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Church MC, Workman JL. The SWI/SNF chromatin remodeling complex: a critical regulator of metabolism. Biochem Soc Trans 2024; 52:1327-1337. [PMID: 38666605 DOI: 10.1042/bst20231141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
The close relationship between chromatin and metabolism has been well-studied in recent years. Many metabolites have been found to be cofactors used to modify chromatin, and these modifications can in turn affect gene transcription. One chromatin-associated factor responsible for regulating transcription is the SWI/SNF complex, an ATP-dependent chromatin remodeler conserved throughout eukaryotes. SWI/SNF was originally described in yeast as regulating genes involved in carbon source metabolism and mating type switching, and its mammalian counterpart has been extensively studied for its role in diseases such as cancer. The yeast SWI/SNF complex is closely associated with activation of stress response genes, many of which have metabolic functions. It is now recognized that this is a conserved function of the complex, and recent work has shown that mammalian SWI/SNF is also a key regulator of metabolic transcription. Emerging evidence suggests that loss of SWI/SNF introduces vulnerabilities to cells due to this metabolic influence, and that this may present opportunities for treatment of SWI/SNF-deficient cancers.
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Affiliation(s)
- Michael C Church
- Stowers Institute of Medical Research, 1000 E 50th Street, Kansas City, MO 64118, U.S.A
| | - Jerry L Workman
- Stowers Institute of Medical Research, 1000 E 50th Street, Kansas City, MO 64118, U.S.A
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2
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Xi Y, Abuduxiku M, Qu M. GRN knockdown regulates the expression and alternative splicing of genes associated with aphasia-related diseases in PC12 cells. Brain Res 2024; 1840:149031. [PMID: 38823507 DOI: 10.1016/j.brainres.2024.149031] [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: 01/16/2024] [Revised: 05/15/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Prior research has shown that granulin precursor (GRN, also termed PGRN) is closely linked to aphasia. However, there has been little research on the mechanism of action of GRN in post-stroke aphasia (PSA). METHODS In this study, RT-qPCR was used to identify variations in gene expression, while RNA sequencing (RNA-seq) was utilized to acquire transcriptional profiles. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were employed for bioinformatics analysis. RESULTS GRN was considerably more active in PSA subjects. After silencing the GRN, 197 transcripts had differential expression, and 237 alternative splicing events (ASEs) were substantially affected. The analysis of differentially expressed genes (DEGs) using GO and KEGG approaches showed that these genes have various molecular functions and are significantly enriched in metabolic signaling pathways. Regarding Alternative Splicing (AS), the GO and KEGG analyses revealed numerous functional genes involved in transcription and metabolism. CONCLUSIONS The knockdown of GRN has been shown to be associated with alterations in transcription, metabolism, and ASEs, potentially impacting transcriptional and metabolic pathways through its involvement in AS. Furthermore, GRN knockdown is associated with nervous system disease-related gene transcription and AS processes, as well as its involvement in G protein-coupled receptor (GPCR) and wingless/integrated (Wnt) signaling pathways, which impact the initiation and resolution of PSA.
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Affiliation(s)
- Yanling Xi
- Department of Rehabilitation Medicine, Shanghai Pudong New Area Guangming Hospital of Traditional Chinese Medicine, China
| | - Munire Abuduxiku
- Department of Rehabilitation Medicine, The Affiliated Hospital of Traditional Chinese Medicine of Xinjiang Medical University, China
| | - Mei Qu
- Department of Rehabilitation Medicine, Shanghai Pudong New Area Guangming Hospital of Traditional Chinese Medicine, China.
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3
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Singh AK, Allington G, Viviano S, McGee S, Kiziltug E, Ma S, Zhao S, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus. Brain 2024; 147:1553-1570. [PMID: 38128548 PMCID: PMC10994532 DOI: 10.1093/brain/awad405] [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: 04/28/2023] [Revised: 10/01/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023] Open
Abstract
Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery in children. Recent studies have implicated SMARCC1, a component of the BRG1-associated factor (BAF) chromatin remodelling complex, as a candidate congenital hydrocephalus gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, congenital hydrocephalus-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo. Here, we aimed to assess the prevalence of SMARCC1 variants in an expanded patient cohort, describe associated clinical and radiographic phenotypes, and assess the impact of Smarcc1 depletion in a novel Xenopus tropicalis model of congenital hydrocephalus. To do this, we performed a genetic association study using whole-exome sequencing from a cohort consisting of 2697 total ventriculomegalic trios, including patients with neurosurgically-treated congenital hydrocephalus, that total 8091 exomes collected over 7 years (2016-23). A comparison control cohort consisted of 1798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents were sourced from the Simons Simplex Collection. Enrichment and impact on protein structure were assessed in identified variants. Effects on the human fetal brain transcriptome were examined with RNA-sequencing and Smarcc1 knockdowns were generated in Xenopus and studied using optical coherence tomography imaging, in situ hybridization and immunofluorescence. SMARCC1 surpassed genome-wide significance thresholds, yielding six rare, protein-altering de novo variants localized to highly conserved residues in key functional domains. Patients exhibited hydrocephalus with aqueductal stenosis; corpus callosum abnormalities, developmental delay, and cardiac defects were also common. Xenopus knockdowns recapitulated both aqueductal stenosis and cardiac defects and were rescued by wild-type but not patient-specific variant SMARCC1. Hydrocephalic SMARCC1-variant human fetal brain and Smarcc1-variant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2. These results suggest de novo variants in SMARCC1 cause a novel human BAFopathy we term 'SMARCC1-associated developmental dysgenesis syndrome', characterized by variable presence of cerebral ventriculomegaly, aqueductal stenosis, developmental delay and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodelling complex for human brain morphogenesis and provide evidence for a 'neural stem cell' paradigm of congenital hydrocephalus pathogenesis. These results highlight utility of trio-based whole-exome sequencing for identifying pathogenic variants in sporadic congenital structural brain disorders and suggest whole-exome sequencing may be a valuable adjunct in clinical management of congenital hydrocephalus patients.
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Affiliation(s)
- Amrita K Singh
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Garrett Allington
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Genetics, Yale University, New Haven, CT 06510, USA
| | - Stephen Viviano
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | | | - Emre Kiziltug
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shaojie Ma
- Department of Genetics, Yale University, New Haven, CT 06510, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Shujuan Zhao
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Departments of Genetics and Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Kedous Y Mekbib
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John P Shohfi
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Phan Q Duy
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Charuta G Furey
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - Benjamin C Reeves
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah Smith
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - André M M Sousa
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Adriana Cherskov
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - August Allocco
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | | | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
- UCL Centre for Advanced Research Computing, University College London, London, WC1H 9RN, UK
| | - Syed R A Rizvi
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
| | - Seth L Alper
- Division of Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nenad Sestan
- Department of Genetics, Yale University, New Haven, CT 06510, USA
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Hermela Shimelis
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Lauren K Walsh
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Andres Moreno-De-Luca
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
- Department of Radiology, Diagnostic Medicine Institute, Geisinger, Danville, PA, 17822, USA
| | - Sheng Chih Jin
- Departments of Genetics and Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | | | - Engin Deniz
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
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4
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Yuan B, Wang WB, Wang YT, Zhao XQ. Regulatory mechanisms underlying yeast chemical stress response and development of robust strains for bioproduction. Curr Opin Biotechnol 2024; 86:103072. [PMID: 38330874 DOI: 10.1016/j.copbio.2024.103072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/10/2024]
Abstract
Yeast is widely studied in producing biofuels and biochemicals using renewable biomass. Among various yeasts, Saccharomyces cerevisiae has been particularly recognized as an important yeast cell factory. However, economic bioproduction using S. cerevisiae is challenged by harsh environments during fermentation, among which inhibitory chemicals in the culture media or toxic products are common experiences. Understanding the stress-responsive mechanisms is conducive to developing robust yeast strains. Here, we review recent progress in mechanisms underlying yeast stress response, including regulation of cell wall integrity, membrane transport, antioxidative system, and gene transcription. We highlight epigenetic regulation of stress response and summarize manipulation of yeast stress tolerance for improved bioproduction. Prospects in the application of machine learning to improve production efficiency are also discussed.
