq data generated a spatially resolved, single cell dataset with 24 unique liver cell phenotypes. We determined that cell-cell interactions predicted using ligand-receptor analysis of snRNASeq data poorly correlated with celullar relationships identified using spatial transcriptomics. Our study provides a framework for generating spatially resolved, single cell datasets to study gene expression and cell-cell interactions in biobanked clinical samples with advanced liver disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shengmei Zhou
- Children's Hospital Los Angeles, University of Southern California Los Angeles
| | | | | | - Burcin Ekser
- Indiana University School of Medicine, Indiana University
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16
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Rosa LF, Haasis E, Knauss A, Guseva D, Bischoff SC. Serotonin reuptake transporter deficiency promotes liver steatosis and impairs intestinal barrier function in obese mice fed a Western-style diet. Neurogastroenterol Motil 2023; 35:e14611. [PMID: 37246491 DOI: 10.1111/nmo.14611] [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: 11/28/2022] [Revised: 03/23/2023] [Accepted: 05/01/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND Intestinal barrier dysfunctions have been associated with liver steatosis and metabolic diseases. Besides nutritional factors, like a Western-style diet (WSD), serotonin has been linked with leaky gut. Therefore, we aimed to evaluate the role of serotonin in the pathogenesis of intestinal barrier dysfunctions and liver steatosis in mice fed high-fat and high-sugar diets. METHODS 6-8 weeks old male serotonin reuptake transporter knockout mice (SERT-/- ) and wild-type controls (SERT+/+ ) were fed either a WSD or a control diet (CD) ad libitum with or without fructose 30% (F) added to the drinking water for 12 weeks. Markers of liver steatosis and intestinal barrier function were assessed. KEY RESULTS SERT-/- mice showed increased weight gain compared with SERT+/+ mice when fed a WSD ± F for 12 weeks (p < 0.05), whereby SERT-/- mice exhibited reduced energy (-21%) intake. Furthermore, SERT knockout resulted in a more pronounced liver steatosis (p < 0.05), enhanced levels of endotoxin in portal vein plasma (p < 0.05), and increased liver expression of Tnf and Myd88 (p < 0.05), when mice were fed a WSD ± F. Finally, SERT-/- mice, when compared with SERT+/+ mice, had a decreased mRNA expression of Muc2 (p < 0.01), Ocln (p < 0.05), Cldn5 (p = 0.054) and 7 (p < 0.01), Defa5 (p < 0.05) and other antimicrobial peptides in the ileum. On the protein level, ZO-1 (p < 0.01) and DEFA5 protein (p < 0.0001) were decreased. CONCLUSION AND INFERENCES Our data demonstrate that SERT knockout causes weight gain, liver steatosis, and leaky gut, especially in mice fed a WSD. Therefore, SERT induction could be a novel therapeutic approach to improve metabolic diseases associated with intestinal barrier dysfunction.
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Affiliation(s)
- Louisa Filipe Rosa
- Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Eva Haasis
- Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Annkathrin Knauss
- Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Daria Guseva
- Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Stephan C Bischoff
- Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
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17
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Puppo M, Valluru MK, Croset M, Ceresa D, Iuliani M, Khan A, Wicinski J, Charafe-Jauffret E, Ginestier C, Pantano F, Ottewell PD, Clézardin P. MiR-662 is associated with metastatic relapse in early-stage breast cancer and promotes metastasis by stimulating cancer cell stemness. Br J Cancer 2023; 129:754-771. [PMID: 37443350 PMCID: PMC10449914 DOI: 10.1038/s41416-023-02340-9] [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: 09/28/2022] [Revised: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Breast cancer (BC) metastasis, which often occurs in bone, contributes substantially to mortality. MicroRNAs play a fundamental role in BC metastasis, although microRNA-regulated mechanisms driving metastasis progression remain poorly understood. METHODS MiRome analysis in serum from BC patients was performed by TaqMan™ low-density array. MiR-662 was overexpressed following MIMIC-transfection or lentivirus transduction. Animal models were used to investigate the role of miR-662 in BC (bone) metastasis. The effect of miR-662-overexpressing BC cell conditioned medium on osteoclastogenesis was investigated. ALDEFLUOR assays were performed to study BC stemness. RNA-sequencing transcriptomic analysis of miR-662-overexpressing BC cells was performed to evaluate gene expression changes. RESULTS High levels of hsa-miR-662 (miR-662) in serum from BC patients, at baseline (time of surgery), were associated with future recurrence in bone. At an early-stage of the metastatic disease, miR-662 could mask the presence of BC metastases in bone by inhibiting the differentiation of bone-resorbing osteoclasts. Nonetheless, metastatic miR-662-overexpressing BC cells then progressed as overt osteolytic metastases thanks to increased stem cell-like traits. CONCLUSIONS MiR-662 is involved in BC metastasis progression, suggesting it may be used as a prognostic marker to identify BC patients at high risk of metastasis.
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Affiliation(s)
- Margherita Puppo
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.
- INSERM, Research Unit UMR_S1033, LyOS, Faculty of Medicine Lyon-Est, Lyon, France.
