1
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Karin M, Kim JY. MASH as an emerging cause of hepatocellular carcinoma: current knowledge and future perspectives. Mol Oncol 2024. [PMID: 38874196 DOI: 10.1002/1878-0261.13685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 04/15/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
Hepatocellular carcinoma is one of the deadliest and fastest-growing cancers. Among HCC etiologies, metabolic dysfunction-associated fatty liver disease (MAFLD) has served as a major HCC driver due to its great potential for increasing cirrhosis. The obesogenic environment fosters a positive energy balance and results in a continuous rise of obesity and metabolic syndrome. However, it is difficult to understand how metabolic complications lead to the poor prognosis of liver diseases and which molecular mechanisms are underpinning MAFLD-driven HCC development. Thus, suitable preclinical models that recapitulate human etiologies are essentially required. Numerous preclinical models have been created but not many mimicked anthropometric measures and the course of disease progression shown in the patients. Here we review the literature on adipose tissues, liver-related HCC etiologies and recently discovered genetic mutation signatures found in MAFLD-driven HCC patients. We also critically review current rodent models suggested for MAFLD-driven HCC study.
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Affiliation(s)
- Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ju Youn Kim
- Department of Molecular and Life Science, Hanyang University ERICA, Ansan, Korea
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2
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Dashti Z, Yousefi Z, Kiani P, Taghizadeh M, Maleki MH, Borji M, Vakili O, Shafiee SM. Autophagy and the unfolded protein response shape the non-alcoholic fatty liver landscape: decoding the labyrinth. Metabolism 2024; 154:155811. [PMID: 38309690 DOI: 10.1016/j.metabol.2024.155811] [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: 11/28/2023] [Revised: 01/23/2024] [Accepted: 01/28/2024] [Indexed: 02/05/2024]
Abstract
The incidence of nonalcoholic fatty liver disease (NAFLD) is on the rise, mirroring a global surge in diabetes and metabolic syndrome, as its major leading causes. NAFLD represents a spectrum of liver disorders, ranging from nonalcoholic fatty liver (NAFL) to nonalcoholic steatohepatitis (NASH), which can potentially progress to cirrhosis and hepatocellular carcinoma (HCC). Mechanistically, we know the unfolded protein response (UPR) as a protective cellular mechanism, being triggered under circumstances of endoplasmic reticulum (ER) stress. The hepatic UPR is turned on in a broad spectrum of liver diseases, including NAFLD. Recent data also defines molecular mechanisms that may underlie the existing correlation between UPR activation and NAFLD. More interestingly, subsequent studies have demonstrated an additional mechanism, i.e. autophagy, to be involved in hepatic steatosis, and thus NAFLD pathogenesis, principally by regulating the insulin sensitivity, hepatocellular injury, innate immunity, fibrosis, and carcinogenesis. All these findings suggest possible mechanistic roles for autophagy in the progression of NAFLD and its complications. Both UPR and autophagy are dynamic and interconnected fluxes that act as protective responses to minimize the harmful effects of hepatic lipid accumulation, as well as the ER stress during NAFLD. The functions of UPR and autophagy in the liver, together with findings of decreased hepatic autophagy in correlation with conditions that predispose to NAFLD, such as obesity and aging, suggest that autophagy and UPR, alone or combined, may be novel therapeutic targets against the disease. In this review, we discuss the current evidence on the interplay between autophagy and the UPR in connection to the NAFLD pathogenesis.
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Affiliation(s)
- Zahra Dashti
- Department of Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Zeynab Yousefi
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Pouria Kiani
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Motahareh Taghizadeh
- Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hasan Maleki
- Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Borji
- Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran; Autophagy Research Center, Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Sayed Mohammad Shafiee
- Autophagy Research Center, Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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3
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Meroueh C, Warasnhe K, Tizhoosh HR, Shah VH, Ibrahim SH. Digital pathology and spatial omics in steatohepatitis: Clinical applications and discovery potentials. Hepatology 2024:01515467-990000000-00815. [PMID: 38517078 DOI: 10.1097/hep.0000000000000866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Steatohepatitis with diverse etiologies is the most common histological manifestation in patients with liver disease. However, there are currently no specific histopathological features pathognomonic for metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, or metabolic dysfunction-associated steatotic liver disease with increased alcohol intake. Digitizing traditional pathology slides has created an emerging field of digital pathology, allowing for easier access, storage, sharing, and analysis of whole-slide images. Artificial intelligence (AI) algorithms have been developed for whole-slide images to enhance the accuracy and speed of the histological interpretation of steatohepatitis and are currently employed in biomarker development. Spatial biology is a novel field that enables investigators to map gene and protein expression within a specific region of interest on liver histological sections, examine disease heterogeneity within tissues, and understand the relationship between molecular changes and distinct tissue morphology. Here, we review the utility of digital pathology (using linear and nonlinear microscopy) augmented with AI analysis to improve the accuracy of histological interpretation. We will also discuss the spatial omics landscape with special emphasis on the strengths and limitations of established spatial transcriptomics and proteomics technologies and their application in steatohepatitis. We then highlight the power of multimodal integration of digital pathology augmented by machine learning (ML)algorithms with spatial biology. The review concludes with a discussion of the current gaps in knowledge, the limitations and premises of these tools and technologies, and the areas of future research.
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Affiliation(s)
- Chady Meroueh
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Khaled Warasnhe
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Hamid R Tizhoosh
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Vijay H Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Samar H Ibrahim
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Pediatric Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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4
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Herranz JM, López-Pascual A, Clavería-Cabello A, Uriarte I, Latasa MU, Irigaray-Miramon A, Adán-Villaescusa E, Castelló-Uribe B, Sangro B, Arechederra M, Berasain C, Avila MA, Fernández-Barrena MG. Comprehensive analysis of epigenetic and epitranscriptomic genes' expression in human NAFLD. J Physiol Biochem 2023; 79:901-924. [PMID: 37620598 PMCID: PMC10636027 DOI: 10.1007/s13105-023-00976-y] [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: 06/15/2023] [Accepted: 07/19/2023] [Indexed: 08/26/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a multifactorial condition with a complex etiology. Its incidence is increasing globally in parallel with the obesity epidemic, and it is now considered the most common liver disease in Western countries. The precise mechanisms underlying the development and progression of NAFLD are complex and still poorly understood. The dysregulation of epigenetic and epitranscriptomic mechanisms is increasingly recognized to play pathogenic roles in multiple conditions, including chronic liver diseases. Here, we have performed a comprehensive analysis of the expression of epigenetic and epitranscriptomic genes in a total of 903 liver tissue samples corresponding to patients with normal liver, obese patients, and patients with non-alcoholic fatty liver (NAFL) and non-alcoholic steatohepatitis (NASH), advancing stages in NAFLD progression. We integrated ten transcriptomic datasets in an unbiased manner, enabling their robust analysis and comparison. We describe the complete landscape of epigenetic and epitranscriptomic genes' expression along the course of the disease. We identify signatures of genes significantly dysregulated in association with disease progression, particularly with liver fibrosis development. Most of these epigenetic and epitranscriptomic effectors have not been previously described in human NAFLD, and their altered expression may have pathogenic implications. We also performed a comprehensive analysis of the expression of enzymes involved in the metabolism of the substrates and cofactors of epigenetic and epitranscriptomic effectors. This study provides novel information on NAFLD pathogenesis and may also guide the identification of drug targets to treat this condition and its progression towards hepatocellular carcinoma.
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Affiliation(s)
- Jose M Herranz
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Amaya López-Pascual
- Hepatology Unit, CCUN, Navarra University Clinic, Pamplona, Spain
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Alex Clavería-Cabello
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Iker Uriarte
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - M Ujúe Latasa
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Ainara Irigaray-Miramon
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Elena Adán-Villaescusa
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Borja Castelló-Uribe
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Bruno Sangro
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Hepatology Unit, CCUN, Navarra University Clinic, Pamplona, Spain
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - María Arechederra
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Carmen Berasain
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Matías A Avila
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Maite G Fernández-Barrena
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain.
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain.
