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Zhao Z, Geisbrecht ER. Stage-specific modulation of Drosophila gene expression with muscle GAL4 promoters. Fly (Austin) 2025; 19:2447617. [PMID: 39772988 PMCID: PMC11730430 DOI: 10.1080/19336934.2024.2447617] [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: 10/15/2024] [Revised: 12/19/2024] [Accepted: 12/20/2024] [Indexed: 01/11/2025] Open
Abstract
The bipartite GAL4/UAS system is the most widely used method for targeted gene expression in Drosophila melanogaster and facilitates rapid in vivo genetic experimentation. Defining precise gene expression patterns for tissues and/or cell types under GAL4 control will continue to evolve to suit experimental needs. However, the precise spatial and temporal expression patterns for some commonly used muscle tissue promoters are still unclear. This missing information limits the precise timing of experiments during development. Here, we focus on three muscle-enriched GAL4 drivers (Mef2-GAL4, C57-GAL4 and G7-GAL4) to better inform selection of the most appropriate muscle promoter for experimental needs. Specifically, C57-GAL4 and G7-GAL4 turn on in the first or second instar larval stages, respectively, and can be used to bypass myogenesis for studies of muscle function after development.
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Affiliation(s)
- Ziwei Zhao
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
| | - Erika R Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
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2
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Saeki K, Ozato K. Transcription factors that define the epigenome structures and transcriptomes in microglia. Exp Hematol 2025:104814. [PMID: 40425139 DOI: 10.1016/j.exphem.2025.104814] [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: 02/28/2025] [Revised: 05/08/2025] [Accepted: 05/10/2025] [Indexed: 05/29/2025]
Abstract
Microglia, the resident macrophages of the brain, play critical roles in maintaining brain health. Recent genome-wide analyses, including ATAC-seq, ChIP-seq/CUT&RUN, and single-cell RNA-seq, have identified key transcription factors that define the transcriptome programs of microglia. Four transcription factors-PU.1, IRF8, SALL1, and SMAD4-form enhancer complexes and act as lineage-determining factors, shaping microglial identity. These factors co-bind with other lineage-determining transcription factors, directing one towards designated regions that program microglia while inhibiting the other from binding to DNA. Other transcription factors, such as BATF3 and MAFB, contribute to transcriptional cascades in microglia. TGF-β is a crucial cytokine driving these transcription factors to bind DNA and maintain homeostatic microglia. These findings provide insights into the physiological aspects of microglia and their roles in neuroinflammatory and neurodegenerative diseases. TEASER ABSTRACT: eTOC blurb: In this article, we compiled more than 100 transcription factors expressed in microglia. Our analysis illustrates that some transcription factors are under a distinct hierarchical rank and are sequentially activated to achieve microglia specific transcriptome programs. This article offers a new scope on the mechanistic foundation underlying microglia's complex activity.
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Affiliation(s)
- Keita Saeki
- Section on Molecular Genetics of Immunity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Keiko Ozato
- Section on Molecular Genetics of Immunity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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3
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Sudarsanam S, Guzman-Clavel LE, Dar N, Ziak J, Shahid N, Jin XO, Kolodkin AL. Mef2c Controls Postnatal Callosal Axon Targeting by Regulating Sensitivity to Ephrin Repulsion. J Neurosci 2025; 45:e0201252025. [PMID: 40228894 PMCID: PMC12096051 DOI: 10.1523/jneurosci.0201-25.2025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Revised: 03/31/2025] [Accepted: 04/07/2025] [Indexed: 04/16/2025] Open
Abstract
Intracortical circuits, including long-range callosal projections, are crucial for information processing. The development of neuronal connectivity in the cerebral cortex is contingent on ordered emergence of neuronal classes followed by the formation of class-specific axon projections. However, the genetic determinants of intracortical axon targeting are still unclear. We find that the transcription factor myocyte enhancer factor 2-c (Mef2c) directs the development of somatosensory cortical (S1) Layer 4 and 5 identity in murine postmitotic pyramidal neurons during embryogenesis. During postnatal development, Mef2c expression shifts to Layer 2/3 callosal projection neurons (L2/3 CPNs). At this later developmental stage, we identify a novel function for Mef2c in contralateral homotopic domain targeting by S1-L2/3 CPN axons. We employ functional manipulation of EphrinA-EphA signaling in Mef2c mutant CPNs and demonstrate that Mef2c represses EphA6 to desensitize S1-L2/3 CPN axons to EphrinA5 repulsion at their contralateral targets. Our work uncovers dual roles for Mef2c in cortical development: regulation of laminar subtype specification during embryogenesis and axon targeting in postnatal callosal neurons.
