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Jiang J, Cheng R, Song A, Lou Y, Fan G. Multi-omics analysis reveals mechanism of Schisandra chinensis lignans and acteoside on EMT in hepatoma cells via ERK1/2 pathway. Funct Integr Genomics 2024; 24:112. [PMID: 38849609 DOI: 10.1007/s10142-024-01351-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/08/2024] [Accepted: 03/28/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC), a globally common cancer, often presents late and shows high resistance to chemotherapy, resulting in suboptimal treatment efficacy. Components from traditional Chinese medicines have been recognized for their anti-cancer properties. OBJECTIVE Exploring the mechanism of Schisandra chinensis lignans and acteoside in suppressing Epithelial-Mesenchymal Transition (EMT) in hepatoma cells through the Extracellular signal-Regulated Kinases (ERK)1/2 pathway and identifying biomarkers, molecular subtypes, and targets via multi-omics for precision oncology. METHODS Proliferation was assessed using cell counting kit-8 (CCK-8) assays, with scratch and transwell assays for evaluating invasion and migration. Flow cytometry quantified apoptosis rates. Expression levels of CCL20, p-ERK1/2, c-Myc, Vimentin, and E-cadherin/N-cadherin were analyzed by real-time PCR and Western blot. Tumor volume was calculated with a specific formula, and growth. RESULTS The Schisandra chinensis lignans and acteoside combination decreased CCL20 expression, inhibited hepatoma proliferation and migration, and enhanced apoptosis in a dose- and time-dependent manner. Molecular analysis revealed increased E-cadherin and decreased N-cadherin, p-ERK1/2, c-Myc, and Vimentin expression, indicating ERK1/2 pathway modulation. In vivo, treated nude mice showed significantly reduced tumor growth and volume. CONCLUSION Schisandra chinensis lignans and acteoside potentially counteract CCL20-induced EMT, invasion, and migration in hepatocellular carcinoma cells via the ERK1/2 pathway, enhancing apoptosis. Multi-omics analysis further aids in pinpointing novel biomarkers for precision cancer therapy.
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Affiliation(s)
- Jingjing Jiang
- Department of Pharmacy, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
| | - Ru Cheng
- Department of Pharmacy, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
| | - Aoqi Song
- Department of Pharmacy, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
| | - Yuefen Lou
- Department of Pharmacy, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China.
| | - Guorong Fan
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080, China.
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Ma Y, Harris J, Li P, Jiang C, Sun H, Cao H. An Integrative Transcriptome Subtraction Strategy to Identify Human lncRNAs That Specifically Play a Role in Activation of Human Hepatic Stellate Cells. Noncoding RNA 2024; 10:34. [PMID: 38921831 PMCID: PMC11206700 DOI: 10.3390/ncrna10030034] [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: 03/06/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
Fibrotic liver features excessive deposition of extracellular matrix (ECM), primarily produced from "activated" hepatic stellate cells (HSCs). While targeting human HSCs (hHSCs) in fibrosis therapeutics shows promise, the overall understanding of hHSC activation remains limited, in part because it is very challenging to define the role of human long non-coding RNAs (lncRNAs) in hHSC activation. To address this challenge, we identified another cell type that acts via a diverse gene network to promote fibrogenesis. Then, we identified the lncRNAs that were differentially regulated in activated hHSCs and the other profibrotic cell. Next, we conducted concurrent analysis to identify those lncRNAs that were specifically involved in fibrogenesis. We tested and confirmed that transdifferentiation of vascular smooth muscle cells (VSMCs) represents such a process. By overlapping TGFβ-regulated lncRNAs in multiple sets of hHSCs and VSMCs, we identified a highly selected list of lncRNA candidates that could specifically play a role in hHSC activation. We experimentally characterized one human lncRNA, named CARMN, which was significantly regulated by TGFβ in all conditions above. CARMN knockdown significantly reduced the expression levels of a panel of marker genes for hHSC activation, as well as the levels of ECM deposition and hHSC migration. Conversely, gain of function of CARMN using CRISPR activation (CRISPR-a) yielded the completely opposite effects. Taken together, our work addresses a bottleneck in identifying human lncRNAs that specifically play a role in hHSC activation and provides a framework to effectively select human lncRNAs with significant pathophysiological role.