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5
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Sanchez-Quant E, Richter ML, Colomé-Tatché M, Martinez-Jimenez CP. Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug challenge. Genome Biol 2023; 24:234. [PMID: 37848949 PMCID: PMC10583437 DOI: 10.1186/s13059-023-03075-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Xenobiotics are primarily metabolized by hepatocytes in the liver, and primary human hepatocytes are the gold standard model for the assessment of drug efficacy, safety, and toxicity in the early phases of drug development. Recent advances in single-cell genomics demonstrate liver zonation and ploidy as main drivers of cellular heterogeneity. However, little is known about the impact of hepatocyte specialization on liver function upon metabolic challenge, including hepatic metabolism, detoxification, and protein synthesis. RESULTS Here, we investigate the metabolic capacity of individual human hepatocytes in vitro. We assess how chronic accumulation of lipids enhances cellular heterogeneity and impairs the metabolisms of drugs. Using a phenotyping five-probe cocktail, we identify four functional subgroups of hepatocytes responding differently to drug challenge and fatty acid accumulation. These four subgroups display differential gene expression profiles upon cocktail treatment and xenobiotic metabolism-related specialization. Notably, intracellular fat accumulation leads to increased transcriptional variability and diminishes the drug-related metabolic capacity of hepatocytes. CONCLUSIONS Our results demonstrate that, upon a metabolic challenge such as exposure to drugs or intracellular fat accumulation, hepatocyte subgroups display different and heterogeneous transcriptional responses.
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Affiliation(s)
- Eva Sanchez-Quant
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Maria Lucia Richter
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), 85354, Freising, Germany.
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 82152, Munich, Germany.
| | - Celia Pilar Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany.
- TUM School of Medicine, Technical University of Munich, Munich (TUM), 80333, Munich, Germany.
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6
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Garcia NA, Mellergaard M, Gonzalez-King H, Salomon C, Handberg A. Comprehensive Strategy for Identifying Extracellular Vesicle Surface Proteins as Biomarkers for Non-Alcoholic Fatty Liver Disease. Int J Mol Sci 2023; 24:13326. [PMID: 37686134 PMCID: PMC10487973 DOI: 10.3390/ijms241713326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a liver disorder that has become a global health concern due to its increasing prevalence. There is a need for reliable biomarkers to aid in the diagnosis and prognosis of NAFLD. Extracellular vesicles (EVs) are promising candidates in biomarker discovery, as they carry proteins that reflect the pathophysiological state of the liver. In this review, we developed a list of EV proteins that could be used as diagnostic biomarkers for NAFLD. We employed a multi-step strategy that involved reviewing and comparing various sources of information. Firstly, we reviewed papers that have studied EVs proteins as biomarkers in NAFLD and papers that have studied circulating proteins as biomarkers in NAFLD. To further identify potential candidates, we utilized the EV database Vesiclepedia.org to qualify each protein. Finally, we consulted the Human Protein Atlas to search for candidates' localization, focusing on membrane proteins. By integrating these sources of information, we developed a comprehensive list of potential EVs membrane protein biomarkers that could aid in diagnosing and monitoring NAFLD. In conclusion, our multi-step strategy for identifying EV-based protein biomarkers for NAFLD provides a comprehensive approach that can also be applied to other diseases. The protein candidates identified through this approach could have significant implications for the development of non-invasive diagnostic tests for NAFLD and improve the management and treatment of this prevalent liver disorder.
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Affiliation(s)
| | - Maiken Mellergaard
- Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg Hobrovej 18-22, 9000 Aalborg, Denmark
- Department of Clinical Medicine, The Faculty of Medicine, Aalborg University, 9000 Aalborg, Denmark
| | - Hernan Gonzalez-King
- Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Carlos Salomon
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland, Brisbane, QLD 4029, Australia
| | - Aase Handberg
- Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg Hobrovej 18-22, 9000 Aalborg, Denmark
- Department of Clinical Medicine, The Faculty of Medicine, Aalborg University, 9000 Aalborg, Denmark
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7
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Correia CM, Præstholm SM, Havelund JF, Pedersen FB, Siersbæk MS, Ebbesen MF, Gerhart-Hines Z, Heeren J, Brewer J, Larsen S, Blagoev B, Færgeman NJ, Grøntved L. Acute Deletion of the Glucocorticoid Receptor in Hepatocytes Disrupts Postprandial Lipid Metabolism in Male Mice. Endocrinology 2023; 164:bqad128. [PMID: 37610219 DOI: 10.1210/endocr/bqad128] [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: 04/17/2023] [Revised: 07/09/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
Hepatic lipid metabolism is highly dynamic, and disruption of several circadian transcriptional regulators results in hepatic steatosis. This includes genetic disruption of the glucocorticoid receptor (GR) as the liver develops. To address the functional role of GR in the adult liver, we used an acute hepatocyte-specific GR knockout model to study temporal hepatic lipid metabolism governed by GR at several preprandial and postprandial circadian timepoints. Lipidomics analysis revealed significant temporal lipid metabolism, where GR disruption results in impaired regulation of specific triglycerides, nonesterified fatty acids, and sphingolipids. This correlates with increased number and size of lipid droplets and mildly reduced mitochondrial respiration, most noticeably in the postprandial phase. Proteomics and transcriptomics analyses suggest that dysregulated lipid metabolism originates from pronounced induced expression of enzymes involved in fatty acid synthesis, β-oxidation, and sphingolipid metabolism. Integration of GR cistromic data suggests that induced gene expression is a result of regulatory actions secondary to direct GR effects on gene transcription.
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Affiliation(s)
- Catarina Mendes Correia
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Stine Marie Præstholm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Jesper Foged Havelund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Felix Boel Pedersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Majken Storm Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Morten Frendø Ebbesen
- DaMBIC, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Zach Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jonathan Brewer
- DaMBIC, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Steen Larsen
- Xlab, Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Nils Joakim Færgeman
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
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8
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Chen C, Wang J, Pan D, Wang X, Xu Y, Yan J, Wang L, Yang X, Yang M, Liu G. Applications of multi-omics analysis in human diseases. MedComm (Beijing) 2023; 4:e315. [PMID: 37533767 PMCID: PMC10390758 DOI: 10.1002/mco2.315] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 08/04/2023] Open
Abstract
Multi-omics usually refers to the crossover application of multiple high-throughput screening technologies represented by genomics, transcriptomics, single-cell transcriptomics, proteomics and metabolomics, spatial transcriptomics, and so on, which play a great role in promoting the study of human diseases. Most of the current reviews focus on describing the development of multi-omics technologies, data integration, and application to a particular disease; however, few of them provide a comprehensive and systematic introduction of multi-omics. This review outlines the existing technical categories of multi-omics, cautions for experimental design, focuses on the integrated analysis methods of multi-omics, especially the approach of machine learning and deep learning in multi-omics data integration and the corresponding tools, and the application of multi-omics in medical researches (e.g., cancer, neurodegenerative diseases, aging, and drug target discovery) as well as the corresponding open-source analysis tools and databases, and finally, discusses the challenges and future directions of multi-omics integration and application in precision medicine. With the development of high-throughput technologies and data integration algorithms, as important directions of multi-omics for future disease research, single-cell multi-omics and spatial multi-omics also provided a detailed introduction. This review will provide important guidance for researchers, especially who are just entering into multi-omics medical research.
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Affiliation(s)
- Chongyang Chen
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
- Co‐innovation Center of NeurodegenerationNantong UniversityNantongChina
| | - Jing Wang
- Shenzhen Key Laboratory of Modern ToxicologyShenzhen Medical Key Discipline of Health Toxicology (2020–2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Donghui Pan
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Xinyu Wang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Yuping Xu
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Junjie Yan
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Lizhen Wang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Xifei Yang
- Shenzhen Key Laboratory of Modern ToxicologyShenzhen Medical Key Discipline of Health Toxicology (2020–2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Min Yang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Gong‐Ping Liu
- Co‐innovation Center of NeurodegenerationNantong UniversityNantongChina
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Ministry of Education of China and Hubei Province for Neurological DisordersTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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9
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Panda S. The Untapped Potential of Circadian Timing as a Variable for Discoveries and Reproducibility. Cell Mol Gastroenterol Hepatol 2023; 16:497-498. [PMID: 37423258 PMCID: PMC10444953 DOI: 10.1016/j.jcmgh.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/11/2023]
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10
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de Assis LVM, Demir M, Oster H. Nonalcoholic Steatohepatitis Disrupts Diurnal Liver Transcriptome Rhythms in Mice. Cell Mol Gastroenterol Hepatol 2023; 16:341-354. [PMID: 37270062 PMCID: PMC10444956 DOI: 10.1016/j.jcmgh.2023.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND & AIMS The liver ensures organismal homeostasis through modulation of physiological functions over the course of the day. How liver diseases such as nonalcoholic steatohepatitis (NASH) affect daily transcriptome rhythms in the liver remains elusive. METHODS To start closing this gap, we evaluated the impact of NASH on the diurnal regulation of the liver transcriptome in mice. In addition, we investigated how stringent consideration of circadian rhythmicity affects the outcomes of NASH transcriptome analyses. RESULTS Comparative rhythm analysis of the liver transcriptome from diet-induced NASH and control mice showed an almost 3-hour phase advance in global gene expression rhythms. Rhythmically expressed genes associated with DNA repair and cell-cycle regulation showed increased overall expression and circadian amplitude. In contrast, lipid and glucose metabolism-associated genes showed loss of circadian amplitude, reduced overall expression, and phase advances in NASH livers. Comparison of NASH-induced liver transcriptome responses between published studies showed little overlap (12%) in differentially expressed genes (DEGs). However, by controlling for sampling time and using circadian analytical tools, a 7-fold increase in DEG detection was achieved compared with methods without time control. CONCLUSIONS NASH had a strong effect on circadian liver transcriptome rhythms with phase- and amplitude-specific effects for key metabolic and cell repair pathways, respectively. Accounting for circadian rhythms in NASH transcriptome studies markedly improves DEG detection and enhances reproducibility.