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Affiliation(s)
- Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ya-Ting Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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5
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Zhang MM, Yuan B, Wang YT, Zhang FL, Liu CG, Zhao XQ. Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance. J Proteome Res 2024. [PMID: 38396335 DOI: 10.1021/acs.jproteome.3c00617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Acetic acid is a prevalent inhibitor in lignocellulosic hydrolysate, which represses microbial growth and bioproduction. Histone modification and chromatin remodeling have been revealed to be critical for regulating eukaryotic metabolism. However, related studies in chronic acetic acid stress responses remain unclear. Our previous studies revealed that overexpression of the histone H4 methyltransferase Set5p enhanced acetic acid stress tolerance of the budding yeast Saccharomyces cerevisiae. In this study, we examined the role of Set5p in acetic acid stress by analyzing global protein expression. Significant activation of intracellular protein expression under the stress was discovered, and the functions of the differential proteins were mainly involved in chromatin modification, signal transduction, and carbohydrate metabolism. Notably, a substantial increase of Set5p expression was observed in response to acetic acid stress. Functional studies demonstrated that the restriction of the telomere capping protein Rtc3p, as well as Ies3p and Taf14p, which are related to chromatin regulation, was critical for yeast stress response. This study enriches the understanding of the epigenetic regulatory mechanisms underlying yeast stress response mediated by histone-modifying enzymes. The results also benefit the development of robust yeast strains for lignocellulosic bioconversion.
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Affiliation(s)
- Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ya-Ting Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng-Li Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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6
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Li J, Hou W, Zhao Q, Han W, Cui H, Xiao S, Zhu L, Qu J, Liu X, Cong W, Shen J, Zhao Y, Gao S, Huang G, Kong Q. Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals. Natl Sci Rev 2024; 11:nwad295. [PMID: 38327665 PMCID: PMC10849771 DOI: 10.1093/nsr/nwad295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 11/04/2023] [Accepted: 11/13/2023] [Indexed: 02/09/2024] Open
Abstract
Lactate is present at a high level in the microenvironment of mammalian preimplantation embryos in vivo and in vitro. However, its role in preimplantation development is unclear. Here, we report that lactate is highly enriched in the nuclei of early embryos when major zygotic genome activation (ZGA) occurs in humans and mice. The inhibition of its production and uptake results in developmental arrest at the 2-cell stage, major ZGA failure, and loss of lactate-derived H3K18lac, which could be rescued by the addition of Lac-CoA and recapitulated by overexpression of H3K18R mutation. By profiling the landscape of H3K18lac during mouse preimplantation development, we show that H3K18lac is enriched on the promoter regions of most major ZGA genes and correlates with their expressions. In humans, H3K18lac is also enriched in ZGA markers and temporally concomitant with their expressions. Taken together, we profile the landscapes of H3K18lac in mouse and human preimplantation embryos, and demonstrate the important role for H3K18lac in major ZGA, showing that a conserved metabolic mechanism underlies preimplantation development of mammalian embryos.
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Affiliation(s)
- Jingyu Li
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Weibo Hou
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Qi Zhao
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Wei Han
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Hongdi Cui
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Songling Xiao
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Ling Zhu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Jiadan Qu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Xiaoyu Liu
- Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Weitao Cong
- School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Jingling Shen
- Institute of Life Sciences, College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 2000237, China
| | - Shaorong Gao
- Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Guoning Huang
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Qingran Kong
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
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7
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Chen Y, Fan C, Liu J. Investigating the shared genetic architecture between COVID-19 and obesity: a large-scale genome wide cross-trait analysis. Front Endocrinol (Lausanne) 2024; 15:1325939. [PMID: 38352709 PMCID: PMC10862482 DOI: 10.3389/fendo.2024.1325939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024] Open
Abstract
Observational studies have reported high comorbidity between obesity and severe COVID-19. The aim of this study is to explore whether genetic factors are involved in the co-occurrence of the two traits. Based on the available genome-wide association studies (GWAS) summary statistics, we explored the genetic correlation and performed cross-trait meta-analysis (CPASSOC) and colocalization analysis (COLOC) to detect pleiotropic single nucleotide polymorphisms (SNPs). At the genetic level, we obtained genes detected by Functional mapping and annotation (FUMA) and the Multi-marker Analysis of GenoMic Annotation (MAGMA). Potential functional genes were further investigated by summary-data-based Mendelian randomization (SMR). Finally, the casualty was identiied using the latent causal variable model (LCV). A significant positive genetic correlation was revealed between obesity and COVID-19. We found 331 shared genetic SNPs by CPASSOC and 13 shared risk loci by COLOC. At the genetic level, We obtained 3546 pleiotropic genes, among which 107 genes were found to be significantly expressed by SMR. Lastly, we observed these genes were mainly enriched in immune pathways and signaling transduction. These indings could provide new insights into the etiology of comorbidity and have implications for future therapeutic trial.
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Affiliation(s)
- Yanjing Chen
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunhua Fan
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun Liu
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Medical Imaging in Hunan Province, Changsha, Hunan, China
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8
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Tian Y, Lautrup S, Law PWN, Dinh ND, Fang EF, Chan WY. WRN loss accelerates abnormal adipocyte metabolism in Werner syndrome. Cell Biosci 2024; 14:7. [PMID: 38184705 PMCID: PMC10770995 DOI: 10.1186/s13578-023-01183-4] [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: 01/23/2023] [Accepted: 12/09/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND Metabolic dysfunction is one of the main symptoms of Werner syndrome (WS); however, the underlying mechanisms remain unclear. Here, we report that loss of WRN accelerates adipogenesis at an early stage both in vitro (stem cells) and in vivo (zebrafish). Moreover, WRN depletion causes a transient upregulation of late-stage of adipocyte-specific genes at an early stage. METHODS In an in vivo study, we generated wrn-/- mutant zebrafish and performed histological stain and Oil Red O staining to assess the fat metabolism. In an in vitro study, we used RNA-seq and ATAC-seq to profile the transcriptional features and chromatin accessibility in WRN depleted adipocytes. Moreover, we performed ChIP-seq to further study the regulatory mechanisms of metabolic dysfunction in WS. RESULTS Our findings show that mechanistically WRN deficiency causes SMARCA5 upregulation. SMARCA5 is crucial in chromatin remodeling and gene regulation. Additionally, rescuing WRN could normalize SMARCA5 expression and adipocyte differentiation. Moreover, we find that nicotinamide riboside (NR) supplementation restores adipocyte metabolism in both stem cells and zebrafish models. CONCLUSIONS Our findings unravel a new mechanism for the influence of WRN in the early stage of adipogenesis and provide a possible treatment for metabolic dysfunction in WS. These data provide promising insights into potential therapeutics for ageing and ageing-related diseases.
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Affiliation(s)
- Yuyao Tian
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Sofie Lautrup
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Patrick Wai Nok Law
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Ngoc-Duy Dinh
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Evandro Fei Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Wai-Yee Chan
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
- Hong Kong Branch CAS Center of Excellence for Animal Evolution and Genetics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
- CUHK-SDU University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
- MOE Key Laboratory of Regenerative Medicine (CUHK-Jinan University), The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
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9
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Kou F, Wu L, Zheng Y, Yi Y, Ji Z, Huang Z, Guo S, Yang L. HMGB1/SET/HAT1 complex-mediated SASH1 repression drives glycolysis and metastasis in lung adenocarcinoma. Oncogene 2023; 42:3407-3421. [PMID: 37794134 DOI: 10.1038/s41388-023-02850-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
High-mobility group box 1 (HMGB1) can enhance the stability and accessibility of nucleus binding sites to nucleosomes and transcription factors. Recently, HMGB1 has been recognized as a positive regulator of tumor glutamine, and its overexpression has been correlated with tumorigenesis and cancer progression. However, functions and mechanisms of HMGB1 in regulation of glycolysis during cancer progression in lung adenocarcinoma (LUAD) is still unclear. Here, we found that intracellular HMGB1 was consistently upregulated in LUAD specimens, and positively relevant to tumor grade and poor survival. HMGB1 facilitated glycolysis and promoted metastasis through physical interaction with SET and HAT1, forming HMGB1/SET/HAT1 complex that inhibited H3K9 and H3K27 acetylation in LUAD. The functional proteins complex coordinated histone modification to suppress the expression of SASH1, thus further facilitating glycolysis and inducing the metastasis in vitro and in vivo. Consistent with this, the expression of SASH1 was negatively correlated with HMGB1, SET and GLUT1, and positively correlated with HAT1 in human LUAD specimens. Clinically, LUAD patients with high expression of HMGB1 and low expression of SASH1 exhibited the worst clinical outcomes. Overall, the findings of this study revealed the critical role of HMGB1 in glycolysis and metastasis by attenuating H3K9ace and H3K27ace through physical interacted with SET and HAT1, which may facilitate future targeted therapies.