- Univ Lyon, Université Claude Bernard Lyon 1, F-69008, Lyon, France.
| | - Manoj Kumar Valluru
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK
- Department of Infection, Immunity and Cardiovascular, Medical School, University of Sheffield, Sheffield, UK
| | - Martine Croset
- INSERM, Research Unit UMR_S1033, LyOS, Faculty of Medicine Lyon-Est, Lyon, France
- Univ Lyon, Université Claude Bernard Lyon 1, F-69008, Lyon, France
- INSERM U1052, CNRS UMR_5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Davide Ceresa
- IRCCS AOU San Martino, Università degli studi di Genova, Genova, Italy
| | - Michele Iuliani
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128, Roma, Italy
- Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128, Roma, Italy
| | - Ashrin Khan
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK
| | - Julien Wicinski
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Emmanuelle Charafe-Jauffret
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Christophe Ginestier
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Francesco Pantano
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128, Roma, Italy
- Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128, Roma, Italy
| | - Penelope Dawn Ottewell
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK
| | - Philippe Clézardin
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.
- INSERM, Research Unit UMR_S1033, LyOS, Faculty of Medicine Lyon-Est, Lyon, France.
- Univ Lyon, Université Claude Bernard Lyon 1, F-69008, Lyon, France.
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18
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Chaudhry A, Noor J, Batool S, Fatima G, Noor R. Advancements in Diagnostic and Therapeutic Interventions of Non-alcoholic Fatty Liver Disease: A Literature Review. Cureus 2023; 15:e44924. [PMID: 37814734 PMCID: PMC10560588 DOI: 10.7759/cureus.44924] [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] [Accepted: 09/08/2023] [Indexed: 10/11/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is one of the most common diseases of the liver globally. Non-alcoholic steatohepatitis (NASH) has a complicated pathophysiology which includes lipid buildup, oxidative stress, endoplasmic reticulum stress, and lipotoxicity. Recently, there has been tremendous improvement in understanding of NASH pathogenesis due to advancements in the scientific field. It is being investigated how non-invasive circulating and imaging biomarkers can help in NAFLD and NASH diagnosis and monitoring the progress. Multiple medications are now undergoing clinical trials for the treatment of NASH, and lifestyle changes have been acknowledged as one of the main treatment methods. The purpose of this review article is to discuss the incidence of NAFLD globally, management issues with NASH, and its relation to the metabolic syndrome. It explains pathophysiology as well as therapeutic strategies using natural items, dietary changes, and pharmaceutical treatments. While emphasizing the necessity for surrogate endpoints to facilitate medication development for NASH, the study also considers the potential of non-invasive imaging biomarkers including magnetic resonance imaging (MRI) and magnetic resonance elastography (MRE).
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Affiliation(s)
| | - Jawad Noor
- Internal Medicine, St. Dominic Hospital, Jackson, USA
| | - Saima Batool
- Pathology, Nishtar Medical University, Multan, PAK
| | - Ghulam Fatima
- Internal Medicine, Medical Unit, Abbasi Shaheed Hospital, Karachi, PAK
| | - Riwad Noor
- Public Health, Nishtar Hospital, Multan, PAK
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19
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Dichtel LE, Tabari A, Mercaldo ND, Corey KE, Husseini J, Osganian SA, Chicote ML, Rao EM, Miller KK, Bredella MA. CT Texture Analysis in Nonalcoholic Fatty Liver Disease (NAFLD). J Clin Exp Hepatol 2023; 13:760-766. [PMID: 37693260 PMCID: PMC10483004 DOI: 10.1016/j.jceh.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/04/2023] [Indexed: 09/12/2023] Open
Abstract
Background Nonalcoholic fatty liver disease (NAFLD) is the most common form of liver disease worldwide. There are limited biomarkers that can detect progression from simple steatosis to nonalcoholic steatohepatitis (NASH). The purpose of our study was to utilize CT texture analysis to distinguish steatosis from NASH. Methods 16 patients with NAFLD (38% male, median (interquartile range): age 57 (48-64) years, BMI 37.5 (35.0-46.8) kg/m2) underwent liver biopsy and abdominal non-contrast CT. CT texture analysis was performed to quantify gray-level tissue summaries (e.g., entropy, kurtosis, skewness, and attenuation) using commercially available software (TexRad, Cambridge England). Logistic regression analyses were performed to quantify the association between steatosis/NASH status and CT texture. ROC curve analysis was performed to determine sensitivity, specificity, AUC, 95% CIs, and cutoff values of texture parameters to differentiate steatosis from NASH. Results By histology, 6/16 (37%) of patients had simple steatosis and 10/16 (63%) had NASH. Patients with NASH had lower entropy (median, interquartile range (IQR): 4.3 (4.1, 4.8) vs. 5.0 (4.9, 5.2), P = 0.013) and lower mean value of positive pixels (MPP) (34.4 (21.8, 52.2) vs. 66.5 (57.0, 70.7), P = 0.009) than those with simple steatosis. Entropy values below 4.73 predict NASH with 100% (95%CI: 67-100%) specificity and 80% (50-100%) sensitivity, AUC: 0.88. MPP values below 54.0 predict NASH with 100% (67-100%) specificity and 100% (50-100%) sensitivity, AUC 0.90. Conclusion Our study provides preliminary evidence that CT texture analysis may serve as a novel imaging biomarker for disease activity in NAFLD and the discrimination of steatosis and NASH.