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Affiliation(s)
| | - Münevver Demir
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany; Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Charité Mitte, Berlin, Germany
| | - Henrik Oster
- Institute of Neurobiology, Center of Brain Behavior and Metabolism, University of Lübeck, Lübeck, Germany.
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11
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Zhu Z, Chen Y, Qin X, Liu S, Wang J, Ren H. Multidimensional landscape of non-alcoholic fatty liver disease-related disease spectrum uncovered by big omics data: Profiling evidence and new perspectives. SMART MEDICINE 2023; 2:e20220029. [PMID: 39188279 PMCID: PMC11236021 DOI: 10.1002/smmd.20220029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/22/2023] [Indexed: 08/28/2024]
Abstract
Characterized by hepatic lipid accumulation, non-alcoholic fatty liver disease (NAFLD) is a multifactorial metabolic disorder that could promote the progression of non-alcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular carcinoma (HCC). Benefiting from recent advances in omics technologies, such as high-throughput sequencing, voluminous profiling data in HCC-integrated molecular science into clinical medicine helped clinicians with rational guidance for treatments. In this review, we conclude the majority of publicly available omics data on the NAFLD-related disease spectrum and bring up new insights to inspire next-generation therapeutics against this increasingly prevalent disease spectrum in the post-genomic era.
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Affiliation(s)
- Zhengyi Zhu
- Department of Hepatobiliary SurgeryAffiliated Drum Tower HospitalMedical SchoolNanjing UniversityNanjingChina
| | - Yuyan Chen
- Department of Hepatobiliary SurgeryAffiliated Drum Tower HospitalMedical SchoolNanjing UniversityNanjingChina
| | - Xueqian Qin
- Department of Hepatobiliary SurgeryAffiliated Drum Tower HospitalMedical SchoolNanjing UniversityNanjingChina
| | - Shujun Liu
- Department of Hepatobiliary SurgeryAffiliated Drum Tower HospitalMedical SchoolNanjing UniversityNanjingChina
| | - Jinglin Wang
- Department of Hepatobiliary SurgeryAffiliated Drum Tower HospitalMedical SchoolNanjing UniversityNanjingChina
| | - Haozhen Ren
- Department of Hepatobiliary SurgeryAffiliated Drum Tower HospitalMedical SchoolNanjing UniversityNanjingChina
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12
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Skytthe MK, Pedersen FB, Wernberg CW, Indira Chandran V, Krag A, Di Caterino T, Mandacaru SC, Blagoev B, Lauridsen MM, Detlefsen S, Graversen JH, Moestrup SK. Obese Patients With Nonalcoholic Fatty Liver Disease Have an Increase in Soluble Plasma CD163 and a Concurrent Decrease in Hepatic Expression of CD163. GASTRO HEP ADVANCES 2023; 2:711-720. [PMID: 39129874 PMCID: PMC11307542 DOI: 10.1016/j.gastha.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/03/2023] [Indexed: 08/13/2024]
Abstract
Background and Aims Macrophages play an important role in the development of nonalcoholic fatty liver disease (NAFLD) and its progression to nonalcoholic steatohepatitis (NASH). In this study, we investigated the hepatic expression of the macrophage scavenger receptor CD163 and the plasma level of its shed soluble form (sCD163) in patients with obesity and NASH, non-NASH NAFLD (NAFL), or healthy livers (no NAFLD). Methods Paired liver biopsies and plasma samples were collected from 61 patients with obesity (body mass index ≥35). Hepatic expression of CD163 was analyzed by immunohistochemistry and data-independent acquisition mass spectrometry, whilst plasma levels of sCD163 were determined by enzyme-linked immunosorbent assay and data-independent acquisition mass spectrometry. NAFLD stage and activity were assessed using the Kleiner fibrosis and NASH Clinical Research Network (NAS-CRN) scoring system. Results sCD163 turned out as a promising predictor of NASH with an area under the receiver-operating characteristic curve of 0.78 [0.65;0.92] (P = .0008). sCD163 increased with more severe NAFLD both in univariate (odds ratio [OR] = 3.31[1.80;6.11], P < .001) and multivariable ordinal logistic regression adjusting for NAFLD risk factors (OR = 2.02 [1.03;3.97], P = .042). On the other hand, hepatic expression of CD163 was negatively associated with more severe NAFLD in univariate ordinal logistic regression determined by immunohistochemistry (OR = 0.91[0.84;0.98], P = .015) and proteomics (OR = 0.13[0.02;0.80], P = .028). Taking NAFLD risk factors into account, hepatic expression of CD163 was only associated with the fibrosis stage (OR = 0.01 [0.0003;0.21], P = .004). Accordingly, hepatic CD163 surface expression and sCD163 were negatively correlated (rho = -0.478, P = .0001). Conclusion An increased plasma sCD163 and a concurrent decreased hepatic expression of CD163 are strongly associated with NAFLD in obese patients.
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Affiliation(s)
| | - Felix Boel Pedersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Charlotte Wilhelmina Wernberg
- Department of Gastroenterology and Hepatology, Liver Research Group, University Hospital of South Denmark, Esbjerg, Denmark
| | | | - Aleksander Krag
- Department of Gastroenterology and Hepatology, Liver Research Group, University Hospital of South Denmark, Esbjerg, Denmark
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
| | - Tina Di Caterino
- Department of Pathology, Odense University Hospital, Odense Denmark
| | - Samuel Coelho Mandacaru
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mette Munk Lauridsen
- Department of Gastroenterology and Hepatology, Liver Research Group, University Hospital of South Denmark, Esbjerg, Denmark
| | - Sönke Detlefsen
- Department of Pathology, Odense University Hospital, Odense Denmark
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | | | - Søren Kragh Moestrup
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Department of Biomedicine, Aarhus University, Aarhus Denmark
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
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13
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Chua D, Low ZS, Cheam GX, Ng AS, Tan NS. Utility of Human Relevant Preclinical Animal Models in Navigating NAFLD to MAFLD Paradigm. Int J Mol Sci 2022; 23:14762. [PMID: 36499091 PMCID: PMC9737809 DOI: 10.3390/ijms232314762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Fatty liver disease is an emerging contributor to disease burden worldwide. The past decades of work established the heterogeneous nature of non-alcoholic fatty liver disease (NAFLD) etiology and systemic contributions to the pathogenesis of the disease. This called for the proposal of a redefinition in 2020 to that of metabolic dysfunction-associated fatty liver disease (MAFLD) to better reflect the current understanding of the disease. To date, several clinical cohort studies comparing NAFLD and MAFLD hint at the relevancy of the new nomenclature in enriching for patients with more severe hepatic injury and extrahepatic comorbidities. However, the underlying systemic pathogenesis is still not fully understood. Preclinical animal models have been imperative in elucidating key biological mechanisms in various contexts, including intrahepatic disease progression, interorgan crosstalk and systemic dysregulation. Furthermore, they are integral in developing novel therapeutics against MAFLD. However, substantial contextual variabilities exist across different models due to the lack of standardization in several aspects. As such, it is crucial to understand the strengths and weaknesses of existing models to better align them to the human condition. In this review, we consolidate the implications arising from the change in nomenclature and summarize MAFLD pathogenesis. Subsequently, we provide an updated evaluation of existing MAFLD preclinical models in alignment with the new definitions and perspectives to improve their translational relevance.