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Affiliation(s)
- Fan Kou
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Department of Interventional Pulmonology, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Lei Wu
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Cancer Center, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Yu Zheng
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Department of Clinical Pharmacology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yeran Yi
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Zhenyu Ji
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Ziqi Huang
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Shiwei Guo
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Lili Yang
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China.
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, China.
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.
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10
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Han S, Luo Y, Liu B, Guo T, Qin D, Luo F. Dietary flavonoids prevent diabetes through epigenetic regulation: advance and challenge. Crit Rev Food Sci Nutr 2023; 63:11925-11941. [PMID: 35816298 DOI: 10.1080/10408398.2022.2097637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The pathophysiology of diabetes has been studied extensively in various countries, but effective prevention and treatment methods are still insufficient. In recent years, epigenetics has received increasing attention from researchers in exploring the etiology and treatment of diabetes. DNA methylation, histone modifications, and non-coding RNAs play critical roles in the occurrence, maintenance, and progression of diabetes and its complications. Therefore, preventing or reversing the epigenetic alterations that occur during the development of diabetes may reduce the individual and societal burden of the disease. Dietary flavonoids serve as natural epigenetic modulators for the discovery of biomarkers for diabetes prevention and the development of alternative therapies. However, there is limited knowledge about the potential beneficial effects of flavonoids on the epigenetics of diabetes. In this review, the multidimensional epigenetic effects of different flavonoid subtypes in diabetes were summarized. Furthermore, it was discussed that parental flavonoid diets might reduce diabetes incidence in offspring, which represent a promising opportunity to prevent diabetes in the future. Future work will depend on exploring anti-diabetic effects of different flavonoids with different epigenetic regulation mechanisms and clinical trials.Highlights• "Epigenetic therapy" could reduce the burden of diabetic patients• "Epigenetic diet" ameliorates diabetes• Targeting epigenetic regulations by dietary flavonoids in the diabetes prevention• Dietary flavonoids prevent diabetes via transgenerational epigenetic inheritance.
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Affiliation(s)
- Shuai Han
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Research Center of Rice Deep Processing and Byproducts, Central South University of Forestry and Technology, Changsha, China
| | - Yi Luo
- Department of Clinic Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Bo Liu
- Central South Food Science Institute of Grain and Oil Co., Ltd., Hunan Grain Group Co., Ltd, Changsha, China
| | - Tianyi Guo
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Research Center of Rice Deep Processing and Byproducts, Central South University of Forestry and Technology, Changsha, China
| | - Dandan Qin
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Research Center of Rice Deep Processing and Byproducts, Central South University of Forestry and Technology, Changsha, China
| | - Feijun Luo
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Research Center of Rice Deep Processing and Byproducts, Central South University of Forestry and Technology, Changsha, China
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11
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Hwang Y, Yun HJ, Jeong JW, Kim M, Joo S, Lee HK, Chang HS, Kim SM, Fang S. Co-inhibition of glutaminolysis and one-carbon metabolism promotes ROS accumulation leading to enhancement of chemotherapeutic efficacy in anaplastic thyroid cancer. Cell Death Dis 2023; 14:515. [PMID: 37573361 PMCID: PMC10423221 DOI: 10.1038/s41419-023-06041-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/14/2023]
Abstract
Anaplastic thyroid cancer (ATC) is one of the most aggressive tumors with an extremely poor prognosis. Based on the several biological features related to glutamine metabolism in ATC, we hypothesized glutaminolysis inhibition induces cell death in ATC cells. However, glutamine metabolism inhibition triggered cell growth arrest independent of cell death in ATC, suggesting that other signaling pathways avoid glutamine metabolism inhibition-induced stress exist. To investigate the functional mechanism against glutamine metabolism inhibition, we conducted mRNA and ATAC-Sequencing data analysis and found that glutamine deprivation increased ATF4-mediated one-carbon metabolism. When we inhibited PHGDH, the first rate-limiting enzyme for one-carbon metabolism, cell growth arrest was promoted upon glutamine metabolism inhibition by accumulating intracellular ROS. We next observed that the co-inhibition of glutamine and one-carbon metabolism could augment the anticancer effects of drugs used in patients with ATC. Finally, single-cell RNA sequencing analysis revealed that one-carbon metabolism was strengthened through the evolutionary process from PTC to ATC. Collectively, our data demonstrate that one-carbon metabolism has a potential role of modulation of cell fate in metabolic stress and can be a therapeutic target for enhancing antitumor effects in ATC.
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Affiliation(s)
- Yeseong Hwang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Hyeok Jun Yun
- Department of Surgery, Thyroid Cancer Center, Institute of Refractory Thyroid Cancer, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Woong Jeong
- Department of Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Minki Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Seyeon Joo
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Hae-Kyung Lee
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hang-Seok Chang
- Department of Surgery, Thyroid Cancer Center, Institute of Refractory Thyroid Cancer, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seok-Mo Kim
- Department of Surgery, Thyroid Cancer Center, Institute of Refractory Thyroid Cancer, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
| | - Sungsoon Fang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea.
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
- Chronic Intractable Disease for Systems Medicine Research Center, Yonsei University College of Medicine, Seoul, Korea.
- Severance Institute for Vascular and Metabolic Research, Yonsei University College of Medicine, Seoul, Korea.
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12
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Menezes AP, Murillo AM, de Castro CG, Bellini NK, Tosi LRO, Thiemann OH, Elias MC, Silber AM, da Cunha JPC. Navigating the boundaries between metabolism and epigenetics in trypanosomes. Trends Parasitol 2023; 39:682-695. [PMID: 37349193 DOI: 10.1016/j.pt.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023]
Abstract
Epigenetic marks enable cells to acquire new biological features that favor their adaptation to environmental changes. These marks are chemical modifications on chromatin-associated proteins and nucleic acids that lead to changes in the chromatin landscape and may eventually affect gene expression. The chemical tags of these epigenetic marks are comprised of intermediate cellular metabolites. The number of discovered associations between metabolism and epigenetics has increased, revealing how environment influences gene regulation and phenotype diversity. This connection is relevant to all organisms but underappreciated in digenetic parasites, which must adapt to different environments as they progress through their life cycles. This review speculates and proposes associations between epigenetics and metabolism in trypanosomes, which are protozoan parasites that cause human and livestock diseases.
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Affiliation(s)
- Ana Paula Menezes
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Ana Milena Murillo
- Laboratório de Bioquímica de Tryps - LabTryps, Departamento de Parasitologia, Universidade de São Paulo, São Paulo-SP, Brazil
| | - Camila Gachet de Castro
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Natalia Karla Bellini
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | | | | | - Maria Carolina Elias
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Ariel Mariano Silber
- Laboratório de Bioquímica de Tryps - LabTryps, Departamento de Parasitologia, Universidade de São Paulo, São Paulo-SP, Brazil.
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil.