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Affiliation(s)
- Laura E. Dichtel
- Harvard Medical School, Boston, MA, USA
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Azadeh Tabari
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Nathaniel D. Mercaldo
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Kathleen E. Corey
- Harvard Medical School, Boston, MA, USA
- Department of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Jad Husseini
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Mark L. Chicote
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth M. Rao
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Karen K. Miller
- Harvard Medical School, Boston, MA, USA
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Miriam A. Bredella
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
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20
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Groeger M, Matsuo K, Heidary Arash E, Pereira A, Le Guillou D, Pino C, Telles-Silva KA, Maher JJ, Hsiao EC, Willenbring H. Modeling and therapeutic targeting of inflammation-induced hepatic insulin resistance using human iPSC-derived hepatocytes and macrophages. Nat Commun 2023; 14:3902. [PMID: 37400454 PMCID: PMC10318012 DOI: 10.1038/s41467-023-39311-w] [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: 10/07/2022] [Accepted: 06/07/2023] [Indexed: 07/05/2023] Open
Abstract
Hepatic insulin resistance is recognized as a driver of type 2 diabetes and fatty liver disease but specific therapies are lacking. Here we explore the potential of human induced pluripotent stem cells (iPSCs) for modeling hepatic insulin resistance in vitro, with a focus on resolving the controversy about the impact of inflammation in the absence of steatosis. For this, we establish the complex insulin signaling cascade and the multiple inter-dependent functions constituting hepatic glucose metabolism in iPSC-derived hepatocytes (iPSC-Heps). Co-culture of these insulin-sensitive iPSC-Heps with isogenic iPSC-derived pro-inflammatory macrophages induces glucose output by preventing insulin from inhibiting gluconeogenesis and glycogenolysis and activating glycolysis. Screening identifies TNFα and IL1β as the mediators of insulin resistance in iPSC-Heps. Neutralizing these cytokines together restores insulin sensitivity in iPSC-Heps more effectively than individual inhibition, reflecting specific effects on insulin signaling and glucose metabolism mediated by NF-κB or JNK. These results show that inflammation is sufficient to induce hepatic insulin resistance and establish a human iPSC-based in vitro model to mechanistically dissect and therapeutically target this metabolic disease driver.
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Affiliation(s)
- Marko Groeger
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Koji Matsuo
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Emad Heidary Arash
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Ashley Pereira
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Dounia Le Guillou
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
- Liver Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Cindy Pino
- Liver Center, University of California San Francisco, San Francisco, CA, 94143, USA
- Genomics CoLab, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Kayque A Telles-Silva
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Human Genome and Stem Cell Research Center, University of Sao Paulo, 05508-090, Sao Paulo, Brazil
| | - Jacquelyn J Maher
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
- Liver Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Edward C Hsiao
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Holger Willenbring
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, CA, 94143, USA.
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA.
- Liver Center, University of California San Francisco, San Francisco, CA, 94143, USA.
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21
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Li Z, Zhang H, Li Q, Feng W, Jia X, Zhou R, Huang Y, Li Y, Hu Z, Hu X, Zhu X, Huang S. GepLiver: an integrative liver expression atlas spanning developmental stages and liver disease phases. Sci Data 2023; 10:376. [PMID: 37301898 PMCID: PMC10257690 DOI: 10.1038/s41597-023-02257-1] [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: 10/03/2022] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Chronic liver diseases usually developed through stepwise pathological transitions under the persistent risk factors. The molecular changes during liver transitions are pivotal to improve liver diagnostics and therapeutics yet still remain elusive. Cumulative large-scale liver transcriptomic studies have been revealing molecular landscape of various liver conditions at bulk and single-cell resolution, however, neither single experiment nor databases enabled thorough investigations of transcriptomic dynamics along the progression of liver diseases. Here we establish GepLiver, a longitudinal and multidimensional liver expression atlas integrating expression profiles of 2469 human bulk tissues, 492 mouse samples, 409,775 single cells from 347 human samples and 27 liver cell lines spanning 16 liver phenotypes with uniformed processing and annotating methods. Using GepLiver, we have demonstrated dynamic changes of gene expression, cell abundance and crosstalk harboring meaningful biological associations. GepLiver can be applied to explore the evolving expression patterns and transcriptomic features for genes and cell types respectively among liver phenotypes, assisting the investigation of liver transcriptomic dynamics and informing biomarkers and targets for liver diseases.