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Affiliation(s)
| | | | | | | | | | - Haiming Cao
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Jaso-Vera ME, Takaoka S, Patel I, Ruan X. Integrative regulation of hLMR1 by dietary and genetic factors in nonalcoholic fatty liver disease and hyperlipidemia. Hum Genet 2024:10.1007/s00439-024-02654-5. [PMID: 38493444 DOI: 10.1007/s00439-024-02654-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 02/05/2024] [Indexed: 03/19/2024]
Abstract
Long non-coding RNA (lncRNA) genes represent a large class of transcripts that are widely expressed across species. As most human lncRNAs are non-conserved, we recently employed a unique humanized liver mouse model to study lncRNAs expressed in human livers. We identified a human hepatocyte-specific lncRNA, hLMR1 (human lncRNA metabolic regulator 1), which is induced by feeding and promotes hepatic cholesterol synthesis. Recent genome-wide association studies (GWAS) found that several single-nucleotide polymorphisms (SNPs) from the hLMR1 gene locus are associated with blood lipids and markers of liver damage. These results suggest that dietary and genetic factors may regulate hLMR1 to affect disease progression. In this study, we first screened for nutritional/hormonal factors and found that hLMR1 was robustly induced by insulin/glucose in cultured human hepatocytes, and this induction is dependent on the transcription factor SREBP1. We then tested if GWAS SNPs genetically linked to hLMR1 could regulate hLMR1 expression. We found that DNA sequences flanking rs9653945, a SNP from the last exon of the hLMR1 gene, functions as an enhancer that can be robustly activated by SREBP1c depending on the presence of rs9653945 major allele (G). We further performed CRISPR base editing in human HepG2 cells and found that rs9653945 major (G) to minor (A) allele modification resulted in blunted insulin/glucose-induced expression of hLMR1. Finally, we performed genotyping and gene expression analyses using a published human NAFLD RNA-seq dataset and found that individuals homozygous for rs9653945-G have a higher expression of hLMR1 and risk of NAFLD. Taken together, our data support a model that rs9653945-G predisposes individuals to insulin/glucose-induced hLMR1, contributing to the development of hyperlipidemia and NAFLD.
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Affiliation(s)
- Marcos E Jaso-Vera
- Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Fundamental Biomedical Research, Johns Hopkins All Childrens Hospital, 600 Fifth Street S., St. Petersburg, FL, 33701, USA
| | - Shohei Takaoka
- Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Fundamental Biomedical Research, Johns Hopkins All Childrens Hospital, 600 Fifth Street S., St. Petersburg, FL, 33701, USA
| | - Ishika Patel
- Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Fundamental Biomedical Research, Johns Hopkins All Childrens Hospital, 600 Fifth Street S., St. Petersburg, FL, 33701, USA
| | - Xiangbo Ruan
- Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Institute for Fundamental Biomedical Research, Johns Hopkins All Childrens Hospital, 600 Fifth Street S., St. Petersburg, FL, 33701, USA.
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4
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Wei Q, Hou YC, Mao FF, Feng JK, Wang X, Cheng SQ. Disulfidptosis-Associated lncRNAs are Potential Biomarkers for Predicting Immune Response and Prognosis Within Individuals Diagnosed with Hepatocellular Carcinoma. Hepat Med 2023; 15:249-264. [PMID: 38162389 PMCID: PMC10757809 DOI: 10.2147/hmer.s435726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) is a prevalent form of cancer that is distributed globally. Disulfidptosis, characterized by the fragility of the actin cytoskeleton, represents a distinct type of cell death and holds promise for novel cancer therapies. Nevertheless, the connection among disulfidptosis-associated long non-coding RNAs (lncRNAs) and HCC is still unexplored. This study uses an in silico approach to provide the novel biomarkers of disulfidptosis-associated lncRNAs for predicting the immune response and prognosis with HCC. Methods In order to address this gap, we integrated transcriptomic data of HCC from The Cancer Genome Atlas (TCGA) and identified genes that exhibit differential expression with disulfidptosis and lncRNAs. Through co-expression analysis, we identified disulfidptosis-related lncRNAs. Afterwards, by employing univariate Cox regression analysis and the least absolute shrinkage and selection operator (LASSO), a model for disulfidptosis-associated lncRNA was constructed. The risk model underwent assessment through the utilization of diverse analytical methodologies, including functional enrichment annotation, Kaplan-Meier analysis, principal component analysis (PCA), immune infiltration and immune status analysis, as well as tumor mutation analysis. Furthermore, we discussed the implications of the model in predicting drug sensitivity. Results Our study culminated in the construction of a disulfidptosis-related lncRNA model comprising four prognostic disulfidptosis-related lncRNAs (ACYTOR, NRAV, AL080248.1, and AC069307.1). This model demonstrates exceptional diagnostic value for HCC patients and holds practical implications for guiding clinicians in personalizing immunotherapy and drug selection based on individual variations. Conclusion In summary, our research introduces a novel predictive tool utilizing disulfidptosis-related lncRNAs, offering potential guidance for the therapeutic management of HCC.
