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Jiang Z. SLC25A19 is required for NADH homeostasis and mitochondrial respiration. Free Radic Biol Med 2024; 222:317-330. [PMID: 38944213 DOI: 10.1016/j.freeradbiomed.2024.06.019] [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: 03/08/2024] [Revised: 05/12/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Mitochondrial transporters facilitate the translocation of metabolites between the cytoplasm and mitochondria and are critical for mitochondrial functional integrity. Although many mitochondrial transporters are associated with metabolic diseases, how they regulate mitochondrial function and their metabolic contributions at the cellular level are largely unknown. Here, we show that mitochondrial thiamine pyrophosphate (TPP) transporter SLC25A19 is required for mitochondrial respiration. SLC25A19 deficiency leads to reduced cell viability, increased integrated stress response (ISR), enhanced glycolysis and elevated cell sensitivity to 2-deoxyglucose (2-DG) treatment. Through a series of biochemical assays, we found that the depletion of mitochondrial NADH is the primary cause of the impaired mitochondrial respiration in SLC25A19 deficient cells. We also showed involvement of SLC25A19 in regulating the enzymatic activities of complexes I and III, the tricarboxylic acid (TCA) cycle, malate-aspartate shuttle and amino acid metabolism. Consistently, addition of idebenone, an analog of coenzyme Q10, restores mitochondrial respiration and cell viability in SLC25A19 deficient cells. Together, our findings provide new insight into the functions of SLC25A19 in mitochondrial and cellular physiology, and suggest that restoring mitochondrial respiration could be a novel strategy for treating SLC25A19-associated disorders.
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Affiliation(s)
- Zongsheng Jiang
- The Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, China.
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2
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Robledo-Cadena DX, Pacheco-Velazquez SC, Vargas-Navarro JL, Padilla-Flores JA, Moreno-Sanchez R, Rodríguez-Enríquez S. Mitochondrial Proteins as Metabolic Biomarkers and Sites for Therapeutic Intervention in Primary and Metastatic Cancers. Mini Rev Med Chem 2024; 24:1187-1202. [PMID: 39004839 DOI: 10.2174/0113895575254320231030051124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/08/2023] [Accepted: 10/05/2023] [Indexed: 07/16/2024]
Abstract
Accelerated aerobic glycolysis is one of the main metabolic alterations in cancer, associated with malignancy and tumor growth. Although glycolysis is one of the most studied properties of tumor cells, recent studies demonstrate that oxidative phosphorylation (OxPhos) is the main ATP provider for the growth and development of cancer. In this last regard, the levels of mRNA and protein of OxPhos enzymes and transporters (including glutaminolysis, acetate and ketone bodies catabolism, free fatty acid β-oxidation, Krebs Cycle, respiratory chain, phosphorylating system- ATP synthase, ATP/ADP translocator, Pi carrier) are altered in tumors and cancer cells in comparison to healthy tissues and organs, and non-cancer cells. Both energy metabolism pathways are tightly regulated by transcriptional factors, oncogenes, and tumor-suppressor genes, all of which dictate their protein levels depending on the micro-environmental conditions and the type of cancer cell, favoring cancer cell adaptation and growth. In the present review paper, variation in the mRNA and protein levels as well as in the enzyme/ transporter activities of the OxPhos machinery is analyzed. An integral omics approach to mitochondrial energy metabolism pathways may allow for identifying their use as suitable, reliable biomarkers for early detection of cancer development and metastasis, and for envisioned novel, alternative therapies.
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Affiliation(s)
- Diana Xochiquetzal Robledo-Cadena
- Departamento de Bioquímica. Instituto Nacional de Cardiología. Juan Badiano No. 1. Col. Sección XVI. 14080. Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México (UNAM), Coyoacán, México City, 04510, México
| | - Silvia Cecilia Pacheco-Velazquez
- Departamento de Bioquímica. Instituto Nacional de Cardiología. Juan Badiano No. 1. Col. Sección XVI. 14080. Ciudad de México, México
| | - Jorge Luis Vargas-Navarro
- Laboratorio de Control Metabólico. Carrera de Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, México
| | - Joaquín Alberto Padilla-Flores
- Laboratorio de Control Metabólico. Carrera de Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, México
| | - Rafael Moreno-Sanchez
- Laboratorio de Control Metabólico. Carrera de Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, México
| | - Sara Rodríguez-Enríquez
- Laboratorio de Control Metabólico, Carrera de Medicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, México
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Sun S, Zhong B, Zeng X, Li J, Chen Q. Transcription factor E4F1 as a regulator of cell life and disease progression. SCIENCE ADVANCES 2023; 9:eadh1991. [PMID: 37774036 PMCID: PMC10541018 DOI: 10.1126/sciadv.adh1991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/31/2023] [Indexed: 10/01/2023]
Abstract
E4F transcription factor 1 (E4F1), a member of the GLI-Kruppel family of zinc finger proteins, is now widely recognized as a transcription factor. It plays a critical role in regulating various cell processes, including cell growth, proliferation, differentiation, apoptosis and necrosis, DNA damage response, and cell metabolism. These processes involve intricate molecular regulatory networks, making E4F1 an important mediator in cell biology. Moreover, E4F1 has also been implicated in the pathogenesis of a range of human diseases. In this review, we provide an overview of the major advances in E4F1 research, from its first report to the present, including studies on its protein domains, molecular mechanisms of transcriptional regulation and biological functions, and implications for human diseases. We also address unresolved questions and potential research directions in this field. This review provides insights into the essential roles of E4F1 in human health and disease and may pave the way for facilitating E4F1 from basic research to clinical applications.