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Affiliation(s)
- Ziteng Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hena Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Qin Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Wanjing Feng
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiya Jia
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Runye Zhou
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yan Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhixiang Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xichun Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xiaodong Zhu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Shenglin Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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22
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Sanchez JI, Parra ER, Jiao J, Solis Soto LM, Ledesma DA, Saldarriaga OA, Stevenson HL, Beretta L. Cellular and Molecular Mechanisms of Liver Fibrosis in Patients with NAFLD. Cancers (Basel) 2023; 15:2871. [PMID: 37296834 PMCID: PMC10252068 DOI: 10.3390/cancers15112871] [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: 04/06/2023] [Revised: 05/08/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The expression of immune- and cancer-related genes was measured in liver biopsies from 107 NAFLD patients. The strongest difference in overall gene expression was between liver fibrosis stages F3 and F4, with 162 cirrhosis-associated genes identified. Strong correlations with fibrosis progression from F1 to F4 were observed for 91 genes, including CCL21, CCL2, CXCL6, and CCL19. In addition, the expression of 21 genes was associated with fast progression to F3/F4 in an independent group of eight NAFLD patients. These included the four chemokines, SPP1, HAMP, CXCL2, and IL-8. A six-gene signature including SOX9, THY-1, and CD3D had the highest performance detecting the progressors among F1/F2 NAFLD patients. We also characterized immune cell changes using multiplex immunofluorescence platforms. Fibrotic areas were strongly enriched in CD3+ T cells compared to CD68+ macrophages. While the number of CD68+ macrophages increased with fibrosis severity, the increase in CD3+ T-cell density was more substantial and progressive from F1 to F4. The strongest correlation with fibrosis progression was observed for CD3+CD45R0+ memory T cells, while the most significant increase in density between F1/F2 and F3/F4 was for CD3+CD45RO+FOXP3+CD8- and CD3+CD45RO-FOXP3+CD8- regulatory T cells. A specific increase in the density of CD68+CD11b+ Kupffer cells with liver fibrosis progression was also observed.
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Affiliation(s)
- Jessica I. Sanchez
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin R. Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jingjing Jiao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luisa M. Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Debora A. Ledesma
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Omar A. Saldarriaga
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Heather L. Stevenson
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Laura Beretta
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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23
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Benegiamo G, von Alvensleben GV, Rodríguez-López S, Goeminne LJ, Bachmann AM, Morel JD, Broeckx E, Ma JY, Carreira V, Youssef SA, Azhar N, Reilly DF, D’Aquino K, Mullican S, Bou-Sleiman M, Auwerx J. The genetic background shapes the susceptibility to mitochondrial dysfunction and NASH progression. J Exp Med 2023; 220:213867. [PMID: 36787127 PMCID: PMC9960245 DOI: 10.1084/jem.20221738] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a global health concern without treatment. The challenge in finding effective therapies is due to the lack of good mouse models and the complexity of the disease, characterized by gene-environment interactions. We tested the susceptibility of seven mouse strains to develop NASH. The severity of the clinical phenotypes observed varied widely across strains. PWK/PhJ mice were the most prone to develop hepatic inflammation and the only strain to progress to NASH with extensive fibrosis, while CAST/EiJ mice were completely resistant. Levels of mitochondrial transcripts and proteins as well as mitochondrial function were robustly reduced specifically in the liver of PWK/PhJ mice, suggesting a central role of mitochondrial dysfunction in NASH progression. Importantly, the NASH gene expression profile of PWK/PhJ mice had the highest overlap with the human NASH signature. Our study exposes the limitations of using a single mouse genetic background in metabolic studies and describes a novel NASH mouse model with features of the human NASH.
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Affiliation(s)
- Giorgia Benegiamo
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland,Giorgia Benegiamo:
| | | | - Sandra Rodríguez-López
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Ludger J.E. Goeminne
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Alexis M. Bachmann
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Jean-David Morel
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Ellen Broeckx
- Janssen Research and Development, LLC, Raritan, NJ, USA
| | - Jing Ying Ma
- Janssen Research and Development, LLC, Raritan, NJ, USA
| | | | | | - Nabil Azhar
- Janssen Research and Development, LLC, Raritan, NJ, USA
| | | | | | | | - Maroun Bou-Sleiman
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland,Correspondence to Johan Auwerx:
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24
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Hironaka T, Takizawa N, Yamauchi Y, Horii Y, Nakaya M. The well-developed actin cytoskeleton and Cthrc1 expression by actin-binding protein drebrin in myofibroblasts promote cardiac and hepatic fibrosis. J Biol Chem 2023; 299:102934. [PMID: 36690273 PMCID: PMC9988570 DOI: 10.1016/j.jbc.2023.102934] [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: 10/15/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
Fibrosis is mainly triggered by inflammation in various tissues, such as heart and liver tissues, and eventually leads to their subsequent dysfunction. Fibrosis is characterized by the excessive accumulation of extracellular matrix proteins (e.g., collagens) produced by myofibroblasts. The well-developed actin cytoskeleton of myofibroblasts, one of the main features differentiating them from resident fibroblasts in tissues under inflammatory conditions, contributes to maintaining their ability to produce excessive extracellular matrix proteins. However, the molecular mechanisms via which the actin cytoskeleton promotes the production of fibrosis-related genes in myofibroblasts remain unclear. In this study, we found, via single-cell analysis, that developmentally regulated brain protein (drebrin), an actin-binding protein, was specifically expressed in cardiac myofibroblasts with a well-developed actin cytoskeleton in fibrotic hearts. Moreover, our immunocytochemistry analysis revealed that drebrin promoted actin cytoskeleton formation and myocardin-related transcription factor-serum response factor signaling. Comprehensive single-cell analysis and RNA-Seq revealed that the expression of collagen triple helix repeat containing 1 (Cthrc1), a fibrosis-promoting secreted protein, was regulated by drebrin in cardiac myofibroblasts via myocardin-related transcription factor-serum response factor signaling. Furthermore, we observed the profibrotic effects of drebrin exerted via actin cytoskeleton formation and the Cthrc1 expression regulation by drebrin in liver myofibroblasts (hepatic stellate cells). Importantly, RNA-Seq demonstrated that drebrin expression levels increased in human fibrotic heart and liver tissues. In summary, our results indicated that the well-developed actin cytoskeleton and Cthrc1 expression due to drebrin in myofibroblasts promoted cardiac and hepatic fibrosis, suggesting that drebrin is a therapeutic target molecule for fibrosis.
