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Parekh P, Sherfey J, Alaybeyoglu B, Cirit M. Pathway-Based Similarity Measurement to Quantify Transcriptomics Similarity Between Human Tissues and Preclinical Models. Clin Pharmacol Ther 2024. [PMID: 39377352 DOI: 10.1002/cpt.3465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 09/14/2024] [Indexed: 10/09/2024]
Abstract
Accurate clinical translation of preclinical research remains challenging, primarily due to species-specific differences and disease and patient heterogeneity. An important recent advancement has been development of microphysiological systems that consist of multiple human cell types that recapitulate key characteristics of their respective human systems, allowing essential physiologic processes to be accurately assessed during drug development. However, an unmet need remains regarding a quantitative method to evaluate the similarity between diverse sample types for various contexts of use (CoU)-specific pathways. To address this gap, this study describes the development of pathway-based similarity measurement (PBSM), which leverages RNA-seq data and pathway-based information to assess the human relevance of preclinical models for specific CoU. PBSM offers a quantitative method to compare the transcriptomic similarity of preclinical models to human tissues, shown here as proof of concept for liver and cardiac tissues, enabling improved model selection and validation. Thus, PBSM can successfully support CoU selection for preclinical models, assess the impact of different gene sets on similarity calculations, and differentiate among various in vitro and in vivo models. PBSM has the potential to reduce the translational gap in drug development by allowing quantitative evaluation of the similarity of preclinical models to human tissues, facilitating model selection, and improving understanding of context-specific applications. PBSM can serve as a foundation for enhancing the physiological relevance of in vitro models and supporting the development of more effective therapeutic interventions.
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Affiliation(s)
| | | | | | - Murat Cirit
- Javelin Biotech, Inc., Woburn, Massachusetts, USA
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Chen X, Wang L, Denning KL, Mazur A, Xu Y, Wang K, Lawrence LM, Wang X, Lu Y. Hepatocyte-Specific PEX16 Abrogation in Mice Leads to Hepatocyte Proliferation, Alteration of Hepatic Lipid Metabolism, and Resistance to High-Fat Diet (HFD)-Induced Hepatic Steatosis and Obesity. Biomedicines 2024; 12:988. [PMID: 38790950 PMCID: PMC11117803 DOI: 10.3390/biomedicines12050988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/15/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Obesity results in hepatic fat accumulation, i.e., steatosis. In addition to fat overload, impaired fatty acid β-oxidation also promotes steatosis. Fatty acid β-oxidation takes place in the mitochondria and peroxisomes. Usually, very long-chain and branched-chain fatty acids are the first to be oxidized in peroxisomes, and the resultant short chain fatty acids are further oxidized in the mitochondria. Peroxisome biogenesis is regulated by peroxin 16 (PEX16). In liver-specific PEX16 knockout (Pex16Alb-Cre) mice, hepatocyte peroxisomes were absent, but hepatocytes proliferated, and liver mass was enlarged. These results suggest that normal liver peroxisomes restrain hepatocyte proliferation and liver sizes. After high-fat diet (HFD) feeding, body weights were increased in PEX16 floxed (Pex16fl/fl) mice and adipose-specific PEX16 knockout (Pex16AdipoQ-Cre) mice, but not in the Pex16Alb-Cre mice, suggesting that the development of obesity is regulated by liver PEX16 but not by adipose PEX16. HFD increased liver mass in the Pex16fl/fl mice but somehow reduced the already enlarged liver mass in the Pex16Alb-Cre mice. The basal levels of serum triglyceride, free fatty acids, and cholesterol were decreased, whereas serum bile acids were increased in the Pex16Alb-Cre mice, and HFD-induced steatosis was not observed in the Pex16Alb-Cre mice. These results suggest that normal liver peroxisomes contribute to the development of liver steatosis and obesity.