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Affiliation(s)
- Silu Sun
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Bing Zhong
- Upper Airways Research Laboratory, Department of Otolaryngology–Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Zeng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
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Yan RG, He Z, Wang FC, Li S, Shang QB, Yang QE. Transcription factor E4F1 dictates spermatogonial stem cell fate decisions by regulating mitochondrial functions and cell cycle progression. Cell Biosci 2023; 13:177. [PMID: 37749649 PMCID: PMC10521505 DOI: 10.1186/s13578-023-01134-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Spermatogonial stem cells (SSCs) provide a foundation for robust and continual spermatogenesis in mammals. SSCs self-renew to maintain a functional stem cell pool and differentiate to supply committed progenitors. Metabolism acts as a crucial determinant of stem cell fates; however, factors linking metabolic programs to SSC development and maintenance are poorly understood. RESULTS We analyzed the chromatin accessibility of undifferentiated spermatogonia at the single-cell level and identified 37 positive TF regulators that may have potential roles in dictating SSC fates. The transcription factor E4F1 is expressed in spermatogonia, and its conditional deletion in mouse germ cells results in progressive loss of the entire undifferentiated spermatogonial pool. Single-cell RNA-seq analysis of control and E4f1-deficient spermatogonia revealed that E4F1 acts as a key regulator of mitochondrial function. E4F1 binds to promotors of genes that encode components of the mitochondrial respiratory chain, including Ndufs5, Cox7a2, Cox6c, and Dnajc19. Loss of E4f1 function caused abnormal mitochondrial morphology and defects in fatty acid metabolism; as a result, undifferentiated spermatogonia were gradually lost due to cell cycle arrest and elevated apoptosis. Deletion of p53 in E4f1-deficient germ cells only temporarily prevented spermatogonial loss but did not rescue the defects in SSC maintenance. CONCLUSIONS Emerging evidence indicates that metabolic signals dictate stem cell fate decisions. In this study, we identified a list of transcription regulators that have potential roles in the fate transitions of undifferentiated spermatogonia in mice. Functional experiments demonstrated that the E4F1-mediated transcription program is a crucial regulator of metabolism and SSC fate decisions in mammals.
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Affiliation(s)
- Rong-Ge Yan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810001, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen He
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810001, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei-Chen Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810001, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuang Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810001, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qin-Bang Shang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810001, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Qi-En Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810001, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810001, China.
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5
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Shao Y, Fan X, Yang X, Li S, Huang L, Zhou X, Zhang S, Zheng M, Sun J. Impact of Cuproptosis-related markers on clinical status, tumor immune microenvironment and immunotherapy in colorectal cancer: A multi-omic analysis. Comput Struct Biotechnol J 2023; 21:3383-3403. [PMID: 37389187 PMCID: PMC10300104 DOI: 10.1016/j.csbj.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 07/01/2023] Open
Abstract
Background Cuproptosis, a novel identified cell death form induced by copper, is characterized by aggregation of lipoylated mitochondrial enzymes and the destabilization of Fe-S cluster proteins. However, the function and potential clinical value of cuproptosis and cuproptosis-related biomarkers in colorectal cancer (CRC) remain largely unknown. Methods A comprehensive multi-omics (transcriptomics, genomics, and single-cell transcriptome) analysis was performed for identifying the influence of 16 cuproptosis-related markers on clinical status, molecular functions and tumor microenvironment (TME) in CRC. A novel cuproptosis-related scoring system (CuproScore) based on cuproptosis-related markers was also constructed to predict the prognosis of CRC individuals, TME and the response to immunotherapy. In addition, our transcriptome cohort of 15 paired CRC tissue, tissue-array, and various assays in 4 kinds of CRC cell lines in vitro were applied for verification. Results Cuproptosis-related markers were closely associated with both clinical prognosis and molecular functions. And the cuproptosis-related molecular phenotypes and scoring system (CuproScore) could distinguish and predict the prognosis of CRC patients, TME, and the response to immunotherapy in both public and our transcriptome cohorts. Besides, the expression, function and clinical significance of these markers were also checked and analyzed in CRC cell lines and CRC tissues in our own cohorts. Conclusions In conclusion, we indicated that cuproptosis and CPRMs played a significant role in CRC progression and in modeling the TME. Inducing cuproptosis may be a useful tool for tumor therapy in the future.
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Affiliation(s)
- Yanfei Shao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaodong Fan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuchun Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ling Huang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xueliang Zhou
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sen Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minhua Zheng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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6
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Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y, Borsari B, Morabito S, Liang HY, McGill CJ, Rahmanian S, Sakr J, Jiang S, Zeng W, Carvalho K, Weimer AK, Dionne LA, McShane A, Bedi K, Elhajjajy SI, Upchurch S, Jou J, Youngworth I, Gabdank I, Sud P, Jolanki O, Strattan JS, Kagda MS, Snyder MP, Hitz BC, Moore JE, Weng Z, Bennett D, Reinholdt L, Ljungman M, Beer MA, Gerstein MB, Pachter L, Guigó R, Wold BJ, Mortazavi A. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540865. [PMID: 37292896 PMCID: PMC10245583 DOI: 10.1101/2023.05.15.540865] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3' end choice. Detecting and quantifying transcript isoforms across tissues, cell types, and species has been extremely challenging because transcripts are much longer than the short reads normally used for RNA-seq. By contrast, long-read RNA-seq (LR-RNA-seq) gives the complete structure of most transcripts. We sequenced 264 LR-RNA-seq PacBio libraries totaling over 1 billion circular consensus reads (CCS) for 81 unique human and mouse samples. We detect at least one full-length transcript from 87.7% of annotated human protein coding genes and a total of 200,000 full-length transcripts, 40% of which have novel exon junction chains. To capture and compute on the three sources of transcript structure diversity, we introduce a gene and transcript annotation framework that uses triplets representing the transcript start site, exon junction chain, and transcript end site of each transcript. Using triplets in a simplex representation demonstrates how promoter selection, splice pattern, and 3' processing are deployed across human tissues, with nearly half of multi-transcript protein coding genes showing a clear bias toward one of the three diversity mechanisms. Evaluated across samples, the predominantly expressed transcript changes for 74% of protein coding genes. In evolution, the human and mouse transcriptomes are globally similar in types of transcript structure diversity, yet among individual orthologous gene pairs, more than half (57.8%) show substantial differences in mechanism of diversification in matching tissues. This initial large-scale survey of human and mouse long-read transcriptomes provides a foundation for further analyses of alternative transcript usage, and is complemented by short-read and microRNA data on the same samples and by epigenome data elsewhere in the ENCODE4 collection.