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Affiliation(s)
- Damien Chua
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore 308232, Singapore
| | - Zun Siong Low
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore 308232, Singapore
| | - Guo Xiang Cheam
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Aik Seng Ng
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore 308232, Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore 637551, Singapore
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14
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Clare K, Dillon JF, Brennan PN. Reactive Oxygen Species and Oxidative Stress in the Pathogenesis of MAFLD. J Clin Transl Hepatol 2022; 10:939-946. [PMID: 36304513 PMCID: PMC9547261 DOI: 10.14218/jcth.2022.00067] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/22/2022] [Accepted: 06/06/2022] [Indexed: 12/04/2022] Open
Abstract
The pathogenesis of metabolic-associated fatty liver disease (MAFLD) is complex and thought to be dependent on multiple parallel hits on a background of genetic susceptibility. The evidence suggests that MAFLD progression is a dynamic two-way process relating to repetitive bouts of metabolic stress and inflammation interspersed with endogenous anti-inflammatory reparative responses. In MAFLD, excessive hepatic lipid accumulation causes the production of lipotoxins that induce mitochondrial dysfunction, endoplasmic reticular stress, and over production of reactive oxygen species (ROS). Models of MAFLD show marked disruption of mitochondrial function and reduced oxidative capacitance with impact on cellular processes including mitophagy, oxidative phosphorylation, and mitochondrial biogenesis. In excess, ROS modify insulin and innate immune signaling and alter the expression and activity of essential enzymes involved in lipid homeostasis. ROS can also cause direct damage to intracellular structures causing hepatocyte injury and death. In select cases, the use of anti-oxidants and ROS scavengers have been shown to diminish the pro-apoptopic effects of fatty acids. Given this link, endogenous anti-oxidant pathways have been a target of interest, with Nrf2 activation showing a reduction in oxidative stress and inflammation in models of MAFLD. Thyroid hormone receptor β (THRβ) agonists and nuclear peroxisome proliferation-activated receptor (PPAR) family have also gained interest in reducing hepatic lipotoxicity and restoring hepatic function in models of MAFLD. Unfortunately, the true interplay between the clinical and molecular components of MAFLD progression remain only partly understood. Most recently, multiomics-based strategies are being adopted for hypothesis-free analysis of the molecular changes in MAFLD. Transcriptome profiling maps the unique genotype-phenotype associations in MAFLD and with various single-cell transcriptome-based projects underway, there is hope of novel physiological insights to MAFLD progression and uncover therapeutic targets.
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Affiliation(s)
- Kathleen Clare
- Royal Alexandra Hospital, Paisley, NHS Greater Glasgow and Clyde, PA2 9PN, UK
| | - John F. Dillon
- University of Dundee, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
| | - Paul N. Brennan
- University of Dundee, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
- University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, EH16 4UU, UK
- Correspondence to: Paul N. Brennan, University of Dundee, Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK. ORCID: https://orcid.org/0000-0001-8368-1478. Tel: +44-7445308786, E-mail:
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15
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Abstract
The human liver is a complex organ made up of multiple specialized cell types that carry out key physiological functions. An incomplete understanding of liver biology limits our ability to develop therapeutics to prevent chronic liver diseases, liver cancers, and death as a result of organ failure. Recently, single-cell modalities have expanded our understanding of the cellular phenotypic heterogeneity and intercellular cross-talk in liver health and disease. This review summarizes these findings and looks forward to highlighting new avenues for the application of single-cell genomics to unravel unknown pathogenic pathways and disease mechanisms for the development of new therapeutics targeting liver pathology. As these technologies mature, their integration into clinical data analysis will aid in patient stratification and in developing treatment plans for patients suffering from liver disease.
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Affiliation(s)
- Jawairia Atif
- Ajmera Transplant Centre, Schwartz Reisman Liver Research Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, Ontario, Canada
| | - Cornelia Thoeni
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ian D. McGilvray
- Ajmera Transplant Centre, Schwartz Reisman Liver Research Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Sonya A. MacParland
- Ajmera Transplant Centre, Schwartz Reisman Liver Research Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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16
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Subramanian R, Tang R, Zhang Z, Joshi V, Miner JN, Lo YH. Multimodal NASH prognosis using 3D imaging flow cytometry and artificial intelligence to characterize liver cells. Sci Rep 2022; 12:11180. [PMID: 35778474 PMCID: PMC9249889 DOI: 10.1038/s41598-022-15364-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
To improve the understanding of the complex biological process underlying the development of non-alcoholic steatohepatitis (NASH), 3D imaging flow cytometry (3D-IFC) with transmission and side-scattered images were used to characterize hepatic stellate cell (HSC) and liver endothelial cell (LEC) morphology at single-cell resolution. In this study, HSC and LEC were obtained from biopsy-proven NASH subjects with early-stage NASH (F2-F3) and healthy controls. Here, we applied single-cell imaging and 3D digital reconstructions of healthy and diseased cells to analyze a spatially resolved set of morphometric cellular and texture parameters that showed regression with disease progression. By developing a customized autoencoder convolutional neural network (CNN) based on label-free cell transmission and side scattering images obtained from a 3D imaging flow cytometer, we demonstrated key regulated cell types involved in the development of NASH and cell classification performance superior to conventional machine learning methods.
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Affiliation(s)
- Ramkumar Subramanian
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rui Tang
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zunming Zhang
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Yu-Hwa Lo
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
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17
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Abstract
We have developed the underrepresented post-translational modification (PTM) database (urPTMdb), a PTM gene set database to accelerate the discovery of enriched protein modifications in experimental data. urPTMdb provides curated lists of proteins reported to be substrates of underrepresented modifications. Their enrichment in proteomics datasets can reveal unexpected PTM regulations. urPTMdb can be implemented in existing workflows, or used in TeaProt, an online Shiny tool that integrates upstream transcription factor enrichment analysis with downstream pathway analysis through an easy-to-use interactive interface. TeaProt annotates user-uploaded data with drug-gene interactions, subcellular localizations, phenotypic functions, gene-disease associations, and enzyme-gene interactions. TeaProt enables gene set enrichment analysis (GSEA) to discover enrichments in gene sets from various resources, including MSigDB, CHEA, and urPTMdb. We demonstrate the utility of urPTMdb and TeaProt through the analysis of a previously published Western diet-induced remodeling of the tongue proteome, which revealed altered cellular processes associated with energy metabolism, interferon alpha/gamma response, adipogenesis, HMGylation substrate enrichment, and transcription regulation through PPARG and CEBPA. Additionally, we analyzed the interactome of ADP-ribose glycohydrolase TARG1, a key enzyme that removes mono-ADP-ribosylation. This analysis identified an enrichment of ADP-ribosylation, ribosomal proteins, and proteins localized in the nucleoli and endoplasmic reticulum. TeaProt and urPTMdb are accessible at https://tea.coffeeprot.com/.
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Affiliation(s)
- Jeffrey Molendijk
- Department
of Anatomy and Physiology, University of
Melbourne, Melbourne, VIC 3010, Australia,. Phone: +61 401 758 489
| | - Rui Yip
- Department
of Anatomy and Physiology, University of
Melbourne, Melbourne, VIC 3010, Australia
| | - Benjamin L. Parker
- Department
of Anatomy and Physiology, University of
Melbourne, Melbourne, VIC 3010, Australia
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18
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Berridge BR. Animal Study Translation: The Other Reproducibility Challenge. ILAR J 2022. [DOI: 10.1093/ilar/ilac005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Animal research is currently an irreplaceable contributor to our efforts to protect and improve public health. Its relevance, importance, and contributions are represented in historical precedent, regulatory expectations, evidence of our rapidly developing understanding of human health and disease, as well as success in the development of novel therapeutics that are improving quality of life and extending human and animal life expectancy. The rapid and evolving success in responding to the current COVID pandemic significantly supported by animal studies is a clear example of the importance of animal research. But there is growing interest in reducing our dependence on animals and challenges to the effective translation of current animal studies to human applications. There are several potential contributors to gaps in the translatability of animal research to humans, including our approaches to choosing or rationalizing the relevance of a particular animal model, our understanding of their biological variability and how that applies to outcomes, the data we collect from animal studies, and even how we manage the animals. These important contributors to the success of animal research are explored in this issue of the ILAR Journal.