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Affiliation(s)
- Qian Wei
- The First Clinical Medicine School, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, People’s Republic of China
| | - Yu-Chao Hou
- Cancer Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Fei-Fei Mao
- Tongji University Cancer Center, Shanghai 10th People’s Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Jin-Kai Feng
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, People’s Republic of China
| | - Xu Wang
- Cancer Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Shu-Qun Cheng
- The First Clinical Medicine School, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, People’s Republic of China
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5
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Yu Q, Wu T, Xu W, Wei J, Zhao A, Wang M, Li M, Chi G. PTBP1 as a potential regulator of disease. Mol Cell Biochem 2023:10.1007/s11010-023-04905-x. [PMID: 38129625 DOI: 10.1007/s11010-023-04905-x] [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: 07/10/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) is a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, which plays a key role in alternative splicing of precursor mRNA and RNA metabolism. PTBP1 is universally expressed in various tissues and binds to multiple downstream transcripts to interfere with physiological and pathological processes such as the tumor growth, body metabolism, cardiovascular homeostasis, and central nervous system damage, showing great prospects in many fields. The function of PTBP1 involves the regulation and interaction of various upstream molecules, including circular RNAs (circRNAs), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). These regulatory systems are inseparable from the development and treatment of diseases. Here, we review the latest knowledge regarding the structure and molecular functions of PTBP1 and summarize its functions and mechanisms of PTBP1 in various diseases, including controversial studies. Furthermore, we recommend future studies on PTBP1 and discuss the prospects of targeting PTBP1 in new clinical therapeutic approaches.
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Affiliation(s)
- Qi Yu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Tongtong Wu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Wenhong Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Junyuan Wei
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Anqi Zhao
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Miaomiao Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Meiying Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China.
| | - Guangfan Chi
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China.
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6
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Ma Y, Cao H. 'Lnc-ing' T reg cells to the aging liver. NATURE AGING 2023; 3:760-761. [PMID: 37291220 DOI: 10.1038/s43587-023-00439-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Yonghe Ma
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Haiming Cao
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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7
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 403] [Impact Index Per Article: 403.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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8
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Fang Z, Fan M, Yuan D, Jin L, Wang Y, Ding L, Xu S, Tu J, Zhang E, Wu X, Chen ZB, Huang W. Downregulation of hepatic lncRNA Gm19619 improves gluconeogenesis and lipogenesis following vertical sleeve gastrectomy in mice. Commun Biol 2023; 6:105. [PMID: 36707678 PMCID: PMC9883214 DOI: 10.1038/s42003-023-04483-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging important epigenetic regulators in metabolic processes. Whether they contribute to the metabolic effects of vertical sleeve gastrectomy (VSG), one of the most effective treatments for sustainable weight loss and metabolic improvement, is unknown. Herein, we identify a hepatic lncRNA Gm19619, which is strongly repressed by VSG but highly up-regulated by diet-induced obesity and overnight-fasting in mice. Forced transcription of Gm19619 in the mouse liver significantly promotes hepatic gluconeogenesis with the elevated expression of G6pc and Pck1. In contrast, AAV-CasRx mediated knockdown of Gm19619 in high-fat diet-fed mice significantly improves hepatic glucose and lipid metabolism. Mechanistically, Gm19619 is enriched along genomic regions encoding leptin receptor (Lepr) and transcription factor Foxo1, as revealed in chromatin isolation by RNA purification (ChIRP) assay and is confirmed to modulate their transcription in the mouse liver. In conclusion, Gm19619 may enhance gluconeogenesis and lipid accumulation in the liver.
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Affiliation(s)
- Zhipeng Fang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Mingjie Fan
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Department of Pediatric, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Dongqiang Yuan
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Lihua Jin
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Yangmeng Wang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Lili Ding
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Senlin Xu
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Jui Tu
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Eryun Zhang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Xiwei Wu
- Integrated Genomic Core, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
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Cuproptosis-Related LncRNA-Based Prediction of the Prognosis and Immunotherapy Response in Papillary Renal Cell Carcinoma. Int J Mol Sci 2023; 24:ijms24021464. [PMID: 36674979 PMCID: PMC9863050 DOI: 10.3390/ijms24021464] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Cuproptosis, a new cell death pattern, is promising as an intervention target to treat tumors. Abnormal long non-coding RNA (lncRNA) expression is closely associated with the occurrence and development of papillary renal cell carcinoma (pRCC). However, cuproptosis-related lncRNAs (CRLs) remain largely unknown as prognostic markers for pRCC. We aimed to forecast the prognosis of pRCC patients by constructing models according to CRLs and to examine the correlation between the signatures and the inflammatory microenvironment. From the Cancer Genome Atlas (TCGA), RNA sequencing, genomic mutations and clinical data of TCGA-KIRP (Kidney renal papillary cell carcinoma) were analyzed. Randomly selected pRCC patients were allotted to the training and testing sets. To determine the independent prognostic impact of the training characteristic, the least absolute shrinkage and selection operator (LASSO) algorithm was utilized, together with univariate and multivariate Cox regression models. Further validation was performed in the testing and whole cohorts. External datasets were utilized to verify the prognostic value of CRLs as well. The CRLs prognostic features in pRCC were established based on the five CRLs (AC244033.2, LINC00886, AP000866.1, MRPS9-AS1 and CKMT2-AS1). The utility of CRLs was evaluated and validated in training, testing and all sets on the basis of the Kaplan-Meier (KM) survival analysis. The risk score could be a robust prognostic factor to forecast clinical outcomes for pRCC patients by the LASSO algorithm and univariate and multivariate Cox regression. Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) data demonstrated that differentially expressed genes (DEGs) are primarily important for immune responses and the PI3K-Akt pathway. Arachidonic acid metabolism was enriched in the high-risk set by Gene Set Enrichment Analysis (GSEA). In addition, Tumor Immune Dysfunction and Exclusion (TIDE) analysis suggested that there was a high risk of immune escape in the high-risk cohort. The immune functions of the low- and high-risk sets differed significantly based on immune microenvironment analysis. Finally, four drugs were screened with a higher sensitivity to the high-risk set. Taken together, a novel model according to five CRLs was set up to forecast the prognosis of pRCC patients, which provides a potential strategy to treat pRCC by a combination of cuproptosis and immunotherapy.