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Affiliation(s)
- Fairlie Reese
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Gabriela Balderrama-Gutierrez
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Dana Wyman
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Muhammed Hasan Çelik
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Elisabeth Rebboah
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Narges Rezaie
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
| | - Beatrice Borsari
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Samuel Morabito
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Heidi Yahan Liang
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Cassandra J McGill
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Sorena Rahmanian
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Jasmine Sakr
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, USA
| | - Shan Jiang
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Weihua Zeng
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Klebea Carvalho
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Annika K Weimer
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Louise A Dionne
- The Jackson Laboratory, The Jackson Laboratory, Bar Harbor, USA
| | - Ariel McShane
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, USA
| | - Karan Bedi
- Department of Biostatistics, University of Michigan, Ann Arbor, USA
- Center for RNA Biomedicine and Rogel Cancer Center, University of Michigan, Ann Arbor, USA
| | - Shaimae I Elhajjajy
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA
| | - Sean Upchurch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Jennifer Jou
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Ingrid Youngworth
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Paul Sud
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Meenakshi S Kagda
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Ben C Hitz
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA
| | - David Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, USA
| | - Laura Reinholdt
- The Jackson Laboratory, The Jackson Laboratory, Bar Harbor, USA
| | - Mats Ljungman
- Center for RNA Biomedicine and Rogel Cancer Center, University of Michigan, Ann Arbor, USA
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan, Ann Arbor, USA
| | - Michael A Beer
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, USA
- Department of Statistics and Data Science, Yale University, New Haven, USA
- Department of Computer Science, Yale University, New Haven, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, USA
| | - Roderic Guigó
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
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7
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Li D, Gao Z, Li Q, Liu X, Liu H. Cuproptosis-a potential target for the treatment of osteoporosis. Front Endocrinol (Lausanne) 2023; 14:1135181. [PMID: 37214253 PMCID: PMC10196240 DOI: 10.3389/fendo.2023.1135181] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/10/2023] [Indexed: 05/24/2023] Open
Abstract
Osteoporosis is an age-related disease of bone metabolism marked by reduced bone mineral density and impaired bone strength. The disease causes the bones to weaken and break more easily. Osteoclasts participate in bone resorption more than osteoblasts participate in bone formation, disrupting bone homeostasis and leading to osteoporosis. Currently, drug therapy for osteoporosis includes calcium supplements, vitamin D, parathyroid hormone, estrogen, calcitonin, bisphosphates, and other medications. These medications are effective in treating osteoporosis but have side effects. Copper is a necessary trace element in the human body, and studies have shown that it links to the development of osteoporosis. Cuproptosis is a recently proposed new type of cell death. Copper-induced cell death regulates by lipoylated components mediated via mitochondrial ferredoxin 1; that is, copper binds directly to the lipoylated components of the tricarboxylic acid cycle, resulting in lipoylated protein accumulation and subsequent loss of iron-sulfur cluster proteins, leading to proteotoxic stress and eventually cell death. Therapeutic options for tumor disorders include targeting the intracellular toxicity of copper and cuproptosis. The hypoxic environment in bone and the metabolic pathway of glycolysis to provide energy in cells can inhibit cuproptosis, which may promote the survival and proliferation of various cells, including osteoblasts, osteoclasts, effector T cells, and macrophages, thereby mediating the osteoporosis process. As a result, our group tried to explain the relationship between the role of cuproptosis and its essential regulatory genes, as well as the pathological mechanism of osteoporosis and its effects on various cells. This study intends to investigate a new treatment approach for the clinical treatment of osteoporosis that is beneficial to the treatment of osteoporosis.
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Affiliation(s)
- Dinglin Li
- Department of Integrated Traditional Chinese and Western Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhonghua Gao
- Department of Geriatrics, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Li
- Department of Integrated Traditional Chinese and Western Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangjie Liu
- Department of Geriatrics, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Liu
- Department of Integrated Traditional Chinese and Western Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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8
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Stacpoole PW, McCall CE. The pyruvate dehydrogenase complex: Life's essential, vulnerable and druggable energy homeostat. Mitochondrion 2023; 70:59-102. [PMID: 36863425 DOI: 10.1016/j.mito.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 03/04/2023]
Abstract
Found in all organisms, pyruvate dehydrogenase complexes (PDC) are the keystones of prokaryotic and eukaryotic energy metabolism. In eukaryotic organisms these multi-component megacomplexes provide a crucial mechanistic link between cytoplasmic glycolysis and the mitochondrial tricarboxylic acid (TCA) cycle. As a consequence, PDCs also influence the metabolism of branched chain amino acids, lipids and, ultimately, oxidative phosphorylation (OXPHOS). PDC activity is an essential determinant of the metabolic and bioenergetic flexibility of metazoan organisms in adapting to changes in development, nutrient availability and various stresses that challenge maintenance of homeostasis. This canonical role of the PDC has been extensively probed over the past decades by multidisciplinary investigations into its causal association with diverse physiological and pathological conditions, the latter making the PDC an increasingly viable therapeutic target. Here we review the biology of the remarkable PDC and its emerging importance in the pathobiology and treatment of diverse congenital and acquired disorders of metabolic integration.
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Affiliation(s)
- Peter W Stacpoole
- Department of Medicine (Division of Endocrinology, Metabolism and Diabetes), and Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL, United States.
| | - Charles E McCall
- Department of Internal Medicine and Translational Sciences, and Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC, United States
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9
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Zhao Q, Qi T. The implications and prospect of cuproptosis-related genes and copper transporters in cancer progression. Front Oncol 2023; 13:1117164. [PMID: 36925927 PMCID: PMC10011146 DOI: 10.3389/fonc.2023.1117164] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/17/2023] [Indexed: 03/08/2023] Open
Abstract
Currently, cancer has become one of the major public health problems worldwide. Apoptosis is an important anti-cancer defense mechanism, which is used in the development of targeted drugs. Because cancer cells have endogenous resistance to apoptosis,the clinical efficacy of related drugs is not ideal. Therefore, non-apoptotic regulatory cell death may bring new therapeutic strategies for cancer treatment. Cuproptosis is a novel form of regulatory cell death which is copper-dependent, regulated and distinct from other known cell death regulatory mechanisms. FDX1,LIAS,and DLAT named cuproptosis-related genes play an essential role in regulating cuproptosis. Meanwhile, abnormal accumulation of copper can be observed in various malignant tumors. The correlation has been established between elevated copper levels in serum and tissues and the progression of several cancers. Copper transporters, CTR1 and Copper-transporting ATPases(ATP7A and ATP7B), are mainly involved in regulating the dynamic balance of copper concentration to maintain copper homeostasis. Thus,cuproptosis-related genes and copper transporters will be the focus of cancer research in future. This review elaborated the basic functions of cuproptosis-related genes and copper transporters by retrievalling PubMed. And then we analyzed their potential relationship with cancer aiming to provide theoretical support and reference in cancer progression, diagnosis and treatment for future study.