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Affiliation(s)
- Brian R Berridge
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences in Research, Triangle Park, North Carolina, USA
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19
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Radhakrishnan S, Yeung SF, Ke JY, Antunes MM, Pellizzon MA. Considerations When Choosing High-Fat, High-Fructose, and High-Cholesterol Diets to Induce Experimental Nonalcoholic Fatty Liver Disease in Laboratory Animal Models. Curr Dev Nutr 2021; 5:nzab138. [PMID: 34993389 PMCID: PMC8718327 DOI: 10.1093/cdn/nzab138] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/29/2021] [Accepted: 11/05/2021] [Indexed: 02/07/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is intricately linked to metabolic disease (including obesity, glucose intolerance, and insulin resistance) and encompasses a spectrum of disorders including steatosis, nonalcoholic steatohepatitis (NASH), and fibrosis. Rodents consuming high-fat (HF; ∼40 kcal% fat including fats containing higher concentrations of saturated and trans fats), high-fructose (HFr), and high-cholesterol (HC) diets display many clinically relevant characteristics of NASH, along with other metabolic disorders. C57BL/6 mice are the most commonly used animal model because they can develop significant metabolic disorders including severe NASH with fibrosis after months of feeding, but other models also are susceptible. The significant number of diets that contain these different factors (i.e., HF, HFr, and HC), either alone or in combination, makes the choice of diet difficult. This methodology review describes the efficacy of these nutrient manipulations on the NAFLD phenotype in mice, rats, guinea pigs, hamsters, and nonhuman primates.
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Affiliation(s)
| | | | - Jia-Yu Ke
- Research Diets, Inc., New Brunswick, NJ, USA
| | - Maísa M Antunes
- Center for Gastrointestinal Biology, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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20
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Dall M, Hassing AS, Niu L, Nielsen TS, Ingerslev LR, Sulek K, Trammell SAJ, Gillum MP, Barrès R, Larsen S, Poulsen SS, Mann M, Ørskov C, Treebak JT. Hepatocyte-specific perturbation of NAD + biosynthetic pathways in mice induces reversible nonalcoholic steatohepatitis-like phenotypes. J Biol Chem 2021; 297:101388. [PMID: 34762911 PMCID: PMC8648833 DOI: 10.1016/j.jbc.2021.101388] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/25/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
Nicotinamide phosphoribosyltransferase (NAMPT) converts nicotinamide to NAD+. As low hepatic NAD+ levels have been linked to the development of nonalcoholic fatty liver disease, we hypothesized that ablation of hepatic Nampt would affect susceptibility to liver injury in response to diet-induced metabolic stress. Following 3 weeks on a low-methionine and choline-free 60% high-fat diet, hepatocyte-specific Nampt knockout (HNKO) mice accumulated less triglyceride than WT littermates but had increased histological scores for liver inflammation, necrosis, and fibrosis. Surprisingly, liver injury was also observed in HNKO mice on the purified control diet. This HNKO phenotype was associated with decreased abundance of mitochondrial proteins, especially proteins involved in oxidoreductase activity. High-resolution respirometry revealed lower respiratory capacity in purified control diet-fed HNKO liver. In addition, fibrotic area in HNKO liver sections correlated negatively with hepatic NAD+, and liver injury was prevented by supplementation with NAD+ precursors nicotinamide riboside and nicotinic acid. MS-based proteomic analysis revealed that nicotinamide riboside supplementation rescued hepatic levels of oxidoreductase and OXPHOS proteins. Finally, single-nucleus RNA-Seq showed that transcriptional changes in the HNKO liver mainly occurred in hepatocytes, and changes in the hepatocyte transcriptome were associated with liver necrosis. In conclusion, HNKO livers have reduced respiratory capacity, decreased abundance of mitochondrial proteins, and are susceptible to fibrosis because of low NAD+ levels. Our data suggest a critical threshold level of hepatic NAD+ that determines the predisposition to liver injury and supports that NAD+ precursor supplementation can prevent liver injury and nonalcoholic fatty liver disease progression.
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Affiliation(s)
- Morten Dall
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Anna S Hassing
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Lili Niu
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas S Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Lars R Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Karolina Sulek
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Samuel A J Trammell
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew P Gillum
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Steen Larsen
- Department of Biomedical Sciences, Xlab, Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark; Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Steen S Poulsen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Cathrine Ørskov
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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21
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De Muynck K, Vanderborght B, Van Vlierberghe H, Devisscher L. The Gut-Liver Axis in Chronic Liver Disease: A Macrophage Perspective. Cells 2021; 10:2959. [PMID: 34831182 PMCID: PMC8616442 DOI: 10.3390/cells10112959] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic liver disease (CLD) is a growing health concern which accounts for two million deaths per year. Obesity, alcohol overconsumption, and progressive cholestasis are commonly characterized by persistent low-grade inflammation and advancing fibrosis, which form the basis for development of end-stage liver disease complications, including hepatocellular carcinoma. CLD pathophysiology extends to the intestinal tract and is characterized by intestinal dysbiosis, bile acid dysregulation, and gut barrier disruption. In addition, macrophages are key players in CLD progression and intestinal barrier breakdown. Emerging studies are unveiling macrophage heterogeneity and driving factors of their plasticity in health and disease. To date, in-depth investigation of how gut-liver axis disruption impacts the hepatic and intestinal macrophage pool in CLD pathogenesis is scarce. In this review, we give an overview of the role of intestinal and hepatic macrophages in homeostasis and gut-liver axis disruption in progressive stages of CLD.
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Affiliation(s)
- Kevin De Muynck
- Gut-Liver Immunopharmacology Unit, Department of Basic and Applied Medical Sciences, Liver Research Center Ghent, Ghent University, 9000 Ghent, Belgium; (K.D.M.); (B.V.)
- Hepatology Research Unit, Department of Internal Medicine and Pediatrics, Liver Research Center Ghent, Ghent University, 9000 Ghent, Belgium;
| | - Bart Vanderborght
- Gut-Liver Immunopharmacology Unit, Department of Basic and Applied Medical Sciences, Liver Research Center Ghent, Ghent University, 9000 Ghent, Belgium; (K.D.M.); (B.V.)
- Hepatology Research Unit, Department of Internal Medicine and Pediatrics, Liver Research Center Ghent, Ghent University, 9000 Ghent, Belgium;
| | - Hans Van Vlierberghe
- Hepatology Research Unit, Department of Internal Medicine and Pediatrics, Liver Research Center Ghent, Ghent University, 9000 Ghent, Belgium;
| | - Lindsey Devisscher
- Gut-Liver Immunopharmacology Unit, Department of Basic and Applied Medical Sciences, Liver Research Center Ghent, Ghent University, 9000 Ghent, Belgium; (K.D.M.); (B.V.)
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22
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Tate T, Xiang T, Wobker SE, Zhou M, Chen X, Kim H, Batourina E, Lin CS, Kim WY, Lu C, Mckiernan JM, Mendelsohn CL. Pparg signaling controls bladder cancer subtype and immune exclusion. Nat Commun 2021; 12:6160. [PMID: 34697317 PMCID: PMC8545976 DOI: 10.1038/s41467-021-26421-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Pparg, a nuclear receptor, is downregulated in basal subtype bladder cancers that tend to be muscle invasive and amplified in luminal subtype bladder cancers that tend to be non-muscle invasive. Bladder cancers derive from the urothelium, one of the most quiescent epithelia in the body, which is composed of basal, intermediate, and superficial cells. We find that expression of an activated form of Pparg (VP16;Pparg) in basal progenitors induces formation of superficial cells in situ, that exit the cell cycle, and do not form tumors. Expression in basal progenitors that have been activated by mild injury however, results in luminal tumor formation. We find that these tumors are immune deserted, which may be linked to down-regulation of Nf-kb, a Pparg target. Interestingly, some luminal tumors begin to shift to basal subtype tumors with time, down-regulating Pparg and other luminal markers. Our findings have important implications for treatment and diagnosis of bladder cancer. PPARg is differentially expressed in bladder cancer subtypes. Here, the authors show in mice that when an activated form of PPARg is expressed in basal bladder cells tumours do not form, however in the presence of injury the basal cells differentiate into luminal cells.
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Affiliation(s)
- Tiffany Tate
- Department of Urology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Tina Xiang
- Department of Urology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Sarah E Wobker
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mi Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Hyunwoo Kim
- Department of Urology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Ekatherina Batourina
- Department of Urology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Chyuan-Sheng Lin
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Transgenic Mouse Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - James M Mckiernan
- Department of Urology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.,New York-Presbyterian Hospital, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Cathy Lee Mendelsohn
- Department of Urology, Columbia University Irving Medical Center, New York, NY, 10032, USA. .,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA. .,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA. .,Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, 10032, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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23
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Niu L, Sulek K, Vasilopoulou CG, Santos A, Wewer Albrechtsen NJ, Rasmussen S, Meier F, Mann M. Defining NASH from a Multi-Omics Systems Biology Perspective. J Clin Med 2021; 10:jcm10204673. [PMID: 34682795 PMCID: PMC8538576 DOI: 10.3390/jcm10204673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/11/2022] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a chronic liver disease affecting up to 6.5% of the general population. There is no simple definition of NASH, and the molecular mechanism underlying disease pathogenesis remains elusive. Studies applying single omics technologies have enabled a better understanding of the molecular profiles associated with steatosis and hepatic inflammation—the commonly accepted histologic features for diagnosing NASH, as well as the discovery of novel candidate biomarkers. Multi-omics analysis holds great potential to uncover new insights into disease mechanism through integrating multiple layers of molecular information. Despite the technical and computational challenges associated with such efforts, a few pioneering studies have successfully applied multi-omics technologies to investigate NASH. Here, we review the most recent technological developments in mass spectrometry (MS)-based proteomics, metabolomics, and lipidomics. We summarize multi-omics studies and emerging omics biomarkers in NASH and highlight the biological insights gained through these integrated analyses.