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10
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LINC01468 drives NAFLD-HCC progression through CUL4A-linked degradation of SHIP2. Cell Death Dis 2022; 8:449. [DOI: 10.1038/s41420-022-01234-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022]
Abstract
AbstractAccumulating evidence suggests that long noncoding RNAs (lncRNAs) are deregulated in hepatocellular carcinoma (HCC) and play a role in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). However, the current understanding of the role of lncRNAs in NAFLD-associated HCC is limited. In this study, transcriptomic profiling analysis of three paired human liver samples from patients with NAFLD-driven HCC and adjacent samples showed that LINC01468 expression was significantly upregulated. In vitro and in vivo gain- and loss-of-function experiments showed that LINC01468 promotes the proliferation of HCC cells through lipogenesis. Mechanistically, LINC01468 binds SHIP2 and promotes cullin 4 A (CUL4A)-linked ubiquitin degradation, thereby activating the PI3K/AKT/mTOR signaling pathway, resulting in the promotion of de novo lipid biosynthesis and HCC progression. Importantly, the SHIP2 inhibitor reversed the sorafenib resistance induced by LINC01468 overexpression. Moreover, ALKBH5-mediated N6-methyladenosine (m6A) modification led to stabilization and upregulation of LINC01468 RNA. Taken together, the findings indicated a novel mechanism by which LINC01468-mediated lipogenesis promotes HCC progression through CUL4A-linked degradation of SHIP2. LINC01468 acts as a driver of HCC progression from NAFLD, highlights the potential of the LINC01468-SHIP2 axis as a therapeutic target for HCC.
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11
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Song Y, Guo F, Zhao Y, Ma X, Wu L, Yu J, Ji H, Shao M, Huang F, Zhao L, Fan X, Xu Y, Wang Q, Qin G. Novel lncRNA-prader willi/angelman region RNA, SNRPN neighbour (PWARSN) aggravates tubular epithelial cell pyroptosis by regulating TXNIP via dual way in diabetic kidney disease. Cell Prolif 2022; 56:e13349. [PMID: 36316968 PMCID: PMC9890532 DOI: 10.1111/cpr.13349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/16/2022] [Accepted: 09/30/2022] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVES Elevated thioredoxin-interacting protein (TXNIP)-induced pyroptosis contributes to the pathology of diabetic kidney disease (DKD). However, the molecular mechanisms in dysregulated TXNIP in DKD remain largely unclear. MATERIALS AND METHODS Transcriptomic analysis identified a novel long noncoding RNA-Prader Willi/Angelman region RNA, SNRPN neighbour (PWARSN)-which was highly expressed in a proximal tubular epithelial cell (PTEC) under high glucose conditions. We focused on revealing the functions of PWARSN in regulating TXNIP-mediated pyroptosis in PTECs by targeting PWARSN expression via lentivirus-mediated overexpression and CRISPR-Cas9-based knockout in vitro and overexpressing PWARSN in the renal cortex by AAV-9 targeted injection in vivo. A number of molecular techniques disclosed the mechanisms of PWARSN in regulating TXNIP induced-pyroptosis in DKD. RESULTS TXNIP-NOD-like receptor thermal protein domain associated protein 3 (NLRP3) inflammasome and PTEC pyroptosis were activated in the renal tubules of patients with DKD and in diabetic mice. Then we explored that PWARSN enhanced TXNIP-driven PTECs pyroptosis in vitro and in vivo. Mechanistically, cytoplasmic PWARSN sponged miR-372-3p to promote TXNIP expression. Moreover, nuclear PWARSN interacted and facilitated RNA binding motif protein X-linked (RBMX) degradation through ubiquitination, resulting in the initiation of TXNIP transcription by reducing H3K9me3-enrichment at the TXNIP promoter. Further analysis indicated that PWARSN might be a potential biomarker for DKD. CONCLUSIONS These findings illustrate distinct dual molecular mechanisms for PWARSN-modulated TXNIP and PTECs pyroptosis in DKD, presenting PWARSN as a promising therapeutic target for DKD.