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Affiliation(s)
- Xue Chen
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Avenue, Huntington, WV 25755, USA; (X.C.); (A.M.)
| | - Long Wang
- Department of Pathology, Guiqian International General Hospital, 1 Dongfeng Ave., Wudang, Guiyang 550018, China (Y.X.)
| | - Krista L. Denning
- Department of Pathology, Joan C. Edwards School of Medicine, Marshall University, 1 John Marshall Drive, Huntington, WV 25755, USA; (K.L.D.)
| | - Anna Mazur
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Avenue, Huntington, WV 25755, USA; (X.C.); (A.M.)
| | - Yujuan Xu
- Department of Pathology, Guiqian International General Hospital, 1 Dongfeng Ave., Wudang, Guiyang 550018, China (Y.X.)
| | - Kesheng Wang
- Department of Family and Community Health, School of Nursing, Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA;
| | - Logan M. Lawrence
- Department of Pathology, Joan C. Edwards School of Medicine, Marshall University, 1 John Marshall Drive, Huntington, WV 25755, USA; (K.L.D.)
| | - Xiaodong Wang
- Department of Pathology, Guiqian International General Hospital, 1 Dongfeng Ave., Wudang, Guiyang 550018, China (Y.X.)
| | - Yongke Lu
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Avenue, Huntington, WV 25755, USA; (X.C.); (A.M.)
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Gebreyesus LH, Choi S, Neequaye P, Mahmoud M, Mahmoud M, Ofosu-Boateng M, Twum E, Nnamani DO, Wang L, Yadak N, Ghosh S, Gonzalez FJ, Gyamfi MA. Pregnane X receptor knockout mitigates weight gain and hepatic metabolic dysregulation in female C57BL/6 J mice on a long-term high-fat diet. Biomed Pharmacother 2024; 173:116341. [PMID: 38428309 PMCID: PMC10983615 DOI: 10.1016/j.biopha.2024.116341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/09/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024] Open
Abstract
Obesity is a significant risk factor for several chronic diseases. However, pre-menopausal females are protected against high-fat diet (HFD)-induced obesity and its adverse effects. The pregnane X receptor (PXR, NR1I2), a xenobiotic-sensing nuclear receptor, promotes short-term obesity-associated liver disease only in male mice but not in females. Therefore, the current study investigated the metabolic and pathophysiological effects of a long-term 52-week HFD in female wild-type (WT) and PXR-KO mice and characterized the PXR-dependent molecular pathways involved. After 52 weeks of HFD ingestion, the body and liver weights and several markers of hepatotoxicity were significantly higher in WT mice than in their PXR-KO counterparts. The HFD-induced liver injury in WT female mice was also associated with upregulation of the hepatic mRNA levels of peroxisome proliferator-activated receptor gamma (Pparg), its target genes, fat-specific protein 27 (Fsp27), and the liver-specific Fsp27b involved in lipid accumulation, apoptosis, and inflammation. Notably, PXR-KO mice displayed elevated hepatic Cyp2a5 (anti-obesity gene), aldo-keto reductase 1b7 (Akr1b7), glutathione-S-transferase M3 (Gstm3) (antioxidant gene), and AMP-activated protein kinase (AMPK) levels, contributing to protection against long-term HFD-induced obesity and inflammation. RNA sequencing analysis revealed a general blunting of the transcriptomic response to HFD in PXR-KO compared to WT mice. Pathway enrichment analysis demonstrated enrichment by HFD for several pathways, including oxidative stress and redox pathway, cholesterol biosynthesis, and glycolysis/gluconeogenesis in WT but not PXR-KO mice. In conclusion, this study provides new insights into the molecular mechanisms by which PXR deficiency protects against long-term HFD-induced severe obesity and its adverse effects in female mice.
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Affiliation(s)
- Lidya H Gebreyesus
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
| | - Sora Choi
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA
| | - Prince Neequaye
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA
| | - Mattia Mahmoud
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA
| | - Mia Mahmoud
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA
| | - Malvin Ofosu-Boateng
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
| | - Elizabeth Twum
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
| | - Daniel O Nnamani
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
| | - Lijin Wang
- Center for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore
| | - Nour Yadak
- Department of Pathology and Laboratory Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Sujoy Ghosh
- Center for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore; Bioinformatics and Computational Biology Core, Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Frank J Gonzalez
- Center for Cancer Research, National Cancer Institute, Building 37, Room 3106, Bethesda, MD 20892, USA
| | - Maxwell A Gyamfi
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA; Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA.