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Affiliation(s)
- Lili Niu
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.S.); (A.S.); (N.J.W.A.); (S.R.); (M.M.)
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; (C.G.V.); (F.M.)
- Correspondence: ; Tel.: +45-3114-6118
| | - Karolina Sulek
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.S.); (A.S.); (N.J.W.A.); (S.R.); (M.M.)
- Systems Medicine, Steno Diabetes Center Copenhagen, 2820 Gentofte, Denmark
| | - Catherine G. Vasilopoulou
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; (C.G.V.); (F.M.)
| | - Alberto Santos
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.S.); (A.S.); (N.J.W.A.); (S.R.); (M.M.)
- Center for Health Data Science, University of Copenhagen, 2200 Copenhagen, Denmark
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Nicolai J. Wewer Albrechtsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.S.); (A.S.); (N.J.W.A.); (S.R.); (M.M.)
- Department of Clinical Biochemistry, Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.S.); (A.S.); (N.J.W.A.); (S.R.); (M.M.)
| | - Florian Meier
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; (C.G.V.); (F.M.)
- Functional Proteomics, Jena University Hospital, 07747 Jena, Germany
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.S.); (A.S.); (N.J.W.A.); (S.R.); (M.M.)
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; (C.G.V.); (F.M.)
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24
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Sembach FE, Ægidius HM, Fink LN, Secher T, Aarup A, Jelsing J, Vrang N, Feldt-Rasmussen B, Rigbolt KTG, Nielsen JC, Østergaard MV. Integrative transcriptomic profiling of a mouse model of hypertension-accelerated diabetic kidney disease. Dis Model Mech 2021; 14:dmm049086. [PMID: 34494644 PMCID: PMC8560499 DOI: 10.1242/dmm.049086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/01/2021] [Indexed: 12/12/2022] Open
Abstract
The current understanding of molecular mechanisms driving diabetic kidney disease (DKD) is limited, partly due to the complex structure of the kidney. To identify genes and signalling pathways involved in the progression of DKD, we compared kidney cortical versus glomerular transcriptome profiles in uninephrectomized (UNx) db/db mouse models of early-stage (UNx only) and advanced [UNxplus adeno-associated virus-mediated renin-1 overexpression (UNx-Renin)] DKD using RNAseq. Compared to normoglycemic db/m mice, db/db UNx and db/db UNx-Renin mice showed marked changes in their kidney cortical and glomerular gene expression profiles. UNx-Renin mice displayed more marked perturbations in gene components associated with the activation of the immune system and enhanced extracellular matrix remodelling, supporting histological hallmarks of progressive DKD in this model. Single-nucleus RNAseq enabled the linking of transcriptome profiles to specific kidney cell types. In conclusion, integration of RNAseq at the cortical, glomerular and single-nucleus level provides an enhanced resolution of molecular signalling pathways associated with disease progression in preclinical models of DKD, and may thus be advantageous for identifying novel therapeutic targets in DKD.
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Affiliation(s)
- Frederikke E. Sembach
- Gubra ApS, Hørsholm Kongevej 11B, 2970 Hørsholm, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | | | | | - Thomas Secher
- Gubra ApS, Hørsholm Kongevej 11B, 2970 Hørsholm, Denmark
| | | | - Jacob Jelsing
- Gubra ApS, Hørsholm Kongevej 11B, 2970 Hørsholm, Denmark
| | - Niels Vrang
- Gubra ApS, Hørsholm Kongevej 11B, 2970 Hørsholm, Denmark
| | - Bo Feldt-Rasmussen
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- Department of Nephrology, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
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25
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Yan Y, Gu T, Christensen SDK, Su J, Lassen TR, Hjortbak MV, Lo IJ, Venø ST, Tóth AE, Song P, Nielsen MS, Bøtker HE, Blagoev B, Drasbek KR, Kjems J. Cyclic Hypoxia Conditioning Alters the Content of Myoblast-Derived Extracellular Vesicles and Enhances Their Cell-Protective Functions. Biomedicines 2021; 9:biomedicines9091211. [PMID: 34572398 PMCID: PMC8471008 DOI: 10.3390/biomedicines9091211] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Remote ischemic conditioning (RIC) is a procedure that can attenuate ischemic-reperfusion injury by conducting brief cycles of ischemia and reperfusion in the arm or leg. Extracellular vesicles (EVs) circulating in the bloodstream can release their content into recipient cells to confer protective function on ischemia-reperfusion injured (IRI) organs. Skeletal muscle cells are potential candidates to release EVs as a protective signal during RIC. In this study, we used C2C12 cells as a model system and performed cyclic hypoxia-reoxygenation (HR) to mimic RIC. EVs were collected and subjected to small RNA profiling and proteomics. HR induced a distinct shift in the miRNA profile and protein content in EVs. HR EV treatment restored cell viability, dampened inflammation, and enhanced tube formation in in vitro assays. In vivo, HR EVs showed increased accumulation in the ischemic brain compared to EVs secreted from normoxic culture (N EVs) in a mouse undergoing transient middle cerebral artery occlusion (tMCAO). We conclude that HR conditioning changes the miRNA and protein profile in EVs released by C2C12 cells and enhances the protective signal in the EVs to recipient cells in vitro.
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Affiliation(s)
- Yan Yan
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark; (Y.Y.); (J.S.); (I.L.); (P.S.)
- Omiics ApS, 8200 Aarhus, Denmark;
| | - Tingting Gu
- Center of Functionally Integrative Neuroscience, Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark; (T.G.); (K.R.D.)
| | - Stine Duelund Kaas Christensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark; (S.D.K.C.); (B.B.)
| | - Junyi Su
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark; (Y.Y.); (J.S.); (I.L.); (P.S.)
| | - Thomas Ravn Lassen
- Department of Cardiology, Aarhus University Hospital, Skejby, 8200 Aarhus, Denmark; (T.R.L.); (M.V.H.); (H.E.B.)
| | - Marie Vognstoft Hjortbak
- Department of Cardiology, Aarhus University Hospital, Skejby, 8200 Aarhus, Denmark; (T.R.L.); (M.V.H.); (H.E.B.)
| | - IJu Lo
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark; (Y.Y.); (J.S.); (I.L.); (P.S.)
| | | | - Andrea Erzsebet Tóth
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (A.E.T.); (M.S.N.)
| | - Ping Song
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark; (Y.Y.); (J.S.); (I.L.); (P.S.)
| | | | - Hans Erik Bøtker
- Department of Cardiology, Aarhus University Hospital, Skejby, 8200 Aarhus, Denmark; (T.R.L.); (M.V.H.); (H.E.B.)
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark; (S.D.K.C.); (B.B.)
| | - Kim Ryun Drasbek
- Center of Functionally Integrative Neuroscience, Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark; (T.G.); (K.R.D.)
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark; (Y.Y.); (J.S.); (I.L.); (P.S.)