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Affiliation(s)
- Yi Song
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina,Academy of Medical SciencesZhengzhou UniversityZhengzhouChina,Institute of Clinical MedicineThe First Affiliated Hospital of Zhengzhou universityZhengzhouChina
| | - Feng Guo
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina,Academy of Medical SciencesZhengzhou UniversityZhengzhouChina,Institute of Clinical MedicineThe First Affiliated Hospital of Zhengzhou universityZhengzhouChina
| | - Yan‐yan Zhao
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Xiao‐jun Ma
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Li‐na Wu
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Ji‐feng Yu
- Department of HematologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Hong‐fei Ji
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Ming‐wei Shao
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Feng‐juan Huang
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Lin Zhao
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Xun‐jie Fan
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina,Academy of Medical SciencesZhengzhou UniversityZhengzhouChina,Institute of Clinical MedicineThe First Affiliated Hospital of Zhengzhou universityZhengzhouChina
| | - Ya‐nan Xu
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina,Institute of Clinical MedicineThe First Affiliated Hospital of Zhengzhou universityZhengzhouChina
| | - Qing‐zhu Wang
- Department of Nuclear MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Gui‐jun Qin
- Department of Endocrinology and MetabolismThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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12
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Lovell CD, Anguera MC. Long Noncoding RNAs That Function in Nutrition: Lnc-ing Nutritional Cues to Metabolic Pathways. Annu Rev Nutr 2022; 42:251-274. [PMID: 35436418 DOI: 10.1146/annurev-nutr-062220-030244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are sensitive to changing environments and play key roles in health and disease. Emerging evidence indicates that lncRNAs regulate gene expression to shape metabolic processes in response to changing nutritional cues. Here we review various lncRNAs sensitive to fasting, feeding, and high-fat diet in key metabolic tissues (liver, adipose, and muscle), highlighting regulatory mechanisms that trigger expression changes of lncRNAs themselves, and how these lncRNAs regulate gene expression of key metabolic genes in specific cell types or across tissues. Determining how lncRNAs respond to changes in nutrition is critical for our understanding of the complex downstream cascades following dietary changes and can shape how we treat metabolic disease. Furthermore, investigating sex biases that might influence lncRNA-regulated responses will likely reveal contributions toward the observed disparities between the sexes in metabolic diseases.
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Affiliation(s)
- Claudia D Lovell
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Montserrat C Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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13
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Sommerauer C, Kutter C. Noncoding RNAs in liver physiology and metabolic diseases. Am J Physiol Cell Physiol 2022; 323:C1003-C1017. [PMID: 35968891 DOI: 10.1152/ajpcell.00232.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The liver holds central roles in detoxification, energy metabolism and whole-body homeostasis but can develop malignant phenotypes when being chronically overwhelmed with fatty acids and glucose. The global rise of metabolic-associated fatty liver disease (MAFLD) is already affecting a quarter of the global population. Pharmaceutical treatment options against different stages of MAFLD do not yet exist and several clinical trials against hepatic transcription factors and other proteins have failed. However, emerging roles of noncoding RNAs, including long (lncRNA) and short noncoding RNAs (sRNA), in various cellular processes pose exciting new avenues for treatment interventions. Actions of noncoding RNAs mostly rely on interactions with proteins, whereby the noncoding RNA fine-tunes protein function in a process termed riboregulation. The developmental stage-, disease stage- and cell type-specific nature of noncoding RNAs harbors enormous potential to precisely target certain cellular pathways in a spatio-temporally defined manner. Proteins interacting with RNAs can be categorized into canonical or non-canonical RNA binding proteins (RBPs) depending on the existence of classical RNA binding domains. Both, RNA- and RBP-centric methods have generated new knowledge of the RNA-RBP interface and added an additional regulatory layer. In this review, we summarize recent advances of how of RBP-lncRNA interactions and various sRNAs shape cellular physiology and the development of liver diseases such as MAFLD and hepatocellular carcinoma.
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Affiliation(s)
- Christian Sommerauer
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, grid.4714.6Karolinska Institute, Stockholm, Sweden
| | - Claudia Kutter
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, grid.4714.6Karolinska Institute, Stockholm, Sweden
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14
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Peltier DC, Roberts A, Reddy P. LNCing RNA to immunity. Trends Immunol 2022; 43:478-495. [DOI: 10.1016/j.it.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 12/29/2022]
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15
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Xu S, Wang Y, Li Z, Hua Q, Jiang M, Fan X. LncRNA GAS5 Knockdown Mitigates Hepatic Lipid Accumulation via Regulating MiR-26a-5p/PDE4B to Activate cAMP/CREB Pathway. Front Endocrinol (Lausanne) 2022; 13:889858. [PMID: 35957809 PMCID: PMC9361042 DOI: 10.3389/fendo.2022.889858] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/23/2022] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Non-alcoholic fatty liver disease (NAFLD) can be attributed to the dysregulation of hepatic lipid metabolism; however, its cellular and molecular mechanisms remain unclear. This study aims to explore the effect of long non-coding RNA growth arrest specific 5 (GAS5) on hepatic lipid metabolism in fatty liver models. METHODS Obese mice, high fat diet-fed mice and free fatty acid-stimulated cells were used for GAS5 expression detection. GAS5 overexpression or knockdown models were established to elucidate the regulatory function of GAS5 in de novo lipogenesis (DNL) and mitochondrial function. Bioinformatic analyses and dual luciferase assays were used to investigate the interaction between GAS5, miR-26a-5p and phosphodiesterase (PDE) 4B. The involvement of the cyclic adenosine monophosphate (cAMP)/cAMP-response element-binding protein (CREB) pathway was evaluated using H89 and forskolin treatment. RESULTS GAS5 was activated in vitro and in vivo fatty liver models. Knockdown of GAS5 reduced lipid droplet accumulation, DNL associated enzymes and preserved mitochondrial function, while GAS5 overexpression exacerbated hepatic lipid accumulation. Mechanistically, GAS5 sponged miR-26a-5p to increase PDE4B expression and subsequently modulated DNL and mitochondrial function via the cAMP/CREB pathway. CONCLUSION Downregulation of GAS5 can activate the cAMP/CREB pathway through miR-26a-5p/PDE4B axis to mitigate hepatic lipid accumulation. This study provides evidence that downregulation of GAS5 may be a potential therapeutic option for the treatment of NAFLD.