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Affiliation(s)
- Qianwen Zhao
- Institute of Medical Sciences, The Second Hospital of Shandong University, Jinan, China
| | - Tonggang Qi
- Institute of Medical Sciences, The Second Hospital of Shandong University, Jinan, China
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10
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Lai MW, Chow N, Checco A, Kunar B, Redmond D, Rafii S, Rabbany SY. Systems Biology Analysis of Temporal Dynamics That Govern Endothelial Response to Cyclic Stretch. Biomolecules 2022; 12:1837. [PMID: 36551265 PMCID: PMC9775567 DOI: 10.3390/biom12121837] [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: 10/21/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Endothelial cells in vivo are subjected to a wide array of mechanical stimuli, such as cyclic stretch. Notably, a 10% stretch is associated with an atheroprotective endothelial phenotype, while a 20% stretch is associated with an atheroprone endothelial phenotype. Here, a systems biology-based approach is used to present a comprehensive overview of the functional responses and molecular regulatory networks that characterize the transition from an atheroprotective to an atheroprone phenotype in response to cyclic stretch. Using primary human umbilical vein endothelial cells (HUVECs), we determined the role of the equibiaxial cyclic stretch in vitro, with changes to the radius of the magnitudes of 10% and 20%, which are representative of physiological and pathological strain, respectively. Following the transcriptome analysis of next-generation sequencing data, we identified four key endothelial responses to pathological cyclic stretch: cell cycle regulation, inflammatory response, fatty acid metabolism, and mTOR signaling, driven by a regulatory network of eight transcription factors. Our study highlights the dynamic regulation of several key stretch-sensitive endothelial functions relevant to the induction of an atheroprone versus an atheroprotective phenotype and lays the foundation for further investigation into the mechanisms governing vascular pathology. This study has significant implications for the development of treatment modalities for vascular disease.
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Affiliation(s)
- Michael W. Lai
- Bioengineering Program, DeMatteis School of Engineering and Applied Science, Hofstra University, New York, NY 11549, USA
| | - Nathan Chow
- Bioengineering Program, DeMatteis School of Engineering and Applied Science, Hofstra University, New York, NY 11549, USA
| | - Antonio Checco
- Bioengineering Program, DeMatteis School of Engineering and Applied Science, Hofstra University, New York, NY 11549, USA
| | - Balvir Kunar
- Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine (WCM), New York, NY 10065, USA
| | - David Redmond
- Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine (WCM), New York, NY 10065, USA
| | - Shahin Rafii
- Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine (WCM), New York, NY 10065, USA
| | - Sina Y. Rabbany
- Bioengineering Program, DeMatteis School of Engineering and Applied Science, Hofstra University, New York, NY 11549, USA
- Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine (WCM), New York, NY 10065, USA
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11
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Ding L, Li W, Tu J, Cao Z, Li J, Cao H, Liang J, Liang Y, Yu Q, Li G. Identification of cuproptosis-related subtypes, cuproptosis-related gene prognostic index in hepatocellular carcinoma. Front Immunol 2022; 13:989156. [PMID: 36177029 PMCID: PMC9513033 DOI: 10.3389/fimmu.2022.989156] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
Cuproptosis is a novel form of cell death, correlated with the tricarboxylic acid (TCA) cycle. However, the metabolic features and the benefit of immune checkpoint inhibitor (ICI) therapy based on cuproptosis have not yet been elucidated in Hepatocellular carcinoma (HCC). First, we identified and validated three cuproptosis subtypes based on 10 cuproptosis-related genes (CRGs) in HCC patients. We explored the correlation between three cuproptosis subtypes and metabolism-related pathways. Besides, a comprehensive immune analysis of three cuproptosis subtypes was performed. Then, we calculated the cuproptosis-related gene prognostic index (CRGPI) score for predicting prognosis and validated its predictive capability by Decision curve analysis (DCA). We as well explored the benefit of ICI therapy of different CRGPI subgroups in two anti-PD1/PD-L1 therapy cohorts (IMvigor210 cohort and GSE176307). Finally, we performed the ridge regression algorithm to calculate the IC50 value for drug sensitivity and Gene set enrichment analysis (GSEA) analysis to explore the potential mechanism. We found that cluster A presented a higher expression of FDX1 and was correlated with metabolism, glycolysis, and TCA cycle pathways, compared with the other two clusters. HCC patients with high CRGPI scores had a worse OS probability, and we further found that the CRGPI-high group had high expression of PD1/PDL1, TMB, and better response (PR/CR) to immunotherapy in the IMvigor210 cohort and GSE176307. These findings highlight the importance of CRGPI serving as a potential biomarker for both prognostic and immunotherapy for HCC patients. Generally, our results provide novel insights about cuproptosis into immune therapeutic strategies.
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Affiliation(s)
- Lei Ding
- The Second Department of General Surgery, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Wei Li
- The Second Department of General Surgery, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Jili Tu
- The Second Department of General Surgery, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Zhixing Cao
- Department of Pathology, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Jizheng Li
- The Second Department of General Surgery, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Haiming Cao
- The Second Department of General Surgery, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Junjie Liang
- The Second Department of General Surgery, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Yiming Liang
- The Second Department of General Surgery, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Qiangfeng Yu
- The Second Department of General Surgery, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China,*Correspondence: Qiangfeng Yu, ; Gencong Li,
| | - Gencong Li
- The Second Department of General Surgery, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China,*Correspondence: Qiangfeng Yu, ; Gencong Li,
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12
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Multi-Level Control of the ATM/ATR-CHK1 Axis by the Transcription Factor E4F1 in Triple-Negative Breast Cancer. Int J Mol Sci 2022; 23:ijms23169217. [PMID: 36012478 PMCID: PMC9409040 DOI: 10.3390/ijms23169217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/01/2022] Open
Abstract
E4F1 is essential for early embryonic mouse development and for controlling the balance between proliferation and survival of actively dividing cells. We previously reported that E4F1 is essential for the survival of murine p53-deficient cancer cells by controlling the expression of genes involved in mitochondria functions and metabolism, and in cell-cycle checkpoints, including CHEK1, a major component of the DNA damage and replication stress responses. Here, combining ChIP-Seq and RNA-Seq approaches, we identified the transcriptional program directly controlled by E4F1 in Human Triple-Negative Breast Cancer cells (TNBC). E4F1 binds and regulates a limited list of direct target genes (57 genes) in these cells, including the human CHEK1 gene and, surprisingly, also two other genes encoding post-transcriptional regulators of the ATM/ATR-CHK1 axis, namely, the TTT complex component TTI2 and the phosphatase PPP5C, that are essential for the folding and stability, and the signaling of ATM/ATR kinases, respectively. Importantly, E4F1 also binds the promoter of these genes in vivo in Primary Derived Xenograft (PDX) of human TNBC. Consequently, the protein levels and signaling of CHK1 but also of ATM/ATR kinases are strongly downregulated in E4F1-depleted TNBC cells resulting in a deficiency of the DNA damage and replicative stress response in these cells. The E4F1-depleted cells fail to arrest into S-phase upon treatment with the replication-stalling agent Gemcitabine, and are highly sensitized to this drug, as well as to other DNA-damaging agents, such as Cisplatin. Altogether, our data indicate that in breast cancer cells the ATM/ATR-CHK1 signaling pathway and DNA damage-stress response are tightly controlled at the transcriptional and post-transcriptional level by E4F1.