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Affiliation(s)
- Takanori Hironaka
- Department of Disease Control, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Noburo Takizawa
- Department of Disease Control, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuto Yamauchi
- Department of Disease Control, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuma Horii
- Department of Disease Control, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Michio Nakaya
- Department of Disease Control, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
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25
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Kwan SY, Slayden AN, Coronado AR, Marquez RC, Chen H, Wei P, Savage MI, Vornik LA, Fox JT, Sei S, Liang D, Stevenson HL, Wilkerson GK, Gagea M, Brown PH, Beretta L. Treatment Strategies and Mechanisms Associated with the Prevention of NASH-Associated HCC by a Toll-like Receptor 4 Inhibitor. Cancer Prev Res (Phila) 2023; 16:17-28. [PMID: 36162136 PMCID: PMC9812917 DOI: 10.1158/1940-6207.capr-22-0332] [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: 07/13/2022] [Revised: 09/08/2022] [Accepted: 09/22/2022] [Indexed: 01/12/2023]
Abstract
We evaluated the cancer preventive efficacy of TAK-242, an inhibitor of Toll-like receptor 4 (TLR4), in a mouse model of hepatocellular carcinoma (HCC) occurring in the context of nonalcoholic steatohepatitis (NASH). We also assessed the cellular events associated with the preventive treatment efficacy. We tested oral administration of TAK-242, at clinically relevant but toxicity-reducing doses and scheduling, in mice with hepatocyte-specific deletion of Pten (HepPten-). The optimal dose and oral gavage formulation of TAK-242 were determined to be 30 mg/kg in 5% DMSO in 30% 2-hydroxypropyl-β-cyclodextrin. Daily oral administration of 30 mg/kg TAK-242 over 18 weeks was well tolerated and resulted in reduced development of tumors (lesions > 7.5 mm3) in HepPten- mice. This effect was accompanied by reduced macrovesicular steatosis and serum levels of alanine aminotransferase. In addition, 30 mg/kg TAK-242 daily treatment of small preexisting adenomas (lesions < 7.5 mm3) over 18 weeks, significantly reduced their progression to HCC. RNA sequencing identified 220 hepatic genes significantly altered upon TAK-242 treatment, that significantly correlated with tumor burden. Finally, cell deconvolution analysis revealed that TAK-242 treatment resulted in reduced hepatic populations of endothelial cells and myeloid-derived immune cells (Kupffer cells, Siglec-H high dendritic cells, and neutrophilic granule protein high neutrophils), while the proportion of mt-Nd4 high hepatocytes significantly increased, suggesting a decrease in hepatic inflammation and concomitant increase in mitochondrial function and oxidative phosphorylation upon TLR4 inhibition. In conclusion, this study identified treatment strategies and novel molecular and cellular mechanisms associated with the prevention of HCC in the context of NASH that merit further investigations. PREVENTION RELEVANCE Means to prevent development of HCC or progression of small adenomas to HCC in patients with NASH are urgently needed to reduce the growing mortality due to HCC. We characterized the chemopreventive effect of oral administration of the TLR4 inhibitor TAK-242 in a model of NASH-associated HCC.