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Affiliation(s)
- Sriram Sudarsanam
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Luis E Guzman-Clavel
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Nyle Dar
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Jakub Ziak
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Naseer Shahid
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Xinyu O Jin
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Alex L Kolodkin
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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4
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Li S, Zhao B, Chen P, Cai Y, Xu H, Yan C, Wang F, Zhang Y. Chromatin accessibility and transcriptomic profiles of sheep pituitary function associated with fecundity. BMC Genomics 2025; 26:508. [PMID: 40394458 PMCID: PMC12090423 DOI: 10.1186/s12864-025-11621-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Accepted: 04/21/2025] [Indexed: 05/22/2025] Open
Abstract
BACKGROUND The pituitary gland, a central regulator of the hypothalamic-pituitary-gonadal (HPG) axis, plays a pivotal role in reproductive efficiency by precisely controlling the secretion of gonadotropins, including follicle-stimulating hormone (FSH) and luteinizing hormone (LH). Chromatin accessibility enables physical interactions between promoters and chromatin-binding factors to drive the gene expression. Despite this mechanistic insight, the chromatin accessibility landscape of the sheep pituitary and its functional implications for reproductive traits remain largely unexplored. To address this knowledge gap, we performed an integrated multi-omics analysis of ATAC-seq and RNA-seq profiling of pituitary from sheep with divergent fecundity phenotypes. RESULTS We identified 1,567 differential accessibility regions (DARs) and 768 differentially expressed genes (DEGs). Functional enrichment analysis revealed that the DEGs were significantly associated with key signaling pathways, including neuroactive ligand-receptor interactions, the cAMP signaling pathway, and the calcium signaling pathway, suggesting their critical roles in pituitary-regulated reproductive functions. Based on integrative analysis of ATAC-seq and RNA-seq, we revealed several potentially key genes involved in gonadotropin secretion, such as CMKLR1, TAFA1, and PPP1R17. Furthermore, we identified novel transcription factors (TFs), including NR4A2 and MEF2, which may influence pituitary hormone secretion by modulating chromatin accessibility and gene expression. CONCLUSIONS This study systematically delineated the gene expression and chromatin accessibility of the pituitary and identified some key regulatory genes associated with gonadotropin secretion in sheep. Our integrated multi-omics analysis identifies critical molecular markers that may contribute to the genetic improvement of reproductive efficiency in ovine species.
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Affiliation(s)
- Shanglai Li
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, China
| | - Bingru Zhao
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, China
| | - Peiyong Chen
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, China
| | - Yu Cai
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, China
| | - Hui Xu
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, China
| | - Chenbo Yan
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, China
| | - Feng Wang
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, China
| | - Yanli Zhang
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, China.
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Sigalova OM, Forneris M, Stojanovska F, Zhao B, Viales RR, Rabinowitz A, Hammal F, Ballester B, Zaugg JB, Furlong EEM. Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis. Genome Res 2025; 35:1138-1153. [PMID: 40234030 PMCID: PMC12047541 DOI: 10.1101/gr.279652.124] [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: 06/03/2024] [Accepted: 02/20/2025] [Indexed: 04/17/2025]
Abstract
Understanding how genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F1 crosses with extensive genetic diversity to profile allele-specific binding of four TFs at several time points during Drosophila embryogenesis. Using a combined haplotype test, we identified 9%-18% of TF-bound regions impacted by genetic variation even for essential regulators. By expanding WASP (a tool for allele-specific read mapping) to examine indels, we increased detection of allelically imbalanced peaks by 30%-50%. This fine-grained "mutagenesis" can reconstruct functionalized binding motifs for all factors. To prioritize causal variants, we trained a convolutional neural network (Basenji) to accurately predict binding from DNA sequence. The model can also predict measured allelic imbalance for strong effect variants, providing a mechanistic interpretation for how the variant impacts binding. This reveals unexpected relationships between TFs, including potential cooperative pairs, and mechanisms of tissue-specific recruitment of the ubiquitous factor CTCF.
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Affiliation(s)
- Olga M Sigalova
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Mattia Forneris
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Frosina Stojanovska
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, D-69117 Heidelberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, D-69117 Heidelberg, Germany
| | - Bingqing Zhao
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Rebecca R Viales
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Adam Rabinowitz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Fayrouz Hammal
- Aix Marseille Univ, INSERM, TAGC, 13009 Marseille, France
| | | | - Judith B Zaugg
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, D-69117 Heidelberg, Germany;
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany;
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6
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de Mattos K, Scott-Boyer MP, Droit A, Viger RS, Tremblay JJ. Identification of MEF2A, MEF2C, and MEF2D interactomes in basal and Fsk-stimulated mouse MA-10 Leydig cells. Andrology 2025. [PMID: 40277654 DOI: 10.1111/andr.70051] [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: 11/25/2024] [Revised: 04/06/2025] [Accepted: 04/11/2025] [Indexed: 04/26/2025]
Abstract
BACKGROUND Myocyte enhancer factor 2 transcription factors regulate essential transcriptional programs in various cell types. The activity of myocyte enhancer factor 2 factors is modulated through interactions with cofactors, chromatin remodelers, and other regulatory proteins, which are dependent on cell context and physiological state. In steroidogenic Leydig cells, MEF2A, MEF2C, and MEF2D are key regulators of genes involved in steroid hormone synthesis, reproductive function, and oxidative stress defense. However, the specific network of myocyte enhancer factor 2-interacting proteins in Leydig cells remains unknown. OBJECTIVE To identify the interactome of each MEF2 factor present in Leydig cells. MATERIALS AND METHODS TurboID proximity-mediated biotinylation combined with mass spectrometry and bioinformatic analyses were used to identify the protein‒protein interaction networks of MEF2A, MEF2C, and MEF2D in MA-10 Leydig cells under basal and stimulated conditions. RESULTS We identified 109 potential myocyte enhancer factor 2-interacting proteins, including some previously known myocyte enhancer factor 2 partners. The interactome for each myocyte enhancer factor 2 factor is dynamic and exhibits unique and shared interaction networks between basal and stimulated conditions. Further analysis through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment categorized these interactions, revealing involvement in pathways related to cellular metabolism, transcriptional regulation, and steroidogenesis. DISCUSSION AND CONCLUSION These findings suggest that myocyte enhancer factor 2 factors can participate in diverse transcriptional activities, capable of gene activation or repression, depending on different protein‒protein interactions. In addition, the differential interactome for each myocyte enhancer factor 2 factor suggests unique regulatory roles for each factor in modulating Leydig cell function. Overall, this study provides new mechanistic insights into myocyte enhancer factor 2 action in Leydig cells by identifying interacting partners that likely influence their functions.