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13
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Zhu X, Fu Z, Chen SY, Ong D, Aceto G, Ho R, Steinberger J, Monast A, Pilon V, Li E, Ta M, Ching K, Adams BN, Negri GL, Choiniere L, Fu L, Pavlakis K, Pirrotte P, Avizonis DZ, Trent J, Weissman BE, Klein Geltink RI, Morin GB, Park M, Huntsman DG, Foulkes WD, Wang Y, Huang S. Alanine supplementation exploits glutamine dependency induced by SMARCA4/2-loss. Nat Commun 2023; 14:2894. [PMID: 37210563 DOI: 10.1038/s41467-023-38594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/09/2023] [Indexed: 05/22/2023] Open
Abstract
SMARCA4 (BRG1) and SMARCA2 (BRM) are the two paralogous ATPases of the SWI/SNF chromatin remodeling complexes frequently inactivated in cancers. Cells deficient in either ATPase have been shown to depend on the remaining counterpart for survival. Contrary to this paralog synthetic lethality, concomitant loss of SMARCA4/2 occurs in a subset of cancers associated with very poor outcomes. Here, we uncover that SMARCA4/2-loss represses expression of the glucose transporter GLUT1, causing reduced glucose uptake and glycolysis accompanied with increased dependency on oxidative phosphorylation (OXPHOS); adapting to this, these SMARCA4/2-deficient cells rely on elevated SLC38A2, an amino acid transporter, to increase glutamine import for fueling OXPHOS. Consequently, SMARCA4/2-deficient cells and tumors are highly sensitive to inhibitors targeting OXPHOS or glutamine metabolism. Furthermore, supplementation of alanine, also imported by SLC38A2, restricts glutamine uptake through competition and selectively induces death in SMARCA4/2-deficient cancer cells. At a clinically relevant dose, alanine supplementation synergizes with OXPHOS inhibition or conventional chemotherapy eliciting marked antitumor activity in patient-derived xenografts. Our findings reveal multiple druggable vulnerabilities of SMARCA4/2-loss exploiting a GLUT1/SLC38A2-mediated metabolic shift. Particularly, unlike dietary deprivation approaches, alanine supplementation can be readily applied to current regimens for better treatment of these aggressive cancers.
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Affiliation(s)
- Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Zheng Fu
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Shary Y Chen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Dionzie Ong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Giulio Aceto
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Rebecca Ho
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Jutta Steinberger
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Anie Monast
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Virginie Pilon
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Eunice Li
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Monica Ta
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kyle Ching
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Bianca N Adams
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Gian L Negri
- Canada's Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Luc Choiniere
- Rosalind & Morris Goodman Cancer Institute, Metabolomics Innovation Resource, McGill University, Montreal, QC, Canada
| | - Lili Fu
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Kitty Pavlakis
- Department of Pathology, IASO women's hospital, Athens, Greece
| | - Patrick Pirrotte
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Daina Z Avizonis
- Rosalind & Morris Goodman Cancer Institute, Metabolomics Innovation Resource, McGill University, Montreal, QC, Canada
| | - Jeffrey Trent
- Translational Genomics Research Institute, Division of Integrated Cancer Genomics, Phoenix, AZ, USA
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Ramon I Klein Geltink
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada
| | - William D Foulkes
- Departments of Human Genetics, Medicine and Oncology McGill University, Montreal, QC, Canada
- Division of Medical Genetics, Department of Specialized Medicine and Cancer Research Program, McGill University Health Centre, Montreal, QC, Canada
- Division of Medical Genetics, Department of Specialized Medicine and Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada.
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada.
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14
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Huang Y, Xiao L, Daba MY, Xu D, Wang Y, Li L, Li Q, Liu B, Qin W, Zhang H, Yuan X. Characterization of molecular subtypes based on chromatin regulators and identification of the role of NPAS2 in lung adenocarcinoma. Clin Epigenetics 2023; 15:72. [PMID: 37120564 PMCID: PMC10149025 DOI: 10.1186/s13148-023-01486-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/18/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Chromatin regulators (CRs) are critical epigenetic modifiers and have been reported to play critical roles during the progression of various tumors, but their role in lung adenocarcinoma (LUAD) has not been comprehensively studied. METHODS Differential expression and univariate Cox regression analyses were conducted to identify the prognostic CRs. Consensus clustering was applied to classify the subtypes of LUAD based on prognostic CRs. LASSO-multivariate Cox regression method was used for construction of a prognostic signature and development of chromatin regulator-related gene index (CRGI). The capacity of CRGI to distinguish survival was evaluated via Kaplan-Meier method in multiple datasets. Relationship between CRGI and tumor microenvironment (TME) was evaluated. Additionally, clinical variables and CRGI were incorporated to create a nomogram. The role of the prognostic gene NPAS2 in LUAD was elucidated via clinical samples validation and a series of in vitro and in vivo experiments. RESULTS Two subtypes of LUAD were classified based on 46 prognostic CRs via consensus clustering which had significantly different survival and TME. A prognostic signature consisting of six CRs (MOCS, PBK, CBX3, A1CF, NPAS2, and CTCFL) was developed and proved to be an effective survival predictor in multiple independent datasets. The prognostic signature was also demonstrated to be an indicator of TME and sensitivity to immunotherapy and chemotherapy. The nomogram was suggested to be a simple tool that can predict survival accurately. Clinical samples show that NPAS2 is highly expressed in LUAD tissues, and in vitro and in vivo experiments demonstrated that inhibition of NPAS2 impeded malignant progression of LUAD cells. CONCLUSIONS Our study comprehensively unveiled the functions of CRs in LUAD, developed a classifier to predict survival and response to treatments, and suggested that NPAS2 promoted LUAD progression for the first time.
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Affiliation(s)
- Yongbiao Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lingyan Xiao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Motuma Yigezu Daba
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Duo Xu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Long Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Li
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Wan Qin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Huixian Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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15
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Singh AK, Viviano S, Allington G, McGee S, Kiziltug E, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Ma S, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 -mutant BAFopathy implicates epigenetic dysregulation of neural progenitors in hydrocephalus. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.19.23287455. [PMID: 36993720 PMCID: PMC10055611 DOI: 10.1101/2023.03.19.23287455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Importance Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery. A few familial forms of congenital hydrocephalus (CH) have been identified, but the cause of most sporadic cases of CH remains elusive. Recent studies have implicated SMARCC1 , a component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, as a candidate CH gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, CH-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo . Objectives The aims of this study are to (i) assess the extent to which rare, damaging de novo mutations (DNMs) in SMARCC1 are associated with cerebral ventriculomegaly; (ii) describe the clinical and radiographic phenotypes of SMARCC1 -mutated patients; and (iii) assess the pathogenicity and mechanisms of CH-associated SMARCC1 mutations in vivo . Design setting and participants A genetic association study was conducted using whole-exome sequencing from a cohort consisting of 2,697 ventriculomegalic trios, including patients with neurosurgically-treated CH, totaling 8,091 exomes collected over 5 years (2016-2021). Data were analyzed in 2023. A comparison control cohort consisted of 1,798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents sourced from the Simons simplex consortium. Main outcomes and measures Gene variants were identified and filtered using stringent, validated criteria. Enrichment tests assessed gene-level variant burden. In silico biophysical modeling estimated the likelihood and extent of the variant impact on protein structure. The effect of a CH-associated SMARCC1 mutation on the human fetal brain transcriptome was assessed by analyzing RNA-sequencing data. Smarcc1 knockdowns and a patient-specific Smarcc1 variant were tested in Xenopus and studied using optical coherence tomography imaging, in situ hybridization, and immunofluorescence microscopy. Results SMARCC1 surpassed genome-wide significance thresholds in DNM enrichment tests. Six rare protein-altering DNMs, including four loss-of-function mutations and one recurrent canonical splice site mutation (c.1571+1G>A) were detected in unrelated patients. DNMs localized to the highly conserved DNA-interacting SWIRM, Myb-DNA binding, Glu-rich, and Chromo domains of SMARCC1 . Patients exhibited developmental delay (DD), aqueductal stenosis, and other structural brain and heart defects. G0 and G1 Smarcc1 Xenopus mutants exhibited aqueductal stenosis and cardiac defects and were rescued by human wild-type SMARCC1 but not a patient-specific SMARCC1 mutant. Hydrocephalic SMARCC1 -mutant human fetal brain and Smarcc1 -mutant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2 . Conclusions SMARCC1 is a bona fide CH risk gene. DNMs in SMARCC1 cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)", characterized by cerebral ventriculomegaly, aqueductal stenosis, DD, and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodeling complex for human brain morphogenesis and provide evidence for a "neural stem cell" paradigm of human CH pathogenesis. These results highlight the utility of trio-based WES for identifying risk genes for congenital structural brain disorders and suggest WES may be a valuable adjunct in the clinical management of CH patients. KEY POINTS Question: What is the role of SMARCC1 , a core component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, in brain morphogenesis and congenital hydrocephalus (CH)? Findings: SMARCC1 harbored an exome-wide significant burden of rare, protein-damaging de novo mutations (DNMs) (p = 5.83 × 10 -9 ) in the largest ascertained cohort to date of patients with cerebral ventriculomegaly, including treated CH (2,697 parent-proband trios). SMARCC1 contained four loss-of-function DNMs and two identical canonical splice site DNMs in a total of six unrelated patients. Patients exhibited developmental delay, aqueductal stenosis, and other structural brain and cardiac defects. Xenopus Smarcc1 mutants recapitulated core human phenotypes and were rescued by the expression of human wild-type but not patient-mutant SMARCC1 . Hydrocephalic SMARCC1 -mutant human brain and Smarcc1 -mutant Xenopus brain exhibited similar alterationsin the expression of key transcription factors that regulate neural progenitor cell proliferation. Meaning: SMARCC1 is essential for human brain morphogenesis and is a bona fide CH risk gene. SMARCC1 mutations cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)". These data implicate epigenetic dysregulation of fetal neural progenitors in the pathogenesis of hydrocephalus, with diagnostic and prognostic implications for patients and caregivers.