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Affiliation(s)
| | | | | | | | - Miao Jiang
- *Correspondence: Xiaoming Fan, ; Miao Jiang,
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16
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Luo Y, Lu H, Peng D, Ruan X, Chen YE, Guo Y. Liver-humanized mice: A translational strategy to study metabolic disorders. J Cell Physiol 2022; 237:489-506. [PMID: 34661916 PMCID: PMC9126562 DOI: 10.1002/jcp.30610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/07/2021] [Accepted: 09/11/2021] [Indexed: 01/03/2023]
Abstract
The liver is the metabolic core of the whole body. Tools commonly used to study the human liver metabolism include hepatocyte cell lines, primary human hepatocytes, and pluripotent stem cells-derived hepatocytes in vitro, and liver genetically humanized mouse model in vivo. However, none of these systems can mimic the human liver in physiological and pathological states satisfactorily. Liver-humanized mice, which are established by reconstituting mouse liver with human hepatocytes, have emerged as an attractive animal model to study drug metabolism and evaluate the therapeutic effect in "human liver" in vivo because the humanized livers greatly replicate enzymatic features of human hepatocytes. The application of liver-humanized mice in studying metabolic disorders is relatively less common due to the largely uncertain replication of metabolic profiles compared to humans. Here, we summarize the metabolic characteristics and current application of liver-humanized mouse models in metabolic disorders that have been reported in the literature, trying to evaluate the pros and cons of using liver-humanized mice as novel mouse models to study metabolic disorders.
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Affiliation(s)
- Yonghong Luo
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, Michigan, USA.,Department of Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Haocheng Lu
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Daoquan Peng
- Department of Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xiangbo Ruan
- Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins School of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Y. Eugene Chen
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, Michigan, USA.,Center for Advanced Models and Translational Sciences and Therapeutics, University of Michigan, Ann Arbor, MI 48109, USA.,Address correspondence to: Yanhong Guo, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, Phone: 734-764-1405, . Or Y. Eugene Chen, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, USA. Phone: 734-936-9548,
| | - Yanhong Guo
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, Michigan, USA.,Address correspondence to: Yanhong Guo, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, Phone: 734-764-1405, . Or Y. Eugene Chen, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, USA. Phone: 734-936-9548,
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17
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Song J, Sun Y, Cao H, Liu Z, Xi L, Dong C, Yang R, Shi Y. A novel pyroptosis-related lncRNA signature for prognostic prediction in patients with lung adenocarcinoma. Bioengineered 2021; 12:5932-5949. [PMID: 34488540 PMCID: PMC8806662 DOI: 10.1080/21655979.2021.1972078] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Lung adenocarcinoma (LUAD) has been the major cause of tumor-associated mortality in recent years and has a poor prognosis. Pyroptosis is regulated via the activation of inflammasomes and participates in tumorigenesis. However, the effects of pyroptosis-related lncRNAs (PRlncRNAs) on LUAD have not yet been completely elucidated. Therefore, we attempted to systematically explore patterns of cell pyroptosis to establish a novel signature for predicting LUAD survival. Based on TCGA database, we set up a prognostic model by incorporating PRlncRNAs with differential expression using Cox regression and LASSO regression. Kaplan-Meier analysis was conducted to compare the survival of LUAD patients. We further simplified the risk model and created a nomogram to enhance the prediction of LUAD prognosis. Altogether, 84 PRlncRNAs with differential expression were discovered. Subsequently, a new risk model was constructed based on five PRlncRNAs, GSEC, FAM83A-AS1, AL606489.1, AL034397.3 and AC010980.2. The proposed signature exhibited good performance in prognostic prediction and was related to immunocyte infiltration. The nomogram exactly forecasted the overall survival of patients and had excellent clinical utility. In the present study, the five-lncRNA prognostic risk signature and nomogram are trustworthy and effective indicators for predicting the prognosis of LUAD.