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Affiliation(s)
- Karine de Mattos
- Reproduction, Santé de la Mère et de l'enfant, Centre de Recherche du CHU de Québec, Université Laval, Quebec City, Canada
| | - Marie-Pier Scott-Boyer
- Endocrinologie et Néphrologie, Centre de Recherche du CHU de Québec, Université Laval, Quebec City, Canada
| | - Arnaud Droit
- Endocrinologie et Néphrologie, Centre de Recherche du CHU de Québec, Université Laval, Quebec City, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Robert S Viger
- Reproduction, Santé de la Mère et de l'enfant, Centre de Recherche du CHU de Québec, Université Laval, Quebec City, Canada
- Centre for Research in Reproduction, Development and Intergenerational Health, Department of Obstetrics, Gynecology, and Reproduction, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Jacques J Tremblay
- Reproduction, Santé de la Mère et de l'enfant, Centre de Recherche du CHU de Québec, Université Laval, Quebec City, Canada
- Centre for Research in Reproduction, Development and Intergenerational Health, Department of Obstetrics, Gynecology, and Reproduction, Faculty of Medicine, Université Laval, Quebec City, Canada
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7
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Zhai C, Ding X, Mao L, Ge Y, Huang A, Yang F, Ding Y. MEF2A, MEF2C, and MEF2D as potential biomarkers of pancreatic cancer? BMC Cancer 2025; 25:775. [PMID: 40281485 PMCID: PMC12023379 DOI: 10.1186/s12885-025-14107-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Accepted: 04/08/2025] [Indexed: 04/29/2025] Open
Abstract
BACKGROUND The myocyte enhancer factor-2 (MEF2) family genes were involved in the carcinogenesis and prognosis of multiple human tumors. The impact of MEF2s on the occurrences, progression, and clinical outcome of pancreatic cancer (PAAD) remains unknown. METHODS This study used the CCLE, HPA, EMBL-EBI, and GEPIA2 databases to study MEF2s expression in PAAD patients. We also investigated the relationship between MEF2s expression and methylation through the DiseaseMeth database, and used MEXPRESS to verify the association. Then we utilized the Kaplan-Meier Plotter and GEPIA2 databases to evaluate the prognostic value of MEF2s in PAAD. The cBioPortal database was used to explore the alteration features of MEF2s in PAAD. We then investigated the association between MEF2s expression, immune cells infiltration, and immune infiltration markers using the TIMER database. Finally, Metascape, STRING, and Cytoscape tools were used for functional enrichment analysis. RESULTS MEF2A, MEF2C, and MEF2D were found to be highly expressed in PAAD patients' tissues compared to normal tissues, whereas MEF2B expression did not show significant differential expression. In addition, the protein expression of MEF2A, MEF2C, and MEF2D was higher in PAAD tissues. Negative correlations were observed between the expression level of MEF2A, MEF2C, and MEF2D and the methylation levels in multiple sites. High expression of MEF2A was related to poor overall survival (p = 0.0071) and relapse-free survival (RFS) (p = 0.0089) of PAAD. High expression of MEF2C was associated with worse RFS of PAAD (p = 0.043). MEF2A was a Truncating mutation, and it was shown that the "G27Wfs*8" mutation point was distributed in the SRF-TF domain. Both MEF2C and MEF2D were a Missense mutation. MEF2A, MEF2C, and MEF2D expression was positively corresponded with five immune cells infiltration (CD8 + T cells, B-cells, neutrophils, macrophages, and dendritic cells), especially for CD8 + T cells and macrophages. Among the 20 pathways, hsa05140 (Leishmania infection), hsa04022 (cGMP-PKG signaling pathway), hsa05145 (Toxoplasmosis), hsa04371 (Apelin signaling pathway), and hsa04064 (NF-kappa B signaling pathway), were closely connected with the occurrence and development of PAAD. CONCLUSIONS Our results indicated that the overexpression of MEF2A, MEF2C, and MEF2D in patients with PAAD. MEF2A could be used as a prognostic biomarker for PAAD, MEF2C might be a potential oncogene for PAAD, and MEF2D had potential biological significance.
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Affiliation(s)
- Chunxia Zhai
- Department of Public Health, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Nantong, Jiangsu, 226011, China.
| | - Xiaorong Ding
- Department of Public Health, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Nantong, Jiangsu, 226011, China
| | - Liping Mao
- Department of Oncology, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Nantong, Jiangsu, 226011, China
| | - Yang Ge
- Department of Public Health, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Nantong, Jiangsu, 226011, China
| | - Anqi Huang
- Department of Public Health, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Nantong, Jiangsu, 226011, China
| | - Fan Yang
- Department of Public Health, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Nantong, Jiangsu, 226011, China
| | - Yi Ding
- Department of Public Health, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Nantong, Jiangsu, 226011, China.