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16
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Li X, Mei Q, Yu Q, Wang M, He F, Xiao D, Liu H, Ge F, Yu X, Li S. The TORC1 activates Rpd3L complex to deacetylate Ino80 and H2A.Z and repress autophagy. SCIENCE ADVANCES 2023; 9:eade8312. [PMID: 36888706 PMCID: PMC9995077 DOI: 10.1126/sciadv.ade8312] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Autophagy is a critical process to maintain homeostasis, differentiation, and development. How autophagy is tightly regulated by nutritional changes is poorly understood. Here, we identify chromatin remodeling protein Ino80 and histone variant H2A.Z as the deacetylation targets for histone deacetylase Rpd3L complex and uncover how they regulate autophagy in response to nutrient availability. Mechanistically, Rpd3L deacetylates Ino80 K929, which protects Ino80 from being degraded by autophagy. The stabilized Ino80 promotes H2A.Z eviction from autophagy-related genes, leading to their transcriptional repression. Meanwhile, Rpd3L deacetylates H2A.Z, which further blocks its deposition into chromatin to repress the transcription of autophagy-related genes. Rpd3-mediated deacetylation of Ino80 K929 and H2A.Z is enhanced by the target of rapamycin complex 1 (TORC1). Inactivation of TORC1 by nitrogen starvation or rapamycin inhibits Rpd3L, leading to induction of autophagy. Our work provides a mechanism for chromatin remodelers and histone variants in modulating autophagy in response to nutrient availability.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qianyun Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Min Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Fei He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Duncheng Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Huan Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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17
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Deprez MA, Caligaris M, Rosseels J, Hatakeyama R, Ghillebert R, Sampaio-Marques B, Mudholkar K, Eskes E, Meert E, Ungermann C, Ludovico P, Rospert S, De Virgilio C, Winderickx J. The nutrient-responsive CDK Pho85 primes the Sch9 kinase for its activation by TORC1. PLoS Genet 2023; 19:e1010641. [PMID: 36791155 PMCID: PMC9974134 DOI: 10.1371/journal.pgen.1010641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/28/2023] [Accepted: 01/27/2023] [Indexed: 02/16/2023] Open
Abstract
Yeast cells maintain an intricate network of nutrient signaling pathways enabling them to integrate information on the availability of different nutrients and adjust their metabolism and growth accordingly. Cells that are no longer capable of integrating this information, or that are unable to make the necessary adaptations, will cease growth and eventually die. Here, we studied the molecular basis underlying the synthetic lethality caused by loss of the protein kinase Sch9, a key player in amino acid signaling and proximal effector of the conserved growth-regulatory TORC1 complex, when combined with either loss of the cyclin-dependent kinase (CDK) Pho85 or loss of its inhibitor Pho81, which both have pivotal roles in phosphate sensing and cell cycle regulation. We demonstrate that it is specifically the CDK-cyclin pair Pho85-Pho80 or the partially redundant CDK-cyclin pairs Pho85-Pcl6/Pcl7 that become essential for growth when Sch9 is absent. Interestingly, the respective three CDK-cyclin pairs regulate the activity and distribution of the phosphatidylinositol-3 phosphate 5-kinase Fab1 on endosomes and vacuoles, where it generates phosphatidylinositol-3,5 bisphosphate that serves to recruit both TORC1 and its substrate Sch9. In addition, Pho85-Pho80 directly phosphorylates Sch9 at Ser726, and to a lesser extent at Thr723, thereby priming Sch9 for its subsequent phosphorylation and activation by TORC1. The TORC1-Sch9 signaling branch therefore integrates Pho85-mediated information at different levels. In this context, we also discovered that loss of the transcription factor Pho4 rescued the synthetic lethality caused by loss of Pho85 and Sch9, indicating that both signaling pathways also converge on Pho4, which appears to be wired to a feedback loop involving the high-affinity phosphate transporter Pho84 that fine-tunes Sch9-mediated responses.
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Affiliation(s)
- Marie-Anne Deprez
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Marco Caligaris
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Joëlle Rosseels
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Riko Hatakeyama
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Ruben Ghillebert
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Braga, Portugal
| | - Kaivalya Mudholkar
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Elja Eskes
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Els Meert
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Christian Ungermann
- Department of Biology/Chemistry & Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Braga, Portugal
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- * E-mail: (CDV); (JW)
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
- * E-mail: (CDV); (JW)
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18
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Ferguson LP, Gatchalian J, McDermott ML, Nakamura M, Chambers K, Rajbhandari N, Lytle NK, Rosenthal SB, Hamilton M, Albini S, Wartenberg M, Zlobec I, Galván JA, Karamitopoulou E, Vavinskaya V, Wascher A, Lowy AM, Schürch CM, Puri PL, Bruneau BG, Hargreaves DC, Reya T. Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma. Nat Commun 2023; 14:292. [PMID: 36653361 PMCID: PMC9849267 DOI: 10.1038/s41467-023-35796-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Pancreatic cancer is characterized by extensive resistance to conventional therapies, making clinical management a challenge. Here we map the epigenetic dependencies of cancer stem cells, cells that preferentially evade therapy and drive progression, and identify SWI/SNF complex member SMARCD3 as a regulator of pancreatic cancer cells. Although SWI/SNF subunits often act as tumor suppressors, we show that SMARCD3 is amplified in cancer, enriched in pancreatic cancer stem cells and upregulated in the human disease. Diverse genetic mouse models of pancreatic cancer and stage-specific Smarcd3 deletion reveal that Smarcd3 loss preferentially impacts established tumors, improving survival especially in context of chemotherapy. Mechanistically, SMARCD3 acts with FOXA1 to control lipid and fatty acid metabolism, programs associated with therapy resistance and poor prognosis in cancer. These data identify SMARCD3 as an epigenetic modulator responsible for establishing the metabolic landscape in aggressive pancreatic cancer cells and a potential target for new therapies.
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Affiliation(s)
- L Paige Ferguson
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | | | - Matthew L McDermott
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Mari Nakamura
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Kendall Chambers
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Nirakar Rajbhandari
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Nikki K Lytle
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology and Bioinformatics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Hamilton
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Sonia Albini
- Genethon, 91000, EVRY, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France
| | - Martin Wartenberg
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - José A Galván
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Eva Karamitopoulou
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Vera Vavinskaya
- Department of Pathology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Alexis Wascher
- Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
- Department of Surgery, Division of Surgical Oncology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Andrew M Lowy
- Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
- Department of Surgery, Division of Surgical Oncology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Christian M Schürch
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Pier Lorenzo Puri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Benoit G Bruneau
- Gladstone Institutes, Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | - Tannishtha Reya
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Physiology and Cellular Biophysics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
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19
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Zhou Y, Suo W, Zhang X, Yang Y, Zhao W, Li H, Ni Q. Targeting epigenetics in diabetic cardiomyopathy: Therapeutic potential of flavonoids. Biomed Pharmacother 2023; 157:114025. [PMID: 36399824 DOI: 10.1016/j.biopha.2022.114025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/05/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022] Open
Abstract
The pathophysiological mechanisms of diabetic cardiomyopathy have been extensively studied, but there is still a lack of effective prevention and treatment methods. The ability of flavonoids to protect the heart from diabetic cardiomyopathy has been extensively described. In recent years, epigenetics has received increasing attention from scholars in exploring the etiology and treatment of diabetes and its complications. DNA methylation, histone modifications and non-coding RNAs play key functions in the development, maintenance and progression of diabetic cardiomyopathy. Hence, prevention or reversal of the epigenetic alterations that have occurred during the development of diabetic cardiomyopathy may alleviate the personal and social burden of the disease. Flavonoids can be used as natural epigenetic modulators in alternative therapies for diabetic cardiomyopathy. In this review, we discuss the epigenetic effects of different flavonoid subtypes in diabetic cardiomyopathy and summarize the evidence from preclinical and clinical studies that already exist. However, limited research is available on the potential beneficial effects of flavonoids on the epigenetics of diabetic cardiomyopathy. In the future, clinical trials in which different flavonoids exert their antidiabetic and cardioprotective effects through various epigenetic mechanisms should be further explored.