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Affiliation(s)
- Suet-Ying Kwan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alyssa N. Slayden
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Aubrey R. Coronado
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rosamaria C. Marquez
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Huiqin Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michelle I. Savage
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lana A. Vornik
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer T. Fox
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland, USA
| | - Shizuko Sei
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland, USA
| | - Dong Liang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, Texas, USA
| | - Heather L. Stevenson
- Department of Pathology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Gregory K. Wilkerson
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, Bastrop, Texas, USA
| | - Mihai Gagea
- Department of Veterinary Medicine & Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Powel H. Brown
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Laura Beretta
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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26
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Zimmermann T, Thomas L, Baader-Pagler T, Haebel P, Simon E, Reindl W, Bajrami B, Rist W, Uphues I, Drucker DJ, Klein H, Santhanam R, Hamprecht D, Neubauer H, Augustin R. BI 456906: Discovery and preclinical pharmacology of a novel GCGR/GLP-1R dual agonist with robust anti-obesity efficacy. Mol Metab 2022; 66:101633. [PMID: 36356832 PMCID: PMC9679702 DOI: 10.1016/j.molmet.2022.101633] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/18/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE Obesity and its associated comorbidities represent a global health challenge with a need for well-tolerated, effective, and mechanistically diverse pharmaceutical interventions. Oxyntomodulin is a gut peptide that activates the glucagon receptor (GCGR) and glucagon-like peptide-1 receptor (GLP-1R) and reduces bodyweight by increasing energy expenditure and reducing energy intake in humans. Here we describe the pharmacological profile of the novel glucagon receptor (GCGR)/GLP-1 receptor (GLP-1R) dual agonist BI 456906. METHODS BI 456906 was characterized using cell-based in vitro assays to determine functional agonism. In vivo pharmacological studies were performed using acute and subchronic dosing regimens to demonstrate target engagement for the GCGR and GLP-1R, and weight lowering efficacy. RESULTS BI 456906 is a potent, acylated peptide containing a C18 fatty acid as a half-life extending principle to support once-weekly dosing in humans. Pharmacological doses of BI 456906 provided greater bodyweight reductions in mice compared with maximally effective doses of the GLP-1R agonist semaglutide. BI 456906's superior efficacy is the consequence of increased energy expenditure and reduced food intake. Engagement of both receptors in vivo was demonstrated via glucose tolerance, food intake, and gastric emptying tests for the GLP-1R, and liver nicotinamide N-methyltransferase mRNA expression and circulating biomarkers (amino acids, fibroblast growth factor-21) for the GCGR. The dual activity of BI 456906 at the GLP-1R and GCGR was supported using GLP-1R knockout and transgenic reporter mice, and an ex vivo bioactivity assay. CONCLUSIONS BI 456906 is a potent GCGR/GLP-1R dual agonist with robust anti-obesity efficacy achieved by increasing energy expenditure and decreasing food intake.
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Affiliation(s)
- Tina Zimmermann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Leo Thomas
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Tamara Baader-Pagler
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Peter Haebel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Eric Simon
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Wolfgang Reindl
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Besnik Bajrami
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Wolfgang Rist
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Ingo Uphues
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Daniel J Drucker
- Lunenfeld-Tanenbaum Research Institute, University of Toronto, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.
| | - Holger Klein
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Rakesh Santhanam
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Dieter Hamprecht
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany; Boehringer Ingelheim Research Italia, Via Lorenzini 8, 20139 Milano, Italy.
| | - Heike Neubauer
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
| | - Robert Augustin
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riβ, Germany.
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27
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A liver secretome gene signature-based approach for determining circulating biomarkers of NAFLD severity. PLoS One 2022; 17:e0275901. [PMID: 36260611 PMCID: PMC9581378 DOI: 10.1371/journal.pone.0275901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/25/2022] [Indexed: 11/08/2022] Open
Abstract
Non-invasive biomarkers of non-alcoholic fatty liver disease (NAFLD) supporting diagnosis and monitoring disease progression are urgently needed. The present study aimed to establish a bioinformatics pipeline capable of defining and validating NAFLD biomarker candidates based on paired hepatic global gene expression and plasma bioanalysis from individuals representing different stages of histologically confirmed NAFLD (no/mild, moderate, more advanced NAFLD). Liver secretome gene signatures were generated in a patient cohort of 26 severely obese individuals with the majority having no or mild fibrosis. To this end, global gene expression changes were compared between individuals with no/mild NAFLD and moderate/advanced NAFLD with subsequent filtering for candidate gene products with liver-selective expression and secretion. Four candidate genes, including LPA (lipoprotein A), IGFBP-1 (insulin-like growth factor-binding protein 1), SERPINF2 (serpin family F member 2) and MAT1A (methionine adenosyltransferase 1A), were differentially expressed in moderate/advanced NAFLD, which was confirmed in three independent RNA sequencing datasets from large, publicly available NAFLD studies. The corresponding gene products were quantified in plasma samples but could not discriminate among different grades of NAFLD based on NAFLD activity score. Conclusion: We demonstrate a novel approach based on the liver transcriptome allowing for identification of secreted hepatic gene products as potential circulating diagnostic biomarkers of NAFLD. Using this approach in larger NAFLD patient cohorts may yield potential circulating biomarkers for NAFLD severity.
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28
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Wang Z, Zhao Z, Xia Y, Cai Z, Wang C, Shen Y, Liu R, Qin H, Jia J, Yuan G. Potential biomarkers in the fibrosis progression of nonalcoholic steatohepatitis (NASH). J Endocrinol Invest 2022; 45:1379-1392. [PMID: 35226336 DOI: 10.1007/s40618-022-01773-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/17/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE Fibrosis is the only histological feature reflecting the severity and prognosis of nonalcoholic steatohepatitis (NASH). We aim to explore novel genes associated with fibrosis progression in NASH. METHODS Two human RNA-seq datasets were downloaded from the public database. Weighted gene co-expression network analysis (WGCNA) was used to identify their co-expressed modules and further bioinformatics analysis was performed to identify hub genes within the modules. Finally, based on two single-cell RNA-seq datasets from mice and one microarray dataset from human, we further observed the expression of hub genes in different cell clusters and liver tissues. RESULTS 7 hub genes (SPP1, PROM1, SOX9, EPCAM, THY1, CD34 and MCAM) associated with fibrosis progression were identified. Single-cell RNA-seq analysis revealed that those hub genes were expressed by different cell clusters such as cholangiocytes, natural killer (NK) cells, and hepatic stellate cells (HSCs). We also found that SPP1 and CD34 serve as markers of different HSCs clusters, which are associated with inflammatory response and fibrogenesis, respectively. Further study suggested that SPP1, SOX9, MCAM and THY1 might be related to NASH-associated hepatocellular carcinoma (HCC). Receiver operating characteristic (ROC) analysis showed that the high expression of these genes could well predict the occurrence of HCC. At the same time, there were significant differences in metabolism-related pathway changes between different HCC subtypes, and SOX9 may be involved in these changes. CONCLUSIONS The present study identified novel genes associated with NASH fibrosis and explored their effects on fibrosis from a single-cell perspective that might provide new ideas for the early diagnosis, monitoring, evaluation, and prediction of fibrosis progression in NASH.