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8
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Trudler D, Ghatak S, Bula M, Parker J, Talantova M, Luevanos M, Labra S, Grabauskas T, Noveral SM, Teranaka M, Schahrer E, Dolatabadi N, Bakker C, Lopez K, Sultan A, Patel P, Chan A, Choi Y, Kawaguchi R, Stankiewicz P, Garcia-Bassets I, Kozbial P, Rosenfeld MG, Nakanishi N, Geschwind DH, Chan SF, Lin W, Schork NJ, Ambasudhan R, Lipton SA. Dysregulation of miRNA expression and excitation in MEF2C autism patient hiPSC-neurons and cerebral organoids. Mol Psychiatry 2025; 30:1479-1496. [PMID: 39349966 PMCID: PMC11919750 DOI: 10.1038/s41380-024-02761-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 09/13/2024] [Accepted: 09/20/2024] [Indexed: 03/20/2025]
Abstract
MEF2C is a critical transcription factor in neurodevelopment, whose loss-of-function mutation in humans results in MEF2C haploinsufficiency syndrome (MHS), a severe form of autism spectrum disorder (ASD)/intellectual disability (ID). Despite prior animal studies of MEF2C heterozygosity to mimic MHS, MHS-specific mutations have not been investigated previously, particularly in a human context as hiPSCs afford. Here, for the first time, we use patient hiPSC-derived cerebrocortical neurons and cerebral organoids to characterize MHS deficits. Unexpectedly, we found that decreased neurogenesis was accompanied by activation of a micro-(mi)RNA-mediated gliogenesis pathway. We also demonstrate network-level hyperexcitability in MHS neurons, as evidenced by excessive synaptic and extrasynaptic activity contributing to excitatory/inhibitory (E/I) imbalance. Notably, the predominantly extrasynaptic (e)NMDA receptor antagonist, NitroSynapsin, corrects this aberrant electrical activity associated with abnormal phenotypes. During neurodevelopment, MEF2C regulates many ASD-associated gene networks, suggesting that treatment of MHS deficits may possibly help other forms of ASD as well.
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Affiliation(s)
- Dorit Trudler
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
| | - Swagata Ghatak
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
- School of Biological Sciences, National Institute of Science Education and Research (NISER)-Bhubaneswar, an Off Campus Center of Homi Bhabha National Institute, Jatani, Odisha, India
| | - Michael Bula
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - James Parker
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
| | - Maria Talantova
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
| | - Melissa Luevanos
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Sergio Labra
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Titas Grabauskas
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah Moore Noveral
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Mayu Teranaka
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
| | - Emily Schahrer
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Nima Dolatabadi
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
| | - Clare Bakker
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Kevin Lopez
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
| | - Abdullah Sultan
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
| | - Parth Patel
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Agnes Chan
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Yongwook Choi
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Riki Kawaguchi
- Departments of Psychiatry and Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ivan Garcia-Bassets
- Howard Hughes Medical Institute, School and Department of Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Piotr Kozbial
- Howard Hughes Medical Institute, School and Department of Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, School and Department of Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Nobuki Nakanishi
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, Center for Autism Research and Treatment, Program in Neurobehavioral Genetics, Department of Human Genetics, Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Shing Fai Chan
- Center for Neuroscience, Aging, and Stem Cell Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Department of Medicine, Indiana University-Purdue University, Indianapolis, IN, USA
| | - Wei Lin
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Nicholas J Schork
- Translational Genomics Research Institute, Phoenix, AZ, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rajesh Ambasudhan
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA
| | - Stuart A Lipton
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA, USA.
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA, USA.
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Sun J, Chen X, Ruan Y, Xu J, Xu H. MEF2A promoter methylation negatively regulates mRNA transcription and affects myoblast physiological function in cattle. Genomics 2025; 117:111016. [PMID: 40024578 DOI: 10.1016/j.ygeno.2025.111016] [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: 11/25/2024] [Revised: 01/27/2025] [Accepted: 02/17/2025] [Indexed: 03/04/2025]
Abstract
This study investigates the regulatory effects of methylation in the promoter region of the bovine MEF2A gene on its transcription levels and the impact on bovine myoblasts. Transcription levels and promoter methylation status of MEF2A in the same tissues of calves and adult cattle were assessed using qRT-PCR and BSP methods. The results indicated that MEF2A expression levels in calves were significantly lower than those in adult cattle (P < 0.05), while the methylation rate of MEF2A was significantly higher in calves (P < 0.05), suggesting a correlation between high methylation levels and reduced gene expression. Subsequently, MEF2A overexpression and interference vectors were transfected into bovine myoblasts to examine the effects of altered MEF2A expression on its promoter methylation status. The findings revealed that MEF2A overexpression significantly reduced the methylation rate (P < 0.01), whereas MEF2A interference increased the methylation rate (P < 0.01), aligning with the expression trends of DNMT1. Furthermore, bovine myoblasts were treated with varying concentrations of the methylation inhibitor 5-Aza-dC to evaluate changes in MEF2A promoter methylation and mRNA levels. The effects on cell cycle progression, apoptosis, and other growth parameters were assessed using flow cytometry, ELISA, and qRT-PCR. Results showed that a concentration of 1 μM 5-Aza-dC effectively reduced MEF2A promoter methylation and significantly upregulated MEF2A expression, leading to accelerated cell cycle progression and increased secretion levels of GH and INS, all differences being statistically significant (P < 0.01). Additionally, 1 μM of 5-Aza-dC promoted apoptosis, with qRT-PCR results for relevant genes supporting this finding. In conclusion, methylation of the MEF2A promoter negatively regulates its mRNA transcription levels, thereby impacting the growth and development of Guanling cattle myoblasts. These results provide valuable insights for the genetic improvement of cattle through marker-assisted selection.