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Affiliation(s)
- Yutong Zhou
- Guang'an Men Hospital, China Academy of Chinese Medicine, Beijing 100053, China
| | - Wendong Suo
- LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Xinai Zhang
- Guang'an Men Hospital, China Academy of Chinese Medicine, Beijing 100053, China
| | - Yanan Yang
- Guang'an Men Hospital, China Academy of Chinese Medicine, Beijing 100053, China
| | - Weizhe Zhao
- College of Traditional Chinese Medicine, Beijing University of Traditional Chinese Medicine, Beijing 100105, China
| | - Hong Li
- LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China.
| | - Qing Ni
- Guang'an Men Hospital, China Academy of Chinese Medicine, Beijing 100053, China.
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20
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Berezin AA, Obradovic Z, Kopp K, Berezina TA, Lichtenauer M, Wernly B, Berezin AE. The Association of Glucose Control with Circulating Levels of Red Blood Cell-Derived Vesicles in Type 2 Diabetes Mellitus Patients with Atrial Fibrillation. Int J Mol Sci 2022; 24:ijms24010729. [PMID: 36614172 PMCID: PMC9820839 DOI: 10.3390/ijms24010729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Hyperglycemia is a trigger for structural alteration of red blood cells (RBCs) and their ability to release extracellular vesicles (EVs). The aim of the study was to elucidate whether glucose control in T2DM patients with concomitant HF and AF affects a circulating number of RBC-derived EVs. We prospectively included 417 T2DM patients with HF, 51 of them had atrial fibrillation and 25 healthy volunteers and 30 T2DM non-HF individuals. Clinical assessment, echocardiography examination and biomarker measures were performed at the baseline of the study. RBC-derived EVs were determined as CD235a+ PS+ particles by flow cytometry. NT-proBNP levels were measured by ELISA. AF patients with glycosylated hemoglobin (HbA1c) < 6.9% had lower levels of CD235a+ PS+ RBC-derived vesicles than those with HbA1c ≥ 7.0%. There were no significant differences in number of CD235a+ PS+ RBC-derived vesicles between patients in entire cohort and in non-AF sub-cohort with HbA1c < 6.9% and HbA1c ≥ 7.0%, respectively. Multivariate linear regression yielded that CD235a+ PS+ RBC-derived vesicles ≥ 545 particles in µL (OR = 1.06; 95% CI = 1.01−1.11, p = 0.044) independently predicted HbA1c ≥ 7.0%. Elevated levels of CD235a+ PS+ RBC-derived EVs independently predicted poor glycaemia control in T2DM patients with HF and AF.
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Affiliation(s)
- Alexander A. Berezin
- Zaporozhye Medical Academy of Postgraduate Education, 20 Vinter Av., 69096 Zaporozhye, Ukraine
- Klinik Barmelweid, Department of Psychosomatic Medicine and Psychotherapy, 5017 Barmelweid, Switzerland
| | - Zeljko Obradovic
- Klinik Barmelweid, Department of Psychosomatic Medicine and Psychotherapy, 5017 Barmelweid, Switzerland
| | - Kristen Kopp
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University of Salzburg, Strubergasse 21, 5020 Salzburg, Austria
| | - Tetiana A. Berezina
- Department of Internal Medicine, Vita Center, 3 Sedov Str., 69000 Zaporozhye, Ukraine
| | - Michael Lichtenauer
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University of Salzburg, Strubergasse 21, 5020 Salzburg, Austria
| | - Bernhard Wernly
- Department of Internal Medicine, General Hospital of Oberndorf, Paracelsusstraβe 37, 5110 Oberndorf bei Salzburg, Austria
- Center for Public Health and Healthcare Research, Paracelsus Medical University of Salzburg, Strubergasse 21, 5020 Salzburg, Austria
- Correspondence:
| | - Alexander E. Berezin
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University of Salzburg, Strubergasse 21, 5020 Salzburg, Austria
- Internal Medicine Department, Zaporozhye State Medical University, 26 Mayakovsky Av., 69035 Zaporozhye, Ukraine
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21
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Singh KS, van der Hooft JJJ, van Wees SCM, Medema MH. Integrative omics approaches for biosynthetic pathway discovery in plants. Nat Prod Rep 2022; 39:1876-1896. [PMID: 35997060 PMCID: PMC9491492 DOI: 10.1039/d2np00032f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic pathways and their genetic regulation have become increasingly important. While genomes provide clues regarding functional associations between genes based on gene clustering, metabolome mining provides a foundational technology to chart natural product structural diversity in plants, and transcriptomics has been successfully used to identify new members of their biosynthetic pathways based on coexpression. Thus far, most approaches utilizing transcriptomics and metabolomics have been targeted towards specific pathways and use one type of omics data at a time. Recent technological advances now provide new opportunities for integration of multiple omics types and untargeted pathway discovery. Here, we review advances in plant biosynthetic pathway discovery using genomics, transcriptomics, and metabolomics, as well as recent efforts towards omics integration. We highlight how transcriptomics and metabolomics provide complementary information to link genes to metabolites, by associating temporal and spatial gene expression levels with metabolite abundance levels across samples, and by matching mass-spectral features to enzyme families. Furthermore, we suggest that elucidation of gene regulatory networks using time-series data may prove useful for efforts to unwire the complexities of biosynthetic pathway components based on regulatory interactions and events.
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Affiliation(s)
- Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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22
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Zong W, Gong Y, Sun W, Li T, Wang ZQ. PARP1: Liaison of Chromatin Remodeling and Transcription. Cancers (Basel) 2022; 14:cancers14174162. [PMID: 36077699 PMCID: PMC9454564 DOI: 10.3390/cancers14174162] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a covalent post-translational modification and plays a key role in the immediate response of cells to stress signals. Poly(ADP-ribose) polymerase 1 (PARP1), the founding member of the PARP superfamily, synthesizes long and branched polymers of ADP-ribose (PAR) onto acceptor proteins, thereby modulating their function and their local surrounding. PARP1 is the most prominent of the PARPs and is responsible for the production of about 90% of PAR in the cell. Therefore, PARP1 and PARylation play a pleotropic role in a wide range of cellular processes, such as DNA repair and genomic stability, cell death, chromatin remodeling, inflammatory response and gene transcription. PARP1 has DNA-binding and catalytic activities that are important for DNA repair, yet also modulate chromatin conformation and gene transcription, which can be independent of DNA damage response. PARP1 and PARylation homeostasis have also been implicated in multiple diseases, including inflammation, stroke, diabetes and cancer. Studies of the molecular action and biological function of PARP1 and PARylation provide a basis for the development of pharmaceutic strategies for clinical applications. This review focuses primarily on the role of PARP1 in the regulation of chromatin remodeling and transcriptional activation.
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Affiliation(s)
- Wen Zong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Correspondence: (W.Z.); or (Z.-Q.W.)
| | - Yamin Gong
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- College of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wenli Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Tangliang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, 07743 Jena, Germany
- Correspondence: (W.Z.); or (Z.-Q.W.)