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13
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Zhao J, Guo S, Schrodi SJ, He D. Cuproptosis and cuproptosis-related genes in rheumatoid arthritis: Implication, prospects, and perspectives. Front Immunol 2022; 13:930278. [PMID: 35990673 PMCID: PMC9386151 DOI: 10.3389/fimmu.2022.930278] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/18/2022] [Indexed: 11/14/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease that severely affects patients' physical and mental health, leading to chronic synovitis and destruction of bone joints. Although various available clinical treatment options exist, patients respond with varying efficacies due to multiple factors, and there is an urgent need to discover new treatment options to improve clinical outcomes. Cuproptosis is a newly characterized form of cell death. Copper causes cuproptosis by binding to lipid-acylated components of the tricarboxylic acid cycle, leading to protein aggregation, loss of iron-sulfur cluster proteins, and eventually proteotoxic stress. Targeting copper cytotoxicity and cuproptosis are considered potential options for treating oncological diseases. The synovial hypoxic environment and the presence of excessive glycolysis in multiple cells appear to act as inhibitors of cuproptosis, which can lead to excessive survival and proliferation of multiple immune cells, such as fibroblast-like synoviocytes, effector T cells, and macrophages, further mediating inflammation and bone destruction in RA. Therefore, in this study, we attempted to elaborate and summarize the linkage of cuproptosis and key genes regulating cuproptosis to the pathological mechanisms of RA and their effects on a variety of immune cells. This study aimed to provide a theoretical basis and support for translating preclinical and experimental results of RA to clinical protocols.
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Affiliation(s)
- Jianan Zhao
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Shicheng Guo
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, United States,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States,*Correspondence: Shicheng Guo, ; Steven J. Schrodi, ; Dongyi He,
| | - Steven J. Schrodi
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, United States,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States,*Correspondence: Shicheng Guo, ; Steven J. Schrodi, ; Dongyi He,
| | - Dongyi He
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China,*Correspondence: Shicheng Guo, ; Steven J. Schrodi, ; Dongyi He,
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14
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Gokcan H, Bedoyan JK, Isayev O. Simulations of Pathogenic E1α Variants: Allostery and Impact on Pyruvate Dehydrogenase Complex-E1 Structure and Function. J Chem Inf Model 2022; 62:3463-3475. [PMID: 35797142 DOI: 10.1021/acs.jcim.2c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyruvate dehydrogenase complex (PDC) deficiency is a major cause of primary lactic acidemia resulting in high morbidity and mortality, with limited therapeutic options. The E1 component of the mitochondrial multienzyme PDC (PDC-E1) is a symmetric dimer of heterodimers (αβ/α'β') encoded by the PDHA1 and PDHB genes, with two symmetric active sites each consisting of highly conserved phosphorylation loops A and B. PDHA1 mutations are responsible for 82-88% of cases. Greater than 85% of E1α residues with disease-causing missense mutations (DMMs) are solvent-inaccessible, with ∼30% among those involved in subunit-subunit interface contact (SSIC). We performed molecular dynamics simulations of wild-type (WT) PDC-E1 and E1 variants with E1α DMMs at R349 and W185 (residues involved in SSIC), to investigate their impact on human PDC-E1 structure. We evaluated the change in E1 structure and dynamics and examined their implications on E1 function with the specific DMMs. We found that the dynamics of phosphorylation Loop A, which is crucial for E1 biological activity, changes with DMMs that are at least about 15 Å away. Because communication is essential for PDC-E1 activity (with alternating active sites), we also investigated the possible communication network within WT PDC-E1 via centrality analysis. We observed that DMMs altered/disrupted the communication network of PDC-E1. Collectively, these results indicate allosteric effect in PDC-E1, with implications for the development of novel small-molecule therapeutics for specific recurrent E1α DMMs such as replacements of R349 responsible for ∼10% of PDC deficiency due to E1α DMMs.
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Affiliation(s)
- Hatice Gokcan
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jirair K Bedoyan
- Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224, United States.,Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, United States
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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15
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RALY regulate the proliferation and expression of immune/inflammatory response genes via alternative splicing of FOS. Genes Immun 2022; 23:246-254. [PMID: 35941292 PMCID: PMC9758052 DOI: 10.1038/s41435-022-00178-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Abstract
RALY is a multifunctional RNA-binding protein involved in cancer metastasis, prognosis, and chemotherapy resistance in various cancers. However, the molecular mechanism of which is still unclear. We have established RALY overexpression cell lines and studied the effect of RALY on proliferation and apoptosis in HeLa cells. Then we used RNA-seq to analyze the transcriptomes data. Lastly, RT-qPCR experiments had performed to confirm the RNA-seq results. We found that the overexpression of RALY in HeLa cells inhibited proliferation. Moreover, the overexpression of RALY changed the gene expression profile, and the significant upregulation of genes involved immune/inflammatory response related biological process by NOD-like receptor signaling pathway cytokine-cytokine receptor interaction. The significant downregulation genes involved innate immune response by the Primary immunodeficiency pathway. Notably, IFIT1, IFIT2, IFTI3, IFI44, HERC4, and OASL expression had inhibited by the overexpression of RALY. Furthermore, RALY negatively regulates the expression of transcription factors FOS and FOSB. Notably, we found that 645 alternative splicing events had regulated by overexpression of RALY, which is highly enriched in transcription regulation, RNA splicing, and cell proliferation biological process by the metabolic pathway. We show that RALY regulates the expression of immune/inflammatory response-related genes via alternative splicing of FOS in HeLa cells. The novel role of RALY in regulating immune/inflammatory gene expression may explain its function in regulating chemotherapy resistance and provides novel insights into further exploring the molecular mechanism of RALY in regulating cancer immunity and chemo/immune therapies.