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Affiliation(s)
- Jinkui Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, PR China; College of Animal Science, Guizhou University, Guiyang 550025, PR China
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, PR China; College of Animal Science, Guizhou University, Guiyang 550025, PR China
| | - Yong Ruan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, PR China; College of Animal Science, Guizhou University, Guiyang 550025, PR China
| | - Jiali Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, PR China; College of Animal Science, Guizhou University, Guiyang 550025, PR China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, PR China; College of Animal Science, Guizhou University, Guiyang 550025, PR China.
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10
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Attwell CL, Maldonado-Lasunción I, Eggers R, Bijleveld BA, Ellenbroek WM, Siersema N, Razenberg L, Lamme D, Fagoe ND, van Kesteren RE, Smit AB, Verhaagen J, Mason MRJ. The transcription factor combination MEF2 and KLF7 promotes axonal sprouting in the injured spinal cord with functional improvement and regeneration-associated gene expression. Mol Neurodegener 2025; 20:18. [PMID: 39923113 PMCID: PMC11807332 DOI: 10.1186/s13024-025-00805-4] [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: 07/08/2024] [Accepted: 01/23/2025] [Indexed: 02/10/2025] Open
Abstract
BACKGROUND Axon regeneration after injury to the central nervous system (CNS) is limited by an inhibitory environment but also because injured neurons fail to initiate expression of regeneration associated genes (RAGs). The potential of strong RAG expression to promote regeneration in the CNS is exemplified by the conditioning lesion model, whereby peripheral nerve injury promotes regeneration of centrally projecting branches of the injured neurons. RAG expression could potentially be induced by delivery of the right set of transcription factors (TFs). We here aim to identify TF combinations that activate this program. METHODS We first analysed binding site motifs in promoters of the RAG program to identify nine candidate growth-promoting TFs. These were systematically screened in vitro to identify combinations that had potent neurite-growth promoting activity. Next, adeno-associated viral vectors were used to express these TF combinations in vivo in L4/L5 dorsal root ganglia to test whether they would promote regeneration in a spinal cord injury model (dorsal column lesion) in female rats. To determine whether they could activate the RAG program we carried out gene expression profiling on laser-dissected dorsal root ganglion neurons specifically expressing these TF combinations, and of DRG neurons that had been axotomized. RESULTS Promoter analysis identified ATF3, Jun, CEBPD, KLF7, MEF2, SMAD1, SOX11, STAT3 and SRF as candidate RAG-activating TFs. In vitro screening identified two TF combinations, KLF7/MEF2 and ATF3/KLF7/MEF2, that had potent neurite-growth promoting activity, the latter being the more powerful. In vivo, KLF7/MEF2, but not ATF3/KLF7/MEF2 or KLF7 or MEF2 alone, promoted axonal sprouting into the dorsal column lesion site and led to improved functional recovery. Gene expression profiling revealed that unexpectedly, the MEF2-VP16 construct used had little transcriptional activity in vivo, suggesting additional steps may be required to achieve full MEF2 activity. All combinations except MEF2 alone induced RAG expression mirroring that induced by axotomy to significant extents, while ATF3/KLF7/MEF2, KLF7 and ATF3, but not KLF7/MEF2 also induced apoptosis-related genes which may hinder regeneration. CONCLUSIONS The TF combination KLF7/MEF2 partially mimics the conditioning lesion effect, inducing axonal sprouting into a dorsal column lesion and driving significant RAG expression, and also promotes functional improvement.
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Affiliation(s)
- Callan L Attwell
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands
| | - Inés Maldonado-Lasunción
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, W12 0NN, UK
| | - Ruben Eggers
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands
| | - Bastiaan A Bijleveld
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands
| | - Ward M Ellenbroek
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands
| | - Natascha Siersema
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands
| | - Lotte Razenberg
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands
| | - Dédé Lamme
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands
| | - Nitish D Fagoe
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands
| | - Ronald E van Kesteren
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognition Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognition Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Joost Verhaagen
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognition Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Matthew R J Mason
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, the Netherlands.