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Affiliation(s)
- Jiahang Song
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, Jiangsu, China.,Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuanyuan Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hui Cao
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, Nanjing Chest Hospital, The Affiliated Nanjing Brain hospital of Nanjing Medical University, and The Pulmonary Nodule Diagnosis and Treatment Research Center of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhengcheng Liu
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, Nanjing Chest Hospital, The Affiliated Nanjing Brain hospital of Nanjing Medical University, and The Pulmonary Nodule Diagnosis and Treatment Research Center of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Xi
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, Nanjing Chest Hospital, The Affiliated Nanjing Brain hospital of Nanjing Medical University, and The Pulmonary Nodule Diagnosis and Treatment Research Center of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changqing Dong
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, Nanjing Chest Hospital, The Affiliated Nanjing Brain hospital of Nanjing Medical University, and The Pulmonary Nodule Diagnosis and Treatment Research Center of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Rusong Yang
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, Nanjing Chest Hospital, The Affiliated Nanjing Brain hospital of Nanjing Medical University, and The Pulmonary Nodule Diagnosis and Treatment Research Center of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ye Shi
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, Nanjing Chest Hospital, The Affiliated Nanjing Brain hospital of Nanjing Medical University, and The Pulmonary Nodule Diagnosis and Treatment Research Center of Nanjing Medical University, Nanjing, Jiangsu, China
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18
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Rey F, Urrata V, Gilardini L, Bertoli S, Calcaterra V, Zuccotti GV, Cancello R, Carelli S. Role of long non-coding RNAs in adipogenesis: State of the art and implications in obesity and obesity-associated diseases. Obes Rev 2021; 22:e13203. [PMID: 33443301 PMCID: PMC8244036 DOI: 10.1111/obr.13203] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 12/14/2022]
Abstract
Obesity is an evolutionary, chronic, and relapsing disease that consists of a pathological accumulation of adipose tissue able to increase morbidity for high blood pressure, type 2 diabetes, metabolic syndrome, and obstructive sleep apnea in adults, children, and adolescents. Despite intense research over the last 20 years, obesity remains today a disease with a complex and multifactorial etiology. Recently, long non-coding RNAs (lncRNAs) are emerging as interesting new regulators as different lncRNAs have been found to play a role in early and late phases of adipogenesis and to be implicated in obesity-associated complications onset. In this review, we discuss the most recent advances on the role of lncRNAs in adipocyte biology and in obesity-associated complications. Indeed, more and more researchers are focusing on investigating the underlying roles that these molecular modulators could play. Even if a significant number of evidence is correlation-based, with lncRNAs being differentially expressed in a specific disease, recent works are now focused on deeply analyzing how lncRNAs can effectively modulate the disease pathogenesis onset and progression. LncRNAs possibly represent new molecular markers useful in the future for both the early diagnosis and a prompt clinical management of patients with obesity.
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Affiliation(s)
- Federica Rey
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
| | - Valentina Urrata
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
| | - Luisa Gilardini
- Obesity Unit-Laboratory of Nutrition and Obesity Research, Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Simona Bertoli
- Obesity Unit-Laboratory of Nutrition and Obesity Research, Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan, Italy.,International Center for the Assessment of Nutritional Status (ICANS), Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Valeria Calcaterra
- Pediatrics and Adolescentology Unit, Department of Internal Medicine, University of Pavia, Pavia, Italy.,Department of Pediatrics, Children's Hospital "V. Buzzi", Milan, Italy
| | - Gian Vincenzo Zuccotti
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy.,Department of Pediatrics, Children's Hospital "V. Buzzi", Milan, Italy
| | - Raffaella Cancello
- Obesity Unit-Laboratory of Nutrition and Obesity Research, Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
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19
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Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have evolved as a critical regulatory mechanism for almost all biological processes. By dynamically interacting with their molecular partners, lncRNAs regulate gene activity at multiple levels ranging from transcription, pre-mRNA splicing, RNA transporting, RNA decay, and translation of mRNA. RESULTS AND CONCLUSIONS Dysregulation of lncRNAs has been associated with human diseases, including cancer, neurodegenerative, and cardiometabolic diseases. However, as lncRNAs are usually much less conserved than mRNAs at the sequence level, most human lncRNAs are either primate or human specific. The pathophysiological significance of human lncRNAs is still mostly unclear due to the persistent limitations in studying human-specific genes. This review will focus on recent discoveries showing human lncRNAs' roles in regulating metabolic homeostasis and the potential of targeting this unique group of genes for treatment of cardiometabolic diseases.