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16
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Lacroix M, Linares LK, Rueda-Rincon N, Bloch K, Di Michele M, De Blasio C, Fau C, Gayte L, Blanchet E, Mairal A, Derua R, Cardona F, Beuzelin D, Annicotte JS, Pirot N, Torro A, Tinahones FJ, Bernex F, Bertrand-Michel J, Langin D, Fajas L, Swinnen JV, Le Cam L. The multifunctional protein E4F1 links P53 to lipid metabolism in adipocytes. Nat Commun 2021; 12:7037. [PMID: 34857760 PMCID: PMC8639890 DOI: 10.1038/s41467-021-27307-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/12/2021] [Indexed: 01/20/2023] Open
Abstract
Growing evidence supports the importance of the p53 tumor suppressor in metabolism but the mechanisms underlying p53-mediated control of metabolism remain poorly understood. Here, we identify the multifunctional E4F1 protein as a key regulator of p53 metabolic functions in adipocytes. While E4F1 expression is upregulated during obesity, E4f1 inactivation in mouse adipose tissue results in a lean phenotype associated with insulin resistance and protection against induced obesity. Adipocytes lacking E4F1 activate a p53-dependent transcriptional program involved in lipid metabolism. The direct interaction between E4F1 and p53 and their co-recruitment to the Steaoryl-CoA Desaturase-1 locus play an important role to regulate monounsaturated fatty acids synthesis in adipocytes. Consistent with the role of this E4F1-p53-Steaoryl-CoA Desaturase-1 axis in adipocytes, p53 inactivation or diet complementation with oleate partly restore adiposity and improve insulin sensitivity in E4F1-deficient mice. Altogether, our findings identify a crosstalk between E4F1 and p53 in the control of lipid metabolism in adipocytes that is relevant to obesity and insulin resistance.
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Affiliation(s)
- Matthieu Lacroix
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.,Equipe labélisée Ligue Contre le Cancer, Paris, France
| | - Laetitia K Linares
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.,Equipe labélisée Ligue Contre le Cancer, Paris, France
| | - Natalia Rueda-Rincon
- KU Leuven-University of Leuven, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
| | - Katarzyna Bloch
- KU Leuven-University of Leuven, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
| | - Michela Di Michele
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.,Equipe labélisée Ligue Contre le Cancer, Paris, France
| | - Carlo De Blasio
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.,Equipe labélisée Ligue Contre le Cancer, Paris, France
| | - Caroline Fau
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.,Equipe labélisée Ligue Contre le Cancer, Paris, France
| | - Laurie Gayte
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.,Equipe labélisée Ligue Contre le Cancer, Paris, France
| | - Emilie Blanchet
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Aline Mairal
- I2MC, Institute of Metabolic and Cardiovascular Diseases, Université de Toulouse, INSERM, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Rita Derua
- KU Leuven-University of Leuven, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Fernando Cardona
- Department of Surgical Specialties, Biochemistry and Immunology School of Medicine, University of Malaga, Malaga, Spain
| | - Diane Beuzelin
- I2MC, Institute of Metabolic and Cardiovascular Diseases, Université de Toulouse, INSERM, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Jean-Sebastien Annicotte
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, Lille, France
| | - Nelly Pirot
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.,BioCampus, RHEM, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Adeline Torro
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Francisco J Tinahones
- CIBER of Physiopathology, Obesity and Nutrition (CIBEROBN), Málaga, Spain; Unidad de Gestion Clinica de Endocrinologia y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clinico Virgen de la Victoria, Málaga, Spain
| | - Florence Bernex
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.,BioCampus, RHEM, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Justine Bertrand-Michel
- I2MC, Institute of Metabolic and Cardiovascular Diseases, Université de Toulouse, INSERM, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Dominique Langin
- I2MC, Institute of Metabolic and Cardiovascular Diseases, Université de Toulouse, INSERM, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France.,Toulouse University Hospitals, Department of Clinical Biochemistry, Toulouse, France
| | - Lluis Fajas
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Johannes V Swinnen
- KU Leuven-University of Leuven, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
| | - Laurent Le Cam
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Univ Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France. .,Equipe labélisée Ligue Contre le Cancer, Paris, France.
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17
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Lahalle A, Lacroix M, De Blasio C, Cissé MY, Linares LK, Le Cam L. The p53 Pathway and Metabolism: The Tree That Hides the Forest. Cancers (Basel) 2021; 13:cancers13010133. [PMID: 33406607 PMCID: PMC7796211 DOI: 10.3390/cancers13010133] [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] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The p53 pathway is a major tumor suppressor pathway that prevents the propagation of abnormal cells by regulating DNA repair, cell cycle progression, cell death, or senescence. The multiple cellular processes regulated by p53 were more recently extended to the control of metabolism, and many studies support the notion that perturbations of p53-associated metabolic activities are linked to cancer development. Converging lines of evidence support the notion that, in addition to p53, other key components of this molecular cascade are also important regulators of metabolism. Here, we illustrate the underestimated complexity of the metabolic network controlled by the p53 pathway and show how its perturbation contributes to human diseases including cancer, aging, and metabolic diseases. Abstract The p53 pathway is functionally inactivated in most, if not all, human cancers. The p53 protein is a central effector of numerous stress-related molecular cascades. p53 controls a safeguard mechanism that prevents accumulation of abnormal cells and their transformation by regulating DNA repair, cell cycle progression, cell death, or senescence. The multiple cellular processes regulated by p53 were more recently extended to the control of metabolism and many studies support the notion that perturbations of p53-associated metabolic activities are linked to cancer development, as well as to other pathophysiological conditions including aging, type II diabetes, and liver disease. Although much less documented than p53 metabolic activities, converging lines of evidence indicate that other key components of this tumor suppressor pathway are also involved in cellular metabolism through p53-dependent as well as p53-independent mechanisms. Thus, at least from a metabolic standpoint, the p53 pathway must be considered as a non-linear pathway, but the complex metabolic network controlled by these p53 regulators and the mechanisms by which their activities are coordinated with p53 metabolic functions remain poorly understood. In this review, we highlight some of the metabolic pathways controlled by several central components of the p53 pathway and their role in tissue homeostasis, metabolic diseases, and cancer.
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Affiliation(s)
- Airelle Lahalle
- Université de Montpellier, F-34090 Montpellier, France; (A.L.); (M.L.); (C.D.B.); (L.K.L.)
- IRCM, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, F-34298 Montpellier, France
- INSERM, Institut National de la Santé et de la Recherche Médicale, U1194, F-24298 Montpellier, France
- Equipe Labellisée Ligue Contre le Cancer, F-75013 Paris, France
| | - Matthieu Lacroix
- Université de Montpellier, F-34090 Montpellier, France; (A.L.); (M.L.); (C.D.B.); (L.K.L.)