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11
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Sudarsanam S, Guzman-Clavel L, Dar N, Ziak J, Shahid N, Jin XO, Kolodkin AL. Mef2c Controls Postnatal Callosal Axon Targeting by Regulating Sensitivity to Ephrin Repulsion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.22.634300. [PMID: 39896513 PMCID: PMC11785193 DOI: 10.1101/2025.01.22.634300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
Cortical connectivity is contingent on ordered emergence of neuron subtypes followed by the formation of subtype-specific axon projections. Intracortical circuits, including long-range callosal projections, are crucial for information processing, but mechanisms of intracortical axon targeting are still unclear. We find that the transcription factor Myocyte enhancer factor 2-c (Mef2c) directs the development of somatosensory cortical (S1) layer 4 and 5 pyramidal neurons during embryogenesis. During early postnatal development, Mef2c expression shifts to layer 2/3 callosal projection neurons (L2/3 CPNs), and we find a novel function for Mef2c in targeting homotopic contralateral cortical regions by S1-L2/3 CPNs. We demonstrate, using functional manipulation of EphA-EphrinA signaling in Mef2c-mutant CPNs, that Mef2c downregulates EphA6 to desensitize S1-L2/3 CPN axons to EphrinA5-repulsion at their contralateral targets. Our work uncovers dual roles for Mef2c in cortical development: regulation of laminar subtype specification during embryogenesis, and axon targeting in postnatal callosal neurons.
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Affiliation(s)
- Sriram Sudarsanam
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- These authors contributed equally
| | - Luis Guzman-Clavel
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- These authors contributed equally
| | - Nyle Dar
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jakub Ziak
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Naseer Shahid
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xinyu O. Jin
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alex L. Kolodkin
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Senior author
- Lead contact
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12
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Wang SY, Wang YX, Guan LS, Shen A, Huang RJ, Yuan SQ, Xiao YL, Wang LS, Lei D, Zhao Y, Lin C, Wang CP, Yuan ZP. Construction of a prognostic model for gastric cancer based on immune infiltration and microenvironment, and exploration of MEF2C gene function. BMC Med Genomics 2025; 18:13. [PMID: 39810215 PMCID: PMC11734330 DOI: 10.1186/s12920-024-02082-4] [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: 11/10/2023] [Accepted: 12/31/2024] [Indexed: 01/16/2025] Open
Abstract
BACKGROUND Advanced gastric cancer (GC) exhibits a high recurrence rate and a dismal prognosis. Myocyte enhancer factor 2c (MEF2C) was found to contribute to the development of various types of cancer. Therefore, our aim is to develop a prognostic model that predicts the prognosis of GC patients and initially explore the role of MEF2C in immunotherapy for GC. METHODS Transcriptome sequence data of GC was obtained from The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO) and PRJEB25780 cohort for subsequent immune infiltration analysis, immune microenvironment analysis, consensus clustering analysis and feature selection for definition and classification of gene M and N. Principal component analysis (PCA) modeling was performed based on gene M and N for the calculation of immune checkpoint inhibitor (ICI) Score. Then, a Nomogram was constructed and evaluated for predicting the prognosis of GC patients, based on univariate and multivariate Cox regression. Functional enrichment analysis was performed to initially investigate the potential biological mechanisms. Through Genomics of Drug Sensitivity in Cancer (GDSC) dataset, the estimated IC50 values of several chemotherapeutic drugs were calculated. Tumor-related transcription factors (TFs) were retrieved from the Cistrome Cancer database and utilized our model to screen these TFs, and weighted correlation network analysis (WGCNA) was performed to identify transcription factors strongly associated with immunotherapy in GC. Finally, 10 patients with advanced GC were enrolled from Sun Yat-sen University Cancer Center, including paired tumor tissues, paracancerous tissues and peritoneal metastases, for preparing sequencing library, in order to perform external validation. RESULTS Lower ICI Score was correlated with improved prognosis in both the training and validation cohorts. First, lower mutant-allele tumor heterogeneity (MATH) was associated with lower ICI Score, and those GC patients with lower MATH and lower ICI Score had the best prognosis. Second, regardless of the T or N staging, the low ICI Score group had significantly higher overall survival (OS) compared to the high ICI Score group. For its mechanisms, consistently, for Camptothecin, Doxorubicin, Mitomycin, Docetaxel, Cisplatin, Vinblastine, Sorafenib and Paclitaxel, all of the IC50 values were significantly lower in the low ICI Score group compared to the high ICI Score group. As a result, based on univariate and multivariate Cox regression, ICI Score was considered to be an independent prognostic factor for GC. And our Nomogram showed good agreement between predicted and actual probabilities. Based on CIBERSORT deconvolution analysis, there was difference of immune cell composition found between high and low ICI Score groups, probably affecting the efficacy of immunotherapy. Then, MEF2C, a tumor-related transcription factor, was screened out by WGCNA analysis. Higher MEF2C expression is significantly correlated with a worse OS. Moreover, its higher expression is also negatively correlated with tumor mutation burden (TMB) and microsatellite instability (MSI), but positively correlated with several immunosuppressive molecules, indicating MEF2C may exert its influence on tumor development by upregulating immunosuppressive molecules. Finally, based on transcriptome sequencing data on 10 paired tumor tissues from Sun Yat-sen University Cancer Center, MEF2C expression was significantly lower in paracancerous tissues compared to tumor tissues and peritoneal metastases, and it was also lower in tumor tissues compared to peritoneal metastases, indicating a potential positive association between MEF2C expression and tumor invasiveness. CONCLUSIONS Our prognostic model can effectively predict outcomes and facilitate stratification GC patients, offering valuable insights for clinical decision-making. The identified transcription factor MEF2C can serve as a biomarker for assessing the efficacy of immunotherapy for GC.