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Kroh A, Walter J, Fragoulis A, Möckel D, Lammers T, Kiessling F, Andruszkow J, Preisinger C, Egbert M, Jiao L, Eickhoff RM, Heise D, Berndt N, Cramer T, Neumann UP, Egners A, Ulmer TF. Hepatocellular loss of mTOR aggravates tumor burden in nonalcoholic steatohepatitis-related HCC. Neoplasia 2023; 46:100945. [PMID: 37976569 PMCID: PMC10685311 DOI: 10.1016/j.neo.2023.100945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023]
Abstract
Obesity and associated nonalcoholic steatohepatitis (NASH) are on the rise globally. NASH became an important driver of hepatocellular carcinoma (HCC) in recent years. Activation of the central metabolic regulator mTOR (mechanistic target of rapamycin) is frequently observed in HCCs. However, mTOR inhibition failed to improve the outcome of HCC therapies, demonstrating the need for a better understanding of the molecular and functional consequences of mTOR blockade. We established a murine NASH-driven HCC model based on long-term western diet feeding combined with hepatocellular mTOR-inactivation. We evaluated tumor load and whole-body fat percentage via µCT-scans, analyzed metabolic blood parameters and tissue proteome profiles. Additionally, we used a bioinformatic model to access liver and HCC mitochondrial metabolic functions. The tumor burden was massively increased via mTOR-knockout. Several signs argue for extensive metabolic reprogramming of glucose, fatty acid, bile acid and cholesterol metabolism. Kinetic modeling revealed reduced oxygen consumption in KO-tumors. NASH-derived HCC pathogenesis is driven by metabolic disturbances and should be considered separately from those caused by other etiologies. We conclude that mTOR functions as tumor suppressor in hepatocytes especially under long-term western diet feeding. However, some of the detrimental consequences of this diet are attenuated by mTOR blockade.
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Affiliation(s)
- Andreas Kroh
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University Hospital, Aachen, Germany.
| | - Jeanette Walter
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University Hospital, Aachen, Germany; Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, RWTH Aachen University Hospital, Aachen, Germany
| | - Athanassios Fragoulis
- Department of Anatomy and Cell Biology, RWTH Aachen University Hospital Aachen, Germany
| | - Diana Möckel
- Institute for Experimental Molecular Imaging (ExMI), RWTH Aachen University Hospital, Aachen, Germany
| | - Twan Lammers
- Institute for Experimental Molecular Imaging (ExMI), RWTH Aachen University Hospital, Aachen, Germany
| | - Fabian Kiessling
- Institute for Experimental Molecular Imaging (ExMI), RWTH Aachen University Hospital, Aachen, Germany
| | - Julia Andruszkow
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Christian Preisinger
- Proteomics Facility, Interdisciplinary Center for Clinical Research (IZKF) Aachen, Medical School, RWTH Aachen University Hospital, Aachen, Germany
| | - Maren Egbert
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University Hospital, Aachen, Germany
| | - Long Jiao
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University Hospital, Aachen, Germany; Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, PR China
| | - Roman M Eickhoff
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University Hospital, Aachen, Germany
| | - Daniel Heise
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University Hospital, Aachen, Germany
| | - Nikolaus Berndt
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany; Institute of Computer-assisted Cardiovascular Medicine, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thorsten Cramer
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University Hospital, Aachen, Germany
| | - Ulf Peter Neumann
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University Hospital, Aachen, Germany; Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Antje Egners
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University Hospital, Aachen, Germany
| | - Tom Florian Ulmer
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University Hospital, Aachen, Germany; Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
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Li X, Zheng L, Zhang B, Deng ZY, Luo T. The Structure Basis of Phytochemicals as Metabolic Signals for Combating Obesity. Front Nutr 2022; 9:913883. [PMID: 35769384 PMCID: PMC9234462 DOI: 10.3389/fnut.2022.913883] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022] Open
Abstract
The consumption of phytochemicals, bioactive compounds in fruits and vegetables, has been demonstrated to ameliorate obesity and related metabolic symptoms by regulating specific metabolic pathways. This review summarizes the progress made in our understanding of the potential of phytochemicals as metabolic signals: we discuss herein selected molecular mechanisms which are involved in the occurrence of obesity that may be regulated by phytochemicals. The focus of our review highlights the regulation of transcription factors toll like receptor 4 (TLR4), nuclear factor (erythroid-derived 2)-like 2 (Nrf2), the peroxisome proliferator-activated receptors (PPARs), fat mass and obesity-associated protein (FTO) and regulation of microRNAs (miRNA). In this review, the effect of phytochemicals on signaling pathways involved in obesity were discussed on the basis of their chemical structure, suggesting molecular mechanisms for how phytochemicals may impact these signaling pathways. For example, compounds with an isothiocyanate group or an α, β-unsaturated carbonyl group may interact with the TLR4 signaling pathway. Regarding Nrf2, we examine compounds possessing an α, β-unsaturated carbonyl group which binds covalently with the cysteine thiols of Keap1. Additionally, phytochemical activation of PPARs, FTO and miRNAs were summarized. This information may be of value to better understand how specific phytochemicals interact with specific signaling pathways and help guide the development of new drugs to combat obesity and related metabolic diseases.