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Affiliation(s)
- Z Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Z Zhao
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Y Xia
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Z Cai
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - C Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Y Shen
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - R Liu
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - H Qin
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - J Jia
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China.
| | - G Yuan
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China.
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29
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Dam TV, Toft NI, Grøntved L. Cell-Type Resolved Insights into the Cis-Regulatory Genome of NAFLD. Cells 2022; 11:cells11050870. [PMID: 35269495 PMCID: PMC8909044 DOI: 10.3390/cells11050870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 11/20/2022] Open
Abstract
The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing rapidly, and unmet treatment can result in the development of hepatitis, fibrosis, and liver failure. There are difficulties involved in diagnosing NAFLD early and for this reason there are challenges involved in its treatment. Furthermore, no drugs are currently approved to alleviate complications, a fact which highlights the need for further insight into disease mechanisms. NAFLD pathogenesis is associated with complex cellular changes, including hepatocyte steatosis, immune cell infiltration, endothelial dysfunction, hepatic stellate cell activation, and epithelial ductular reaction. Many of these cellular changes are controlled by dramatic changes in gene expression orchestrated by the cis-regulatory genome and associated transcription factors. Thus, to understand disease mechanisms, we need extensive insights into the gene regulatory mechanisms associated with tissue remodeling. Mapping cis-regulatory regions genome-wide is a step towards this objective and several current and emerging technologies allow detection of accessible chromatin and specific histone modifications in enriched cell populations of the liver, as well as in single cells. Here, we discuss recent insights into the cis-regulatory genome in NAFLD both at the organ-level and in specific cell populations of the liver. Moreover, we highlight emerging technologies that enable single-cell resolved analysis of the cis-regulatory genome of the liver.
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Zhang L, Li Y, Dong YC, Guan CY, Tian S, Lv XD, Li JH, Su X, Xia HF, Ma X. Transplantation of umbilical cord-derived mesenchymal stem cells promotes the recovery of thin endometrium in rats. Sci Rep 2022; 12:412. [PMID: 35013490 PMCID: PMC8748676 DOI: 10.1038/s41598-021-04454-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/20/2021] [Indexed: 12/25/2022] Open
Abstract
The endometrium plays a critical role in embryo implantation and pregnancy, and a thin uterus is recognized as a key factor in embryo implantation failure. Umbilical cord mesenchymal stem cells (UC-MSCs) have attracted interest for the repair of intrauterine adhesions. The current study investigated the repair of thin endometrium in rats using the UC-MSCs and the mechanisms involved. Rats were injected with 95% ethanol to establish a model of thin endometrium. The rats were randomly divided into normal, sham, model, and UC-MSCs groups. Endometrial morphological alterations were observed by hematoxylin-eosin staining and Masson staining, and functional restoration was assessed by testing embryo implantation. The interaction between UC-MSCs and rat endometrial stromal cells (ESCs) was evaluated using a transwell 3D model and immunocytochemistry. Microarray mRNA and miRNA platforms were used for miRNA-mRNA expression profiling. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses were performed to identify the biological processes, molecular functions, cellular components, and pathways of endometrial injury and UC-MSCs transplantation repair and real-time quantitative reverse transcription PCR (qRT-PCR) was performed to further identify the expression changes of key molecules in the pathways. Endometrium thickness, number of glands, and the embryo implantation numbers were improved, and the degree of fibrosis was significantly alleviated by UC-MSCs treatment in the rat model of thin endometrium. In vitro cell experiments showed that UC-MSCs migrated to injured ESCs and enhanced their proliferation. miRNA microarray chip results showed that expression of 45 miRNAs was downregulated in the injured endometrium and upregulated after UC-MSCs transplantation. Likewise, expression of 39 miRNAs was upregulated in the injured endometrium and downregulated after UC-MSCs transplantation. The miRNA-mRNA interactions showed the changes in the miRNA and mRNA network during the processes of endometrial injury and repair. GO and KEGG analyses showed that the process of endometrial injury was mainly attributed to the decomposition of the extracellular matrix (ECM), protein degradation and absorption, and accompanying inflammation. The process of UC-MSCs transplantation and repair were accompanied by the reconstruction of the ECM, regulation of chemokines and inflammation, and cell proliferation and apoptosis. The key molecules involved in ECM-receptor interaction pathways were further verified by qRT-PCR. Itga1 and Thbs expression decreased in the model group and increased by UC-MSCs transplantation, while Laminin and Collagen expression increased in both the model group and MSCs group, with greater expression observed in the latter. This study showed that UC-MSCs transplantation could promote recovery of thin endometrial morphology and function. Furthermore, it revealed the expression changes of miRNA and mRNA after endometrial injury and UC-MSCs transplantation repair processed, and signaling pathways that may be involved in endometrial injury and repair.