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Affiliation(s)
- Si-Yu Wang
- Department of Oncology, The First People's Hospital of Yibin, No.65, Wenxing Street, Cuiping District, Yibin, 644000, China
| | - Yu-Xin Wang
- The First Hospital of Jilin University, Changchun, 130000, China
| | - Lu-Shun Guan
- China-Japan Union Hospital of Jilin University, Changchun, 130000, China
| | - Ao Shen
- Departments of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Run-Jie Huang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Shu-Qiang Yuan
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Yu-Long Xiao
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Li-Shuai Wang
- Department of Oncology, The First People's Hospital of Yibin, No.65, Wenxing Street, Cuiping District, Yibin, 644000, China
| | - Dan Lei
- Department of Oncology, The First People's Hospital of Yibin, No.65, Wenxing Street, Cuiping District, Yibin, 644000, China
| | - Yin Zhao
- Department of Oncology, The First People's Hospital of Yibin, No.65, Wenxing Street, Cuiping District, Yibin, 644000, China
| | - Chuan Lin
- Department of Oncology, The First People's Hospital of Yibin, No.65, Wenxing Street, Cuiping District, Yibin, 644000, China
| | - Chang-Ping Wang
- Department of Oncology, The First People's Hospital of Yibin, No.65, Wenxing Street, Cuiping District, Yibin, 644000, China
| | - Zhi-Ping Yuan
- Department of Oncology, The First People's Hospital of Yibin, No.65, Wenxing Street, Cuiping District, Yibin, 644000, China.
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13
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Yu M, Thorner K, Parameswaran S, Wei W, Yu C, Lin X, Kopan R, Hass MR. The unique functions of Runx1 in skeletal muscle maintenance and regeneration are facilitated by an ETS interaction domain. Development 2024; 151:dev202556. [PMID: 39508441 DOI: 10.1242/dev.202556] [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: 11/21/2023] [Accepted: 10/22/2024] [Indexed: 11/15/2024]
Abstract
The conserved Runt-related (RUNX) transcription factor family are master regulators of developmental and regenerative processes. Runx1 and Runx2 are expressed in satellite cells (SCs) and in skeletal myotubes. Here, we examined the role of Runx1 in mouse satellite cells to determine the role of Runx1 during muscle differentiation. Conditional deletion of Runx1 in adult SCs negatively impacted self-renewal and impaired skeletal muscle maintenance even though Runx2 expression persisted. Runx1 deletion in C2C12 cells (which retain Runx2 expression) identified unique molecular functions of Runx1 that could not be compensated for by Runx2. The reduced myoblast fusion in vitro caused by Runx1 loss was due in part to ectopic expression of Mef2c, a target repressed by Runx1. Structure-function analysis demonstrated that the ETS-interacting MID/EID region of Runx1, absent from Runx2, is essential for Runx1 myoblast function and for Etv4 binding. Analysis of ChIP-seq datasets from Runx1 (T cells, muscle)- versus Runx2 (preosteoblasts)-dependent tissues identified a composite ETS:RUNX motif enriched in Runx1-dependent tissues. The ETS:RUNX composite motif was enriched in peaks open exclusively in ATAC-seq datasets from wild-type cells compared to ATAC peaks unique to Runx1 knockout cells. Thus, engagement of a set of targets by the RUNX1/ETS complex define the non-redundant functions of Runx1 in mouse muscle precursor cells.
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Affiliation(s)
- Meng Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Konrad Thorner
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sreeja Parameswaran
- Division of Human Genetics, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Wei Wei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Chuyue Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Raphael Kopan
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Matthew R Hass
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Human Genetics, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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14
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Gautam N, Chapagain PP, Adhikari NP, Tiwari PB. Characterization of molecular interactions between HDAC7 and MEF2A. J Biomol Struct Dyn 2024:1-10. [PMID: 39660765 DOI: 10.1080/07391102.2024.2437523] [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: 12/02/2023] [Accepted: 05/17/2024] [Indexed: 12/12/2024]
Abstract
Interactions of transcriptional corepressors such as histone deacetylase 7 (HDAC7), a class IIa HDAC, with myocyte enhancer factor-2 (MEF2) regulate MEF2 activity. Despite previous investigations exploring interactions between HDAC7 and MEF2, a detailed characterization of the HDAC7-MEF2 functional complex is still lacking. Herein, we first modeled the structure of the HDAC7-MEF2A complex and investigated the inter-protein interactions using all-atom molecular dynamics (MD) simulations. We identified specific amino acids within HDAC7 and MEF2A that participate in interactions such as salt bridges, hydrogen bonds, and hydrophobic interactions. Our results reveal a salt bridge formed between LYS96(HDAC7) and ASP63(MEF2A). Our analysis also predicted formations of reliable hydrogen bonds between SER82(HDAC7) and ASP63(MEF2A) as well as LYS96(HDAC7) and ASP63(MEF2A). In addition, clustering of hydrophobic residues at the interface contributes in stabilizing the HDAC7-MEF2A complex. Results from multiple sequence alignment show that most of the HDAC7 residues that are predicted to associate with MEF2A are conserved in at least three class IIa HDACs and all predicted residues in MEF2A are conserved in MEF2s. We also found that the association of DNA to MEF2A has no significant effect on HDAC7-MEF2A interactions. Our results may also provide useful insights into the interactions between other class IIa HDACs and MEF2s.