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Correspondence: ; Tel.: +45-289-920-86
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26
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Zhu Y, Zhang S, Yang C, Xue W, Zhang J, Li J, Zhao J, Xu J, Huang W. [Quantitative analysis of differential proteins in liver tissues of patients with non-alcoholic steatohepatitis using iTRAQ technology]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1381-1387. [PMID: 34658353 DOI: 10.12122/j.issn.1673-4254.2021.09.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To screen differentially expressed proteins (DSPs) in the liver tissues of patients with nonalcoholic steatohepatitis (NASH) using proteomic technologies to identify potential therapeutic targets of NASH. METHODS Liver tissue specimens were obtained from 3 patients with pathologically confirmed NASH and 3 normal control subjects. The total proteins were extracted from the specimens, and iTRAQ reagent was used to label the peptides for liquid chromatography tandem mass spectrometry (LC-MS/MS) detection. The DSPs were identified by comparing the data against UniProt protein database using Mascot2.3.02 software and were annotated and enriched using GO database; KEGG database was used for enrichment of the pathways involving these proteins. Real-time fluorescent quantitative PCR (qPCR) was performed to detect the mRNA expressions of the significant DSPs in NASH. RESULTS By the criteria that a DSP has >1.2 or < 0.8 fold difference between NASH group and the control group and with P < 0.05 as the threshold, a total of 648 significant DSPs in NASH were identified, including 246 up-regulated and 402 down-regulated proteins. GO functional enrichment analysis showed that the DSPs were involved mainly in small molecule metabolism, organic acid metabolism, oxygen acid metabolism and other biological processes, and were enriched in KEGG pathways including the metabolic pathways, complement coagulation cascades, and ribosomes. Among the 25 DEPs with a fold difference >2.0 or < 0.5 (P < 0.05), 6 proteins showed consistent results between qPCR verification and proteomic analysis, including 5 down-regulated proteins: Jumonji protein (JARID2), Lebasillinlike protein (LCA5L), synaptophysin 1 (SYN1) and collagen α-1 (XIII) chain (COL13A1), FYVE, RhoGEF and PH domain protein 5 (FGD5), and 1 upregulated protein glutathione S-transferase Mu 4 (GSTM4). CONCLUSION We identified 648 DEPs inthe liver tissue of patients NASH using iTRAQ technology and bioinformatics methods, and among them JARID2, SYN1, COL13A1, FGD5, and GSTM4 may serve as the key target proteins of NASH.
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Affiliation(s)
- Y Zhu
- Department of Infectious Diseases, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - S Zhang
- Department of Infectious Diseases, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - C Yang
- Department of Infectious Diseases, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - W Xue
- Department of Infectious Diseases, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - J Zhang
- Department of Infectious Diseases, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - J Li
- Department of Infectious Diseases, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - J Zhao
- Department of Infectious Diseases, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - J Xu
- Department of Infectious Diseases, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - W Huang
- Department of Infectious Diseases, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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Liver-fibrosis-activated transcriptional networks govern hepatocyte reprogramming and intra-hepatic communication. Cell Metab 2021; 33:1685-1700.e9. [PMID: 34237252 DOI: 10.1016/j.cmet.2021.06.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/27/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022]
Abstract
Liver fibrosis is a strong predictor of long-term mortality in individuals with metabolic-associated fatty liver disease; yet, the mechanisms underlying the progression from the comparatively benign fatty liver state to advanced non-alcoholic steatohepatitis (NASH) and liver fibrosis are incompletely understood. Using cell-type-resolved genomics, we show that comprehensive alterations in hepatocyte genomic and transcriptional settings during NASH progression, led to a loss of hepatocyte identity. The hepatocyte reprogramming was under tight cooperative control of a network of fibrosis-activated transcription factors, as exemplified by the transcription factor Elf-3 (ELF3) and zinc finger protein GLIS2 (GLIS2). Indeed, ELF3- and GLIS2-controlled fibrosis-dependent hepatokine genes targeting disease-associated hepatic stellate cell gene programs. Thus, interconnected transcription factor networks not only promoted hepatocyte dysfunction but also directed the intra-hepatic crosstalk necessary for NASH and fibrosis progression, implying that molecular "hub-centered" targeting strategies are superior to existing mono-target approaches as currently used in NASH therapy.
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28
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Ma L, Khatib S, Craig AJ, Wang XW. Toward a Liver Cell Atlas: Understanding Liver Biology in Health and Disease at Single-Cell Resolution. Semin Liver Dis 2021; 41:321-330. [PMID: 34130336 DOI: 10.1055/s-0041-1729970] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Single-cell technologies are revolutionizing our understanding of cellular heterogeneity and functional diversity in health and disease. Here, we review the current knowledge and advances in liver biology using single-cell approaches. We focus on the landscape of the composition and the function of cells in a healthy liver in the context of its spatial organization. We also highlight the alterations of the molecular landscape in chronic liver disease and liver cancer, which includes the identification of disease-related cell types, altered cellular functions, dynamic cell-cell interactions, the plasticity of malignant cells, the collective behavior of a cell community, and microenvironmental reprogramming. We anticipate that the uncovered liver cell atlas will help deciphering the molecular and cellular mechanisms driving a healthy liver into a disease state. It also offers insight into the detection of new therapeutic targets and paves the way for effective disease interventions.
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Affiliation(s)
- Lichun Ma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Subreen Khatib
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Amanda J Craig
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.,Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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29
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Saldarriaga OA, Dye B, Pham J, Wanninger TG, Millian D, Kueht M, Freiberg B, Utay N, Stevenson HL. Comparison of liver biopsies before and after direct-acting antiviral therapy for hepatitis C and correlation with clinical outcome. Sci Rep 2021; 11:14506. [PMID: 34267267 PMCID: PMC8282660 DOI: 10.1038/s41598-021-93881-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Direct-acting antivirals (DAA) have replaced interferon (IFN)-based therapies for hepatitis C virus. In this retrospective clinical study, we examined differences in histopathologic features in paired liver biopsies collected from the same patient before and after DAA and correlated these findings with clinical outcome. Biopsies (n = 19) were evaluated by quantitative imaging analysis to measure steatosis and fibrosis. Most patients had decreased steatosis in their post-treatment, follow-up biopsies. However, one patient had a striking increase in steatosis (from 0.86 to 6.32%) and later developed decompensated cirrhosis and hepatocellular carcinoma (HCC). This patient had a marked increase in fibrosis between biopsies, with a CPA of 6.74 to 32.02. Another patient, who already had bridging fibrosis at the time of her pre-treatment biopsy, developed cholangiocarcinoma after DAA. Even though the overall inflammatory activity in the post-treatment biopsies significantly decreased after treatment, 60% of patients had persistent portal lymphocytic inflammation. In summary, DAAs decreased steatosis and hepatic inflammation in most patients, although some may have persistence of lymphocytic portal inflammation. Patients known to have advanced fibrosis at treatment initiation and who have other risk factors for ongoing liver injury, such as steatosis, should be followed closely for the development of adverse outcomes, such as portal hypertension and primary liver cancers.
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Affiliation(s)
- Omar A Saldarriaga
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA
| | - Bradley Dye
- School of Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA
| | - Judy Pham
- School of Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA
| | - Timothy G Wanninger
- School of Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA
| | - Daniel Millian
- School of Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA
| | - Michael Kueht
- Dept. of Surgery, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA
| | - Benjamin Freiberg
- Digital Pathology, Araceli Biosciences, 7425 NE Evergreen Pkwy, Hillsboro, OR, 97124, USA
| | - Netanya Utay
- Department of Internal Medicine, University of Texas Health Science Center at Houston, 7000 Fannin St # 1200, Houston, TX, 77030, USA
| | - Heather L Stevenson
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.
- Department of Pathology, The University of Texas Medical Branch, 712 Texas Avenue, Clinical Services Wing-Room 5.506Q, Galveston, TX, 77555-0416, USA.
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30
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Flessa CM, Kyrou I, Nasiri-Ansari N, Kaltsas G, Papavassiliou AG, Kassi E, Randeva HS. Endoplasmic Reticulum Stress and Autophagy in the Pathogenesis of Non-alcoholic Fatty Liver Disease (NAFLD): Current Evidence and Perspectives. Curr Obes Rep 2021; 10:134-161. [PMID: 33751456 DOI: 10.1007/s13679-021-00431-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Non-alcoholic fatty liver disease (NAFLD) is one of the most common causes of chronic liver disease with rising prevalence worldwide. Herein, we provide a comprehensive overview of the current knowledge supporting the role of ER stress and autophagy processes in NAFLD pathogenesis and progression. We also highlight the interrelation between these two pathways and the impact of ER stress and autophagy modulators on NAFLD treatment. RECENT FINDINGS The pathophysiological mechanisms involved in NAFLD progression are currently under investigation. The endoplasmic reticulum (ER) stress and the concomitant unfolded protein response (UPR) seem to contribute to its pathogenesis mainly due to high ER content in the liver which exerts significant metabolic functions and can be dysregulated. Furthermore, disruption of autophagy processes has also been identified in NAFLD. The crucial role of these two pathways in NAFLD is underlined by the fact that they have recently emerged as promising targets of therapeutic interventions. There is a greater need for finding the natural/chemical compounds and drugs which can modulate the ER stress pathway and autophagy for the treatment of NAFLD. Clarifying the inter-relation between these two pathways and their interaction with inflammatory and apoptotic mechanisms will allow the development of additional therapeutic options which can better target and reprogram the underlying pathophysiological pathways, aiming to attenuate NAFLD progression.