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Rusdiana R, Syarifah S, Pane YS, Widjaja SS, Anggraini DR. The Effects of High Fat Diet on the Liver of the White Rat Model Obesity. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.9383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is the most common form of chronic liver disease with the manifestation of over-accumulation of fat in the liver.
AIM: The purpose of this study was to assess the degree of occurrence of steatosis in rats induced by a standard diet, a high-fat diet, and a modified high-fat diet.
METHODS: This study used 18 white rats of the Wistar strain, divided into three groups, and fed for 9 weeks. Before feeding, all rats were measured their body weight, abdominal circumference, and body length. We measured body weight every week, while body length and waist circumference were measured every 2 weeks. After 9 weeks of diet, all rats were subjected to injection of Ketamine and examined for metabolic markers and histopathological examination of liver organs.
RESULT: There was an increase in body weight of rats in the three groups with the average percentage increase in body weight in the three groups of rats before and after being fed a diet for 9 weeks found in Group 1 29.19% 1 (187−264.40 g), Group 2 by 19.12% (219.33−275 g), and Group 3 24.53% (213.33−275 g). Steatosis in Group 1 was 57.50% of hepatocytes containing macrovesicular fat droplets and called Grade 2 (moderate). In contrast, with a high-fat diet, steatosis occurred around 93.33%−95% of hepatocytes containing macrovesicular fat droplets and called steatosis Grade 3 (severe).
CONCLUSION: The percentage of hepatocytes that had steatosis in obese rats induced by a high-fat diet was more significant than in obese models induced by a standard diet.
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Cicuéndez B, Ruiz-Garrido I, Mora A, Sabio G. Stress kinases in the development of liver steatosis and hepatocellular carcinoma. Mol Metab 2021; 50:101190. [PMID: 33588102 PMCID: PMC8324677 DOI: 10.1016/j.molmet.2021.101190] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/31/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is an important component of metabolic syndrome and one of the most prevalent liver diseases worldwide. This disorder is closely linked to hepatic insulin resistance, lipotoxicity, and inflammation. Although the mechanisms that cause steatosis and chronic liver injury in NAFLD remain unclear, a key component of this process is the activation of stress-activated kinases (SAPKs), including p38 and JNK in the liver and immune system. This review summarizes findings which indicate that the dysregulation of stress kinases plays a fundamental role in the development of steatosis and are important players in inducing liver fibrosis. To avoid the development of steatohepatitis and liver cancer, SAPK activity must be tightly regulated not only in the hepatocytes but also in other tissues, including cells of the immune system. Possible cellular mechanisms of SAPK actions are discussed. Hepatic JNK triggers steatosis and insulin resistance, decreasing lipid oxidation and ketogenesis in HFD-fed mice. Decreased liver expression of p38α/β in HFD increases lipogenesis. Hepatic p38γ/δ drive insulin resistance and inhibit autophagy, which may lead to steatosis. Macrophage p38α/β promote cytokine production and M1 polarization, leading to lipid accumulation in hepatocytes. Myeloid p38γ/δ contribute to cytokine production and neutrophil migration, protecting against steatosis, diabetes and NAFLD. JNK1 and p38γ induce HCC while p38α blocks it. However, deletion of hepatic JNK1/2 induces cholangiocarcinoma. SAPK are potential therapeutic target for metabolic disorders, steatohepatitis and liver cancer.
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Affiliation(s)
- Beatriz Cicuéndez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Irene Ruiz-Garrido
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Alfonso Mora
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain.
| | - Guadalupe Sabio
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain.
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