- IRCM, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, F-34298 Montpellier, France
- INSERM, Institut National de la Santé et de la Recherche Médicale, U1194, F-24298 Montpellier, France
- Equipe Labellisée Ligue Contre le Cancer, F-75013 Paris, France
| | - Carlo De Blasio
- Université de Montpellier, F-34090 Montpellier, France; (A.L.); (M.L.); (C.D.B.); (L.K.L.)
- IRCM, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, F-34298 Montpellier, France
- INSERM, Institut National de la Santé et de la Recherche Médicale, U1194, F-24298 Montpellier, France
- Equipe Labellisée Ligue Contre le Cancer, F-75013 Paris, France
| | - Madi Y. Cissé
- Department of Molecular Metabolism, Harvard, T.H Chan School of Public Health, Boston, MA 02115, USA;
| | - Laetitia K. Linares
- Université de Montpellier, F-34090 Montpellier, France; (A.L.); (M.L.); (C.D.B.); (L.K.L.)
- IRCM, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, F-34298 Montpellier, France
- INSERM, Institut National de la Santé et de la Recherche Médicale, U1194, F-24298 Montpellier, France
| | - Laurent Le Cam
- Université de Montpellier, F-34090 Montpellier, France; (A.L.); (M.L.); (C.D.B.); (L.K.L.)
- IRCM, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, F-34298 Montpellier, France
- INSERM, Institut National de la Santé et de la Recherche Médicale, U1194, F-24298 Montpellier, France
- Equipe Labellisée Ligue Contre le Cancer, F-75013 Paris, France
- Correspondence:
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E4 Transcription Factor 1 (E4F1) Regulates Sertoli Cell Proliferation and Fertility in Mice. Animals (Basel) 2020; 10:ani10091691. [PMID: 32962114 PMCID: PMC7552733 DOI: 10.3390/ani10091691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Male fertility relies on the generation of functional sperm in seminiferous tubules of the testis. In mammals, Sertoli cells are the only somatic cells that directly interact with spermatogenic cells. Compelling evidences suggest that the number of Sertoli cells determines testis size and sperm output, however, molecular mechanisms regulating Sertoli cell proliferation and maturation are not well-understood. Using a Sertoli cell specific loss-of-function approach, here we showed that transcription factor E4F1 played an important role in murine Sertoli cell proliferation. Compared with their littermate control, E4f1 conditional knockout male mice sired a significantly low number of pups. E4f1 deletion resulted in reduced Sertoli cell number and testis size. Further analyses revealed that E4f1 deletion affected Sertoli cell proliferation in the neonatal testis and caused an increase in apoptosis of spermatogenic cells without affecting normal development of spermatogonia, meiotic and post-meiotic germ cells. These findings have shed new light on molecular controlling of spermatogenesis in mice and a similar mechanism likely exists in other animals. Abstract In the mammalian testes, Sertoli cells are the only somatic cells in the seminiferous tubules that provide structural, nutritional and regulatory support for developing spermatogenic cells. Sertoli cells only proliferate during the fetal and neonatal periods and enter a quiescent state after puberty. Functional evidences suggest that the size of Sertoli cell population determines sperm production and fertility. However, factors that direct Sertoli cell proliferation and maturation are not fully understood. Transcription factor E4F1 is a multifunctional protein that serves essential roles in cell fate decisions and because it interacts with pRB, a master regulator of Sertoli cell function, we hypothesized that E4F1 may have a functional role in Sertoli cells. E4f1 mRNA was present in murine testis and immunohistochemical staining confirmed that E4F1 was enriched in mature Sertoli cells. We generated a conditional knockout mouse model using Amh-cre and E4f1flox/flox lines to study E4F1 fucntion in Sertoli cells and the results showed that E4f1 deletion caused a significant reduction in testis size and fertility. Further analyses revealed that meiosis progression and spermiogenesis were normal, however, Sertoli cell proliferation was impaired and germ cell apoptosis was elevated in the testis of E4f1 conditional knockout mice. On the basis of these findings, we concluded that E4F1 was expressed in murine Sertoli cells and served important functions in regulating Sertoli cell proliferation and fertility.
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Buchanan JL, Taylor EB. Mitochondrial Pyruvate Carrier Function in Health and Disease across the Lifespan. Biomolecules 2020; 10:biom10081162. [PMID: 32784379 PMCID: PMC7464753 DOI: 10.3390/biom10081162] [Citation(s) in RCA: 13] [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: 07/18/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 12/25/2022] Open
Abstract
As a nodal mediator of pyruvate metabolism, the mitochondrial pyruvate carrier (MPC) plays a pivotal role in many physiological and pathological processes across the human lifespan, from embryonic development to aging-associated neurodegeneration. Emerging research highlights the importance of the MPC in diverse conditions, such as immune cell activation, cancer cell stemness, and dopamine production in Parkinson’s disease models. Whether MPC function ameliorates or contributes to disease is highly specific to tissue and cell type. Cell- and tissue-specific differences in MPC content and activity suggest that MPC function is tightly regulated as a mechanism of metabolic, cellular, and organismal control. Accordingly, recent studies on cancer and diabetes have identified protein–protein interactions, post-translational processes, and transcriptional factors that modulate MPC function. This growing body of literature demonstrates that the MPC and other mitochondrial carriers comprise a versatile and dynamic network undergirding the metabolism of health and disease.
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Affiliation(s)
- Jane L. Buchanan
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA;
| | - Eric B. Taylor
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA;
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
- Fraternal Order of Eagles Diabetes Research Center (FOEDRC), University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
- Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
- Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
- Correspondence:
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20
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Rooney RJ. Multiple domains in the 50 kDa form of E4F1 regulate promoter-specific repression and E1A trans-activation. Gene 2020; 754:144882. [PMID: 32535047 DOI: 10.1016/j.gene.2020.144882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/25/2020] [Accepted: 06/06/2020] [Indexed: 11/28/2022]
Abstract
The 50 kDa N-terminal product of the cellular transcription factor E4F1 (p50E4F1) mediates E1A289R trans-activation of the adenovirus E4 gene, and suppresses E1A-mediated transformation by sensitizing cells to cell death. This report shows that while both E1A289R and E1A243R stimulate p50E4F1 DNA binding activity, E1A289R trans-activation, as measured using GAL-p50E4F1 fusion proteins, involves a p50E4F1 transcription regulatory (TR) region that must be promoter-bound and is dependent upon E1A CR3, CR1 and N-terminal domains. Trans-activation is promoter-specific, as GAL-p50E4F1 did not stimulate commonly used artificial promoters and was strongly repressive when competing against GAL-VP16. p50E4F1 and E1A289R stably associate in vivo using the p50E4F1 TR region and E1A CR3, although their association in vitro is indirect and paradoxically disrupted by MAP kinase phosphorylation of E1A289R, which stimulates E4 trans-activation in vivo. Multiple cellular proteins, including TBP, bind the p50E4F1 TR region in vitro. The mechanistic implications for p50E4F1 function are discussed.