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Affiliation(s)
- Lu Zhang
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Ying Li
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Yi-Chao Dong
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Chun-Yi Guan
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Shi Tian
- Haidian Maternal and Child Health Hospital, Beijing, China
| | - Xiao-Dan Lv
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Jian-Hui Li
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Xing Su
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Hong-Fei Xia
- National Research Institute for Family Planning, Beijing, 100081, China.
- Graduate School, Peking Union Medical College, Beijing, China.
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, 100081, China.
- Graduate School, Peking Union Medical College, Beijing, China.
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Li Z, Feng J, Zhong J, Lu M, Gao X, Zhang Y. Screening of the Key Genes and Signalling Pathways for Diabetic Nephropathy Using Bioinformatics Analysis. Front Endocrinol (Lausanne) 2022; 13:864407. [PMID: 35923621 PMCID: PMC9340545 DOI: 10.3389/fendo.2022.864407] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND This study aimed to identify biological markers for diabetic nephropathy (DN) and explore their underlying mechanisms. METHODS Four datasets, GSE30528, GSE47183, GSE104948, and GSE96804, were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the "limma" package, and the "RobustRankAggreg" package was used to screen the overlapping DEGs. The hub genes were identified using cytoHubba of Cytoscape. Logistic regression analysis was used to further analyse the hub genes, followed by receiver operating characteristic (ROC) curve analysis to predict the diagnostic effectiveness of the hub genes. Correlation analysis and enrichment analysis of the hub genes were performed to identify the potential functions of the hub genes involved in DN. RESULTS In total, 55 DEGs, including 38 upregulated and 17 downregulated genes, were identified from the three datasets. Four hub genes (FN1, CD44, C1QB, and C1QA) were screened out by the "UpSetR" package, and FN1 was identified as a key gene for DN by logistic regression analysis. Correlation analysis and enrichment analysis showed that FN1 was positively correlated with four genes (COL6A3, COL1A2, THBS2, and CD44) and with the development of DN through the extracellular matrix (ECM)-receptor interaction pathway. CONCLUSIONS We identified four candidate genes: FN1, C1QA, C1QB, and CD44. On further investigating the biological functions of FN1, we showed that FN1 was positively correlated with THBS2, COL1A2, COL6A3, and CD44 and involved in the development of DN through the ECM-receptor interaction pathway. THBS2, COL1A2, COL6A3, and CD44 may be novel biomarkers and target therapeutic candidates for DN.
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Affiliation(s)
- Zukai Li
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Nephrology, Affiliated Huadu Hospital, Southern Medical University (People’s Hospital of Huadu District), Guangzhou, China
| | - Junxia Feng
- The Central Laboratory, Affiliated Huadu Hospital, Southern Medical University (People’s Hospital of Huadu District), Guangzhou, China
| | - Jinting Zhong
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Meizhi Lu
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Nephrology, Affiliated Huadu Hospital, Southern Medical University (People’s Hospital of Huadu District), Guangzhou, China
| | - Xuejuan Gao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Ministry of Education (MOE) Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Yunfang Zhang
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Nephrology, Affiliated Huadu Hospital, Southern Medical University (People’s Hospital of Huadu District), Guangzhou, China
- *Correspondence: Yunfang Zhang,
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Park J, Jeong W, Yun C, Kim H, Oh CM. Serotonergic Regulation of Hepatic Energy Metabolism. Endocrinol Metab (Seoul) 2021; 36:1151-1160. [PMID: 34911172 PMCID: PMC8743581 DOI: 10.3803/enm.2021.1331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/25/2021] [Indexed: 01/01/2023] Open
Abstract
The liver is a vital organ that regulates systemic energy metabolism and many physiological functions. Nonalcoholic fatty liver disease (NAFLD) is the commonest cause of chronic liver disease and end-stage liver failure. NAFLD is primarily caused by metabolic disruption of lipid and glucose homeostasis. Serotonin (5-hydroxytryptamine [5-HT]) is a biogenic amine with several functions in both the central and peripheral systems. 5-HT functions as a neurotransmitter in the brain and a hormone in peripheral tissues to regulate systemic energy homeostasis. Several recent studies have proposed various roles of 5-HT in hepatic metabolism and inflammation using tissue-specific knockout mice and 5-HT-receptor agonists/antagonists. This review compiles the most recent research on the relationship between 5-HT and hepatic metabolism, and the role of 5-HT signaling as a potential therapeutic target in NAFLD.
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Affiliation(s)
- Jiwon Park
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju,
Korea
| | - Wooju Jeong
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju,
Korea
| | - Chahyeon Yun
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju,
Korea
| | - Hail Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon,
Korea
| | - Chang-Myung Oh
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju,
Korea
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