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Affiliation(s)
- Xiangbo Ruan
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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20
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Crone B, Krause AM, Hornsby WE, Willer CJ, Surakka I. Translating genetic association of lipid levels for biological and clinical application. Cardiovasc Drugs Ther 2021; 35:617-626. [PMID: 33604704 PMCID: PMC8272953 DOI: 10.1007/s10557-021-07156-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/09/2021] [Indexed: 12/11/2022]
Abstract
PURPOSE OF REVIEW This review focuses on the foundational evidence from the last two decades of lipid genetics research and describes the current status of data-driven approaches for transethnic GWAS, fine-mapping, transcriptome informed fine-mapping, and disease prediction. RECENT FINDINGS Current lipid genetics research aims to understand the association mechanisms and clinical relevance of lipid loci as well as to capture population specific associations found in global ancestries. Recent genome-wide trans-ethnic association meta-analyses have identified 118 novel lipid loci reaching genome-wide significance. Gene-based burden tests of whole exome sequencing data have identified three genes-PCSK9, LDLR, and APOB-with significant rare variant burden associated with familial dyslipidemia. Transcriptome-wide association studies discovered five previously unreported lipid-associated loci. Additionally, the predictive power of genome-wide genetic risk scores amalgamating the polygenic determinants of lipid levels can potentially be used to increase the accuracy of coronary artery disease prediction. CONCLUSIONS Lipids are one of the most successful group of traits in the era of genome-wide genetic discovery for identification of novel loci and plausible drug targets. However, a substantial fraction of lipid trait heritability remains unexplained. Further analysis of diverse ancestries and state of the art methods for association locus refinement could potentially reveal some of this missing heritability and increase the clinical application of the genomic association results.
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Affiliation(s)
- Bradley Crone
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Amelia M Krause
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Michigan Medicine, Ann Arbor, MI, USA
| | - Whitney E Hornsby
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Michigan Medicine, Ann Arbor, MI, USA
| | - Cristen J Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Michigan Medicine, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Ida Surakka
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Michigan Medicine, Ann Arbor, MI, USA.
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21
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Ma Y, Harris J, Li P, Cao H. Long noncoding RNAs-a new dimension in the molecular architecture of the bile acid/FXR pathway. Mol Cell Endocrinol 2021; 525:111191. [PMID: 33539963 PMCID: PMC8437140 DOI: 10.1016/j.mce.2021.111191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 11/15/2022]
Abstract
Bile acids, regarded as the body's detergent for digesting lipids, also function as critical signaling molecules that regulate cholesterol and triglyceride levels in the body. Bile acids are the natural ligands of the nuclear receptor, FXR, which controls an intricate network of cellular pathways to maintain metabolic homeostasis. In recent years, growing evidence supports that many cellular actions of the bile acid/FXR pathway are mediated by long non-coding RNAs (lncRNAs), and lncRNAs are in turn powerful regulators of bile acid levels and FXR activities. In this review, we highlight the substantial progress made in the understanding of the functional and mechanistic role of lncRNAs in bile acid metabolism and how lncRNAs connect bile acid activity to additional metabolic processes. We also discuss the potential of lncRNA studies in elucidating novel molecular mechanisms of the bile acid/FXR pathway and the promise of lncRNAs as potential diagnostic markers and therapeutic targets for diseases associated with altered bile acid metabolism.
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Affiliation(s)
- Yonghe Ma
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jamie Harris
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ping Li
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Haiming Cao
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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Identification of Accessible Hepatic Gene Signatures for Interindividual Variations in Nutrigenomic Response to Dietary Supplementation of Omega-3 Fatty Acids. Cells 2021; 10:cells10020467. [PMID: 33671567 PMCID: PMC7926558 DOI: 10.3390/cells10020467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/29/2022] Open
Abstract
Dietary supplementation is a widely adapted strategy to maintain nutritional balance for improving health and preventing chronic diseases. Conflicting results in studies of similar design, however, suggest that there is substantial heterogenicity in individuals’ responses to nutrients, and personalized nutrition is required to achieve the maximum benefit of dietary supplementation. In recent years, nutrigenomics studies have been increasingly utilized to characterize the detailed genomic response to a specific nutrient, but it remains a daunting task to define the signatures responsible for interindividual variations to dietary supplements for tissues with limited accessibility. In this work, we used the hepatic response to omega-3 fatty acids as an example to probe such signatures. Through comprehensive analysis of nutrigenomic response to eicosapentaneoid acid (EPA) and/or docosahexaenoic acid (DHA) including both protein coding and long noncoding RNA (lncRNA) genes in human hepatocytes, we defined the EPA- and/or DHA-specific signature genes in hepatocytes. By analyzing gene expression variations in livers of healthy and relevant disease populations, we identified a set of protein coding and lncRNA signature genes whose responses to omega-3 fatty acid exhibit very high interindividual variabilities. The large variabilities of individual responses to omega-3 fatty acids were further validated in human hepatocytes from ten different donors. Finally, we profiled RNAs in exosomes isolated from the circulation of a liver-specific humanized mouse model, in which the humanized liver is the sole source of human RNAs, and confirmed the in vivo detectability of some signature genes, supporting their potential as biomarkers for nutrient response. Taken together, we have developed an efficient and practical procedure to identify nutrient-responsive gene signatures as well as accessible biomarkers for interindividual variations.
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