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23
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Sahoo OS, Pethusamy K, Srivastava TP, Talukdar J, Alqahtani MS, Abbas M, Dhar R, Karmakar S. The metabolic addiction of cancer stem cells. Front Oncol 2022; 12:955892. [PMID: 35957877 PMCID: PMC9357939 DOI: 10.3389/fonc.2022.955892] [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: 05/29/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer stem cells (CSC) are the minor population of cancer originating cells that have the capacity of self-renewal, differentiation, and tumorigenicity (when transplanted into an immunocompromised animal). These low-copy number cell populations are believed to be resistant to conventional chemo and radiotherapy. It was reported that metabolic adaptation of these elusive cell populations is to a large extent responsible for their survival and distant metastasis. Warburg effect is a hallmark of most cancer in which the cancer cells prefer to metabolize glucose anaerobically, even under normoxic conditions. Warburg's aerobic glycolysis produces ATP efficiently promoting cell proliferation by reprogramming metabolism to increase glucose uptake and stimulating lactate production. This metabolic adaptation also seems to contribute to chemoresistance and immune evasion, a prerequisite for cancer cell survival and proliferation. Though we know a lot about metabolic fine-tuning in cancer, what is still in shadow is the identity of upstream regulators that orchestrates this process. Epigenetic modification of key metabolic enzymes seems to play a decisive role in this. By altering the metabolic flux, cancer cells polarize the biochemical reactions to selectively generate "onco-metabolites" that provide an added advantage for cell proliferation and survival. In this review, we explored the metabolic-epigenetic circuity in relation to cancer growth and proliferation and establish the fact how cancer cells may be addicted to specific metabolic pathways to meet their needs. Interestingly, even the immune system is re-calibrated to adapt to this altered scenario. Knowing the details is crucial for selective targeting of cancer stem cells by choking the rate-limiting stems and crucial branch points, preventing the formation of onco-metabolites.
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Affiliation(s)
- Om Saswat Sahoo
- Department of Biotechnology, National Institute of technology, Durgapur, India
| | - Karthikeyan Pethusamy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Joyeeta Talukdar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammed S. Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- BioImaging Unit, Space Research Centre, Michael Atiyah Building, University of Leicester, Leicester, United Kingdom
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha, Saudi Arabia
- Computers and communications Department, College of Engineering, Delta University for Science and Technology, Gamasa, Egypt
| | - Ruby Dhar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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24
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Mignon J, Mottet D, Leyder T, Uversky VN, Perpète EA, Michaux C. Structural characterisation of amyloidogenic intrinsically disordered zinc finger protein isoforms DPF3b and DPF3a. Int J Biol Macromol 2022; 218:57-71. [PMID: 35863661 DOI: 10.1016/j.ijbiomac.2022.07.102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 11/05/2022]
Abstract
Double PHD fingers 3 (DPF3) is a zinc finger protein, found in the BAF chromatin remodelling complex, and is involved in the regulation of gene expression. Two DPF3 isoforms have been identified, respectively named DPF3b and DPF3a. Very limited structural information is available for these isoforms, and their specific functionality still remains poorly studied. In a previous work, we have demonstrated the first evidence of DPF3a being a disordered protein sensitive to amyloid fibrillation. Intrinsically disordered proteins (IDPs) lack a defined tertiary structure, existing as a dynamic conformational ensemble, allowing them to act as hubs in protein-protein interaction networks. In the present study, we have more thoroughly characterised DPF3a in vitro behaviour, as well as unravelled and compared the structural properties of the DPF3b isoform, using an array of predictors and biophysical techniques. Predictions, spectroscopy, and dynamic light scattering have revealed a high content in disorder: prevalence of random coil, aromatic residues partially to fully exposed to the solvent, and large hydrodynamic diameters. DPF3a appears to be more disordered than DPF3b, and exhibits more expanded conformations. Furthermore, we have shown that they both time-dependently aggregate into amyloid fibrils, as revealed by typical circular dichroism, deep-blue autofluorescence, and amyloid-dye binding assay fingerprints. Although spectroscopic and microscopic analyses have unveiled that they share a similar aggregation pathway, DPF3a fibrillates at a faster rate, likely through reordering of its C-terminal domain.
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Affiliation(s)
- Julien Mignon
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
| | - Denis Mottet
- University of Liège, GIGA-Molecular Biology of Diseases, Gene Expression and Cancer Laboratory, B34, Avenue de l'Hôpital, 4000 Liège, Belgium.
| | - Tanguy Leyder
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
| | - Eric A Perpète
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium; Institute of Life, Earth and Environment (ILEE), University of Namur, Namur, Belgium.
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
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25
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Izquierdo-Torres E, Hernández-Oliveras A, Lozano-Arriaga D, Zarain-Herzberg Á. Obesity, the other pandemic: linking diet and carcinogenesis by epigenetic mechanisms. J Nutr Biochem 2022; 108:109092. [PMID: 35718098 DOI: 10.1016/j.jnutbio.2022.109092] [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: 11/21/2021] [Revised: 03/19/2022] [Accepted: 05/30/2022] [Indexed: 11/25/2022]
Abstract
Both obesity and cancer are complex medical conditions that are considered public health problems. The influence of obesity on the predisposition to develop various types of cancer has been observed in a wide variety of studies. Due to their importance as public health problems, and the close relationship between both conditions, it is important to be able to understand and associate them mechanistically. In this review article, we intend to go a little further, by finding relationships between lifestyle, which can lead a person to develop obesity, and how it influences at the cellular and molecular level, affecting gene expression to favor signaling pathways or transcriptional programs involved in cancer. We describe how products of metabolism and intermediate metabolism can affect chromatin structure, participating in the regulation (or dysregulation) of gene expression, and we show an analysis of genes that are responsive to diets high in sugar and fat, and how their epigenetic landscape is altered.
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Affiliation(s)
- Eduardo Izquierdo-Torres
- Departamento de Bioquímica, Facultad de Medicina. Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Andrés Hernández-Oliveras
- Departamento de Bioquímica, Facultad de Medicina. Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Dalia Lozano-Arriaga
- Departamento de Bioquímica, Facultad de Medicina. Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ángel Zarain-Herzberg
- Departamento de Bioquímica, Facultad de Medicina. Universidad Nacional Autónoma de México, Ciudad de México, México.
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26
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Chen Y, Zeng W, Ma W, Ma W, Zhou J. Chromatin Regulators Ahc1p and Eaf3p Positively Influence Nitrogen Metabolism in Saccharomyces cerevisiae. Front Microbiol 2022; 13:883934. [PMID: 35620110 PMCID: PMC9127870 DOI: 10.3389/fmicb.2022.883934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
There is a complex regulatory network of nitrogen metabolism in Saccharomyces cerevisiae, and many details of this regulatory network have not been revealed. This study explored the global regulation of nitrogen metabolism in S. cerevisiae from an epigenetic perspective. Comparative transcriptome analysis of S. cerevisiae S288C treated with 30 nitrogen sources identified nine chromatin regulators (CRs) that responded significantly to different nitrogen sources. Functional analysis showed that among the CRs identified, Ahc1p and Eaf3p promoted the utilization of non-preferred nitrogen sources through global regulation of nitrogen metabolism. Ahc1p regulated nitrogen metabolism through amino acid transport, nitrogen catabolism repression (NCR), and the Ssy1p-Ptr3p-Ssy5p signaling sensor system. Eaf3p regulated nitrogen metabolism via amino acid transport and NCR. The regulatory mechanisms of the effects of Ahc1p and Eaf3p on nitrogen metabolism depended on the function of their histone acetyltransferase complex ADA and NuA4. These epigenetic findings provided new insights for a deeper understanding of the nitrogen metabolism regulatory network in S. cerevisiae.