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Affiliation(s)
- Robert J Rooney
- Department of Genetics, Duke University Medical Center, Durham, NC, USA.
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Popov DV, Makhnovskii PA, Shagimardanova EI, Gazizova GR, Lysenko EA, Gusev OA, Vinogradova OL. Contractile activity-specific transcriptome response to acute endurance exercise and training in human skeletal muscle. Am J Physiol Endocrinol Metab 2019; 316:E605-E614. [PMID: 30779632 DOI: 10.1152/ajpendo.00449.2018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Reduction in daily activity leads to dramatic metabolic disorders, while regular aerobic exercise training is effective for preventing this problem. The purpose of this study was to identify genes that are directly related to contractile activity in human skeletal muscle, regardless of the level of fitness. Transcriptome changes after the one-legged knee extension exercise in exercised and contralateral nonexercised vastus lateralis muscle of seven men were evaluated by RNA-seq. Transcriptome change at baseline after 2 mo of aerobic training (5/wk, 1 h/day) was evaluated as well. Postexercise changes in the transcriptome of exercised muscle were associated with different factors, including circadian oscillations. To reveal transcriptome response specific for endurance-like contractile activity, differentially expressed genes between exercised and nonexercised muscle were evaluated at 1 and 4 h after the one-legged exercise. The contractile activity-specific transcriptome responses were associated only with an increase in gene expression and were regulated mainly by CREB/ATF/AP1-, MYC/MAX-, and E2F-related transcription factors. Endurance training-induced changes (an increase or decrease) in the transcriptome at baseline were more pronounced than transcriptome responses specific for acute contractile activity. Changes after training were associated with widely different biological processes than those after acute exercise and were regulated by different transcription factors (IRF- and STAT-related factors). In conclusion, adaptation to regular exercise is associated not only with a transient (over several hours) increase in expression of many contractile activity-specific genes, but also with a pronounced change (an increase or decrease) in expression of a large number of genes under baseline conditions.
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Affiliation(s)
- Daniil V Popov
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences , Moscow , Russia
- Faculty of Fundamental Medicine, M. V. Lomonosov Moscow State University , Moscow , Russia
| | - Pavel A Makhnovskii
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences , Moscow , Russia
| | - Elena I Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University , Kazan , Russia
| | - Guzel R Gazizova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University , Kazan , Russia
| | - Evgeny A Lysenko
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences , Moscow , Russia
- Faculty of Fundamental Medicine, M. V. Lomonosov Moscow State University , Moscow , Russia
| | - Oleg A Gusev
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University , Kazan , Russia
- Cluster for Science, Technology and Innovation Hub, RIKEN, Wako , Japan
| | - Olga L Vinogradova
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences , Moscow , Russia
- Faculty of Fundamental Medicine, M. V. Lomonosov Moscow State University , Moscow , Russia
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Dietary butyrate glycerides modulate intestinal microbiota composition and serum metabolites in broilers. Sci Rep 2018; 8:4940. [PMID: 29563518 PMCID: PMC5862971 DOI: 10.1038/s41598-018-22565-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/13/2018] [Indexed: 12/21/2022] Open
Abstract
Butyrate can modulate the immune response and energy expenditure of animals and enhance intestinal health. The present study investigated changes in the intestinal microbiota composition and serum metabolites of young broilers in response to 3,000 ppm butyrate in the form of butyrate glycerides (BG) via pyrosequencing of bacterial 16S rRNA genes and nuclear magnetic resonance (NMR). The dietary treatment did not affect the alpha diversity of intestinal microbiota, but altered its composition. Thirty-nine key operational taxonomic units (OTUs) in differentiating cecal microbiota community structures between BG treated and untreated chickens were also identified. Bifidobacterium was, in particular, affected by the dietary treatment significantly, showing an increase in not only the abundance (approximately 3 fold, P ≤ 0.05) but also the species diversity. The (NMR)-based analysis revealed an increase in serum concentrations of alanine, low-density and very low-density lipoproteins, and lipids (P ≤ 0.05) by BG. More interestingly, the dietary treatment also boosted (P ≤ 0.05) serum concentrations of bacterial metabolites, including choline, glycerophosphorylcholine, dimethylamine, trimethylamine, trimethylamine-N-oxide, lactate, and succinate. In conclusion, the data suggest the modulation of intestinal microbiota and serum metabolites by BG dietary treatment and potential contribution of intestinal bacteria to lipid metabolism/energy homeostasis in broilers.
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E4F1-mediated control of pyruvate dehydrogenase activity is essential for skin homeostasis. Proc Natl Acad Sci U S A 2016; 113:11004-9. [PMID: 27621431 DOI: 10.1073/pnas.1602751113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The multifunctional protein E4 transcription factor 1 (E4F1) is an essential regulator of epidermal stem cell (ESC) maintenance. Here, we found that E4F1 transcriptionally regulates a metabolic program involved in pyruvate metabolism that is required to maintain skin homeostasis. E4F1 deficiency in basal keratinocytes resulted in deregulated expression of dihydrolipoamide acetyltransferase (Dlat), a gene encoding the E2 subunit of the mitochondrial pyruvate dehydrogenase (PDH) complex. Accordingly, E4f1 knock-out (KO) keratinocytes exhibited impaired PDH activity and a redirection of the glycolytic flux toward lactate production. The metabolic reprogramming of E4f1 KO keratinocytes associated with remodeling of their microenvironment and alterations of the basement membrane, led to ESC mislocalization and exhaustion of the ESC pool. ShRNA-mediated depletion of Dlat in primary keratinocytes recapitulated defects observed upon E4f1 inactivation, including increased lactate secretion, enhanced activity of extracellular matrix remodeling enzymes, and impaired clonogenic potential. Altogether, our data reveal a central role for Dlat in the metabolic program regulated by E4F1 in basal keratinocytes and illustrate the importance of PDH activity in skin homeostasis.
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