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Affiliation(s)
- Christina-Maria Flessa
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM), University Hospitals Coventry and Warwickshire NHS Trust, Coventry, CV2 2DX, UK
| | - Ioannis Kyrou
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM), University Hospitals Coventry and Warwickshire NHS Trust, Coventry, CV2 2DX, UK
- Aston Medical Research Institute, Aston Medical School, College of Health and Life Sciences, Aston University, B4 7ET, Birmingham, UK
- Division of Translational and Experimental Medicine, Metabolic and Vascular Health, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Narjes Nasiri-Ansari
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | - Gregory Kaltsas
- Endocrine Unit, 1st Department of Propaedeutic and Internal Medicine, Laiko Hospital, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | - Eva Kassi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece.
- Endocrine Unit, 1st Department of Propaedeutic and Internal Medicine, Laiko Hospital, National and Kapodistrian University of Athens, 11527, Athens, Greece.
| | - Harpal S Randeva
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM), University Hospitals Coventry and Warwickshire NHS Trust, Coventry, CV2 2DX, UK.
- Division of Translational and Experimental Medicine, Metabolic and Vascular Health, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
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31
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López-Moreno A, Acuña I, Torres-Sánchez A, Ruiz-Moreno Á, Cerk K, Rivas A, Suárez A, Monteoliva-Sánchez M, Aguilera M. Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies. Nutrients 2021; 13:1617. [PMID: 34065873 PMCID: PMC8151043 DOI: 10.3390/nu13051617] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/12/2022] Open
Abstract
The combination of diet, lifestyle, and the exposure to food obesogens categorized into "microbiota disrupting chemicals" (MDC) could determine obesogenic-related dysbiosis and modify the microbiota diversity that impacts on individual health-disease balances, inducing altered pathogenesis phenotypes. Specific, complementary, and combined treatments are needed to face these altered microbial patterns and the specific misbalances triggered. In this sense, searching for next-generation beneficial microbes or next-generation probiotics (NGP) by microbiota culturing, and focusing on their demonstrated, extensive scope and well-defined functions could contribute to counteracting and repairing the effects of obesogens. Therefore, this review presents a perspective through compiling information and key strategies for directed searching and culturing of NGP that could be administered for obesity and endocrine-related dysbiosis by (i) observing the differential abundance of specific microbiota taxa in obesity-related patients and analyzing their functional roles, (ii) developing microbiota-directed strategies for culturing these taxa groups, and (iii) applying the successful compiled criteria from recent NGP clinical studies. New isolated or cultivable microorganisms from healthy gut microbiota specifically related to obesogens' neutralization effects might be used as an NGP single strain or in consortia, both presenting functions and the ability to palliate metabolic-related disorders. Identification of holistic approaches for searching and using potential NGP, key aspects, the bias, gaps, and proposals of solutions are also considered in this review.
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Affiliation(s)
- Ana López-Moreno
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
| | - Inmaculada Acuña
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Alfonso Torres-Sánchez
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
| | - Ángel Ruiz-Moreno
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
| | - Klara Cerk
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
| | - Ana Rivas
- IBS, Instituto de Investigación Biosanitaria, 18012 Granada, Spain;
- Department of Nutrition and Food Science, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Antonio Suárez
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Mercedes Monteoliva-Sánchez
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
- IBS, Instituto de Investigación Biosanitaria, 18012 Granada, Spain;
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Dutt M, Ng YK, Molendijk J, Karimkhanloo H, Liao L, Blazev R, Montgomery MK, Watt MJ, Parker BL. Western Diet Induced Remodelling of the Tongue Proteome. Proteomes 2021; 9:proteomes9020022. [PMID: 34066295 PMCID: PMC8163156 DOI: 10.3390/proteomes9020022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/03/2021] [Accepted: 05/08/2021] [Indexed: 12/14/2022] Open
Abstract
The tongue is a heavily innervated and vascularized striated muscle that plays an important role in vocalization, swallowing and digestion. The surface of the tongue is lined with papillae which contain gustatory cells expressing various taste receptors. There is growing evidence to suggest that our perceptions of taste and food preference are remodelled following chronic consumption of Western diets rich in carbohydrate and fats. Our sensitivity to taste and also to metabolising Western diets may be a key factor in the rising prevalence of obesity; however, a systems-wide analysis of the tongue is lacking. Here, we defined the proteomic landscape of the mouse tongue and quantified changes following chronic consumption of a chow or Western diet enriched in lipid, fructose and cholesterol for 7 months. We observed a dramatic remodelling of the tongue proteome including proteins that regulate fatty acid and mitochondrial metabolism. Furthermore, the expressions of several receptors, metabolic enzymes and hormones were differentially regulated, and are likely to provide novel therapeutic targets to alter taste perception and food preference to combat obesity.
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Helmstädter M, Schmidt J, Kaiser A, Weizel L, Proschak E, Merk D. Differential Therapeutic Effects of FXR Activation, sEH Inhibition, and Dual FXR/sEH Modulation in NASH in Diet-Induced Obese Mice. ACS Pharmacol Transl Sci 2021; 4:966-979. [PMID: 33860214 DOI: 10.1021/acsptsci.1c00041] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 12/11/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is an epidemic chronic liver disease and may progress over nonalcoholic steatohepatitis (NASH) to liver cirrhosis and hepatocellular carcinoma. The multiple metabolic, environmental, and genetic factors that are involved in NAFLD/NASH pathogenesis and progression suggest a need for multimechanistic interventions. We have developed and preliminarily characterized a concept of dual farnesoid X receptor (FXR) and soluble epoxide hydrolase (sEH) modulation as a promising polypharmacological strategy to counteract NASH. Here we report the profiling of FXR activation, sEH inhibition, and simultaneous FXR/sEH modulation as an interventional treatment in pre-established NASH in mice with diet-induced obesity (DIO). We found that full FXR activation was required to obtain antisteatosis effects but also worsened ballooning degeneration and fibrosis. In contrast, sEH inhibition and dual FXR/sEH modulation, despite a lack of antisteatosis activity, had anti-inflammatory effects and efficiently counteracted hepatic fibrosis. These results demonstrate great therapeutic potential of sEH inhibition to counteract hepatic fibrosis and validate the designed polypharmacology concept of dual FXR/sEH modulation as a potentially superior avenue for the effective treatment of the multifactorial condition NASH.
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Affiliation(s)
- Moritz Helmstädter
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Jurema Schmidt
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Astrid Kaiser
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Lilia Weizel
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Daniel Merk
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
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Park SR, Cho CS, Xi J, Kang HM, Lee JH. Holistic characterization of single-hepatocyte transcriptome responses to high-fat diet. Am J Physiol Endocrinol Metab 2021; 320:E244-E258. [PMID: 33103450 PMCID: PMC8260362 DOI: 10.1152/ajpendo.00391.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
During nutritional overload and obesity, hepatocyte function is grossly altered, and a subset of hepatocytes begins to accumulate fat droplets, leading to nonalcoholic fatty liver disease (NAFLD). Recent single-cell studies revealed how nonparenchymal cells, such as macrophages, hepatic stellate cells, and endothelial cells, heterogeneously respond to NAFLD. However, it remains to be characterized how hepatocytes, the major constituents of the liver, respond to nutritional overload in NAFLD. Here, using droplet-based, single-cell RNA sequencing (Drop-seq), we characterized how the transcriptomic landscape of individual hepatocytes is altered in response to high-fat diet (HFD) and NAFLD. We showed that the entire hepatocyte population undergoes substantial transcriptome changes upon HFD, although the patterns of alteration were highly heterogeneous, with zonation-dependent and -independent effects. Periportal (zone 1) hepatocytes downregulated many zone 1-specific marker genes, whereas a small number of genes mediating gluconeogenesis were upregulated. Pericentral (zone 3) hepatocytes also downregulated many zone 3-specific genes; however, they upregulated several genes that promote HFD-induced fat droplet formation, consistent with findings that zone 3 hepatocytes accumulate more lipid droplets. Zone 3 hepatocytes also upregulated ketogenic pathways as an adaptive mechanism to HFD. Interestingly, many of the top HFD-induced genes, which encode proteins regulating lipid metabolism, were strongly co-expressed with each other in a subset of hepatocytes, producing a variegated pattern of spatial co-localization that is independent of metabolic zonation. In conclusion, our data set provides a useful resource for understanding hepatocellular alteration during NAFLD at single cell level.
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Affiliation(s)
- Sung Rye Park
- Department of Molecular and Integrative Physiology and Institute for Gerontology, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Chun-Seok Cho
- Department of Molecular and Integrative Physiology and Institute for Gerontology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jingyue Xi
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology and Institute for Gerontology, University of Michigan Medical School, Ann Arbor, Michigan
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