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Affiliation(s)
- Yu Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Weizhu Zeng
- Science Center for Future Foods, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Wenjian Ma
- Science Center for Future Foods, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Wei Ma
- Science Center for Future Foods, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
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27
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Sebastian C, Vong JSL, Mayekar MK, Tummala KS, Singh I. Editorial: Metabolism and Epigenetics. Front Genet 2022; 13:877538. [PMID: 35360874 PMCID: PMC8960136 DOI: 10.3389/fgene.2022.877538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Carlos Sebastian
- Department of Cell Biology, Physiology and Immunology, School of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Joaquim S. L. Vong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | - Krishna S. Tummala
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, , United States
| | - Indrabahadur Singh
- Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- *Correspondence: Indrabahadur Singh,
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28
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Xu G, Guo H, Yan M, Jia Z, Li Z, Chen M, Bao X. An actin‐like protein
Po
ARP9
involves in the regulation of development and cellulase and amylase expression in
Penicillium oxalicum. J Appl Microbiol 2022; 132:2894-2905. [DOI: 10.1111/jam.15466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/28/2021] [Accepted: 01/23/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Gen Xu
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Hao Guo
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Mengdi Yan
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Zhilei Jia
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Zhonghai Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Mei Chen
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Xiaoming Bao
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
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29
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Kumar S. SWI/SNF (BAF) complexes: From framework to a functional role in endothelial mechanotransduction. CURRENT TOPICS IN MEMBRANES 2021; 87:171-198. [PMID: 34696885 DOI: 10.1016/bs.ctm.2021.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Endothelial cells (ECs) are constantly subjected to an array of mechanical cues, especially shear stress, due to their luminal placement in the blood vessels. Blood flow can regulate various aspects of endothelial biology and pathophysiology by regulating the endothelial processes at the transcriptomic, proteomic, miRNomic, metabolomics, and epigenomic levels. ECs sense, respond, and adapt to altered blood flow patterns and shear profiles by specialized mechanisms of mechanosensing and mechanotransduction, resulting in qualitative and quantitative differences in their gene expression. Chromatin-regulatory proteins can regulate transcriptional activation by modifying the organization of nucleosomes at promoters, enhancers, silencers, insulators, and locus control regions. Recent research efforts have illustrated that SWI/SNF (SWItch/Sucrose Non-Fermentable) or BRG1/BRM-associated factor (BAF) complex regulates DNA accessibility and chromatin structure. Since the discovery, the gene-regulatory mechanisms of the BAF complex associated with chromatin remodeling have been intensively studied to investigate its role in diverse disease phenotypes. Thus far, it is evident that (1) the SWI/SNF complex broadly regulates the activity of transcriptional enhancers to control lineage-specific differentiation and (2) mutations in the BAF complex proteins lead to developmental disorders and cancers. It is unclear if blood flow can modulate the activity of SWI/SNF complex to regulate EC differentiation and reprogramming. This review emphasizes the integrative role of SWI/SNF complex from a structural and functional standpoint with a special reference to cardiovascular diseases (CVDs). The review also highlights how regulation of this complex by blood flow can lead to the discovery of new therapeutic interventions for the treatment of endothelial dysfunction in vascular diseases.
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Affiliation(s)
- Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia Institute of Technology, Atlanta, GA, United States.
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30
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Xiao Z, Locasale JW. Epigenomic links from metabolism-methionine and chromatin architecture. Curr Opin Chem Biol 2021; 63:11-18. [PMID: 33667809 PMCID: PMC9889272 DOI: 10.1016/j.cbpa.2021.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/12/2021] [Accepted: 01/31/2021] [Indexed: 02/03/2023]
Abstract
Chromatin and associated epigenetic marks provide important platforms for gene regulation in response to metabolic changes associated with environmental exposures, including physiological stress, nutritional deprivation, and starvation. Numerous studies have shown that fluctuations of key metabolites can influence chromatin modifications, but their effects on chromatin structure (e.g. chromatin compaction, nucleosome arrangement, and chromatin loops) and how they appropriately deposit specific chemical modification on chromatin are largely unknown. Here, focusing on methionine metabolism, we discuss recent developments of metabolic effects on chromatin modifications and structure, as well as consequences on gene regulation.
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Affiliation(s)
- Zhengtao Xiao
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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31
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Vaziri A, Dus M. Brain on food: The neuroepigenetics of nutrition. Neurochem Int 2021; 149:105099. [PMID: 34133954 DOI: 10.1016/j.neuint.2021.105099] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/29/2021] [Accepted: 06/10/2021] [Indexed: 12/17/2022]
Abstract
Humans have known for millennia that nutrition has a profound influence on health and disease, but it is only recently that we have begun mapping the mechanisms via which the dietary environment impacts brain physiology and behavior. Here we review recent evidence on the effects of energy-dense and methionine diets on neural epigenetic marks, gene expression, and behavior in invertebrate and vertebrate model organisms. We also discuss limitations, open questions, and future directions in the emerging field of the neuroepigenetics of nutrition.
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Affiliation(s)
- Anoumid Vaziri
- Molecular, Cellular and Developmental Biology Graduate Program, The University of Michigan, Ann Arbor, USA; Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, USA
| | - Monica Dus
- Molecular, Cellular and Developmental Biology Graduate Program, The University of Michigan, Ann Arbor, USA; Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, USA.
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32
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Samo N, Ebert A, Kopka J, Mozgová I. Plant chromatin, metabolism and development - an intricate crosstalk. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102002. [PMID: 33497897 DOI: 10.1016/j.pbi.2021.102002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Chromatin structure influences DNA accessibility and underlying gene expression. Disturbances of chromatin structure often result in pleiotropic developmental phenotypes. Interactions between chromatin modifications and development have been the main focus of epigenetic studies. Recent years brought major advance in uncovering and understanding connections between chromatin organisation in the nucleus and metabolic processes that take place in the cytoplasm or other cellular compartments. Products of primary metabolism and cell redox states influence chromatin-modifying complexes, and chromatin modifiers in turn affect expression of metabolic genes. Current evidence indicates that complex interaction loops between these biological system layers exist. Applying interdisciplinary and holistic approaches will decipher causality and molecular mechanisms of the dynamic crosstalk between chromatin structure, metabolism and plant growth and development.
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Affiliation(s)
- Naseem Samo
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Alina Ebert
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Iva Mozgová
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic.
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33
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Xu M, Yao J, Shi Y, Yi H, Zhao W, Lin X, Yang Z. The SRCAP chromatin remodeling complex promotes oxidative metabolism during prenatal heart development. Development 2021; 148:237772. [PMID: 33913477 DOI: 10.1242/dev.199026] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Mammalian heart development relies on cardiomyocyte mitochondrial maturation and metabolism. Embryonic cardiomyocytes make a metabolic shift from anaerobic glycolysis to oxidative metabolism by mid-gestation. VHL-HIF signaling favors anaerobic glycolysis but this process subsides by E14.5. Meanwhile, oxidative metabolism becomes activated but its regulation is largely elusive. Here, we first pinpointed a crucial temporal window for mitochondrial maturation and metabolic shift, and uncovered the pivotal role of the SRCAP chromatin remodeling complex in these processes in mouse. Disruption of this complex massively suppressed the transcription of key genes required for the tricarboxylic acid cycle, fatty acid β-oxidation and ubiquinone biosynthesis, and destroyed respirasome stability. Furthermore, we found that the SRCAP complex functioned through H2A.Z deposition to activate transcription of metabolic genes. These findings have unveiled the important physiological functions of the SRCAP complex in regulating mitochondrial maturation and promoting oxidative metabolism during heart development, and shed new light on the transcriptional regulation of ubiquinone biosynthesis.
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Affiliation(s)
- Mingjie Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Jie Yao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Yingchao Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Huijuan Yi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Wukui Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China.,MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210093, China.,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210093, China
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34
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Shan CM, Bao K, Diedrich J, Chen X, Lu C, Yates JR, Jia S. The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin. Cell Rep 2020; 33:108561. [PMID: 33378674 PMCID: PMC7896557 DOI: 10.1016/j.celrep.2020.108561] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/31/2020] [Accepted: 12/03/2020] [Indexed: 12/21/2022] Open
Abstract
One key aspect of epigenetic inheritance is that chromatin structures can be stably inherited through generations after the removal of the signals that establish such structures. In fission yeast, the RNA interference (RNAi) pathway is critical for the targeting of histone methyltransferase Clr4 to pericentric repeats to establish heterochromatin. However, pericentric heterochromatin cannot be properly inherited in the absence of RNAi, suggesting the existence of mechanisms that counteract chromatin structure inheritance. Here, we show that mutations of components of the INO80 chromatin-remodeling complex allow pericentric heterochromatin inheritance in RNAi mutants. The ability of INO80 to counter heterochromatin inheritance is attributed to one subunit, Iec5, which promotes histone turnover at heterochromatin but has little effects on nucleosome positioning at heterochromatin, gene expression, or the DNA damage response. These analyses demonstrate the importance of the INO80 chromatin-remodeling complex in controlling heterochromatin inheritance and maintaining the proper heterochromatin landscape of the genome.
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Affiliation(s)
- Chun-Min Shan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Kehan Bao
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Jolene Diedrich
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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