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Affiliation(s)
- Narayan Gautam
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Tri-Chandra Multiple Campus, Tribhuvan University, Ghantaghar, Kathmandu, Nepal
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Narayan P Adhikari
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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15
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Sukhan ZP, Cho Y, Hossen S, Cho DH, Kho KH. Molecular Characterization, Expression Analysis, and CRISPR/Cas9 Mediated Gene Disruption of Myogenic Regulatory Factor 4 (MRF4) in Nile Tilapia. Curr Issues Mol Biol 2024; 46:13725-13745. [PMID: 39727948 PMCID: PMC11727018 DOI: 10.3390/cimb46120820] [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: 11/08/2024] [Revised: 11/28/2024] [Accepted: 12/02/2024] [Indexed: 12/28/2024] Open
Abstract
Myogenic regulator factors (MRFs) are essential for skeletal muscle development in vertebrates, including fish. This study aimed to characterize the role of myogenic regulatory factor 4 (MRF4) in muscle development in Nile tilapia by cloning NT-MRF4 from muscle tissues. To explore the function of NT-MRF4, CRISPR/Cas9 gene editing was employed. The NT-MRF4 cDNA was 1146 bp long and had encoded 225 amino acids, featuring a myogenic basic domain, a helix-loop-helix domain, and a nuclear localization signal. NT-MRF4 mRNA was exclusively expressed in adult muscle tissues, with expression also observed during embryonic and larval stages. Food-deprived Nile tilapia exhibited significantly lower NT-MRF4 mRNA levels than the controls while re-feeding markedly increased expression. The CRISPR/Cas9 gene editing of NT-MRF4 successfully generated two types of gene disruption, leading to a frame-shift mutation in the NT-MRF4 protein. Expression analysis of MRF and MEF2 genes in gene-edited (GE) Nile tilapia revealed that MyoG expressions nearly doubled compared to wild-type (WT) fish, suggesting that MyoG compensates for the loss of MRF4 function. Additionally, MEF2b, MEF2d, and MEF2a expressions significantly increased in GE Nile tilapia, supporting continued muscle development. Overall, these findings suggest that NT-MRF4 regulates muscle development, while MyoG may compensate for its inactivation to sustain normal muscle growth.
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Affiliation(s)
| | | | | | | | - Kang Hee Kho
- Department of Fisheries Science, Chonnam National University, Yeosu 59626, Republic of Korea; (Z.P.S.); (Y.C.); (S.H.); (D.H.C.)
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16
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Ocampo-Ortega SA, Sierra-Sanchez VM, Blancas-Napoles CM, González-Carteño A, Mera-Jiménez E, Macías-Pérez ME, Hernandez-Guerra A, Romero-Nava R, Huang F, Hong E, Villafaña S. Evaluation of an Antisense Oligonucleotide Targeting CAG Repeats: A Patient-Customized Therapy Study for Huntington's Disease. Life (Basel) 2024; 14:1607. [PMID: 39768315 PMCID: PMC11677511 DOI: 10.3390/life14121607] [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: 10/23/2024] [Revised: 11/16/2024] [Accepted: 11/28/2024] [Indexed: 01/11/2025] Open
Abstract
Huntington's disease is a genetic disorder characterized by progressive neuronal cell damage in some areas of the brain; symptoms are commonly associated with chorea, rigidity and dystonia. The symptoms in Huntington's Disease are caused by a pathological increase in the number of Cytokine-Adenine-Guanine (CAG) repeats on the first exon of the Huntingtin gene, which causes a protein to have an excessive number of glutamine residues; this alteration leads to a change in the protein's conformation and function. Therefore, the purpose of this work was to design, synthesize and evaluate an antisense oligonucleotide (ASO; 95 nucleotides) HTT 90-5 directed to the Huntingtin CAG repeats in primary leukocyte culture cells from a patient with Huntington's Disease; approximately 500,000 leukocytes per well extracted from venous blood were used, to which 100 pMol of ASO were administered, and the expression of Huntingtin was subsequently evaluated at 72 h by RT-PCR. Our results showed that the administration of the HTT 90-5 antisense decreased the expression of Huntingtin mRNA in the primary culture leukocyte cells from our patient. These results suggest that the use of long antisense targeting the CAG Huntingtin cluster may be an option to decrease the expression of Huntingtin and probably could be adjusted depending on the number of CAG repeats in the cluster.
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Affiliation(s)
- Sergio Adrian Ocampo-Ortega
- Laboratorio de Terapia Génica Experimental, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico; (S.A.O.-O.); (V.M.S.-S.); (C.M.B.-N.); (A.G.-C.); (A.H.-G.); (R.R.-N.)
| | - Vivany Maydel Sierra-Sanchez
- Laboratorio de Terapia Génica Experimental, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico; (S.A.O.-O.); (V.M.S.-S.); (C.M.B.-N.); (A.G.-C.); (A.H.-G.); (R.R.-N.)
| | - Citlali Margarita Blancas-Napoles
- Laboratorio de Terapia Génica Experimental, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico; (S.A.O.-O.); (V.M.S.-S.); (C.M.B.-N.); (A.G.-C.); (A.H.-G.); (R.R.-N.)
| | - Asdrúbal González-Carteño
- Laboratorio de Terapia Génica Experimental, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico; (S.A.O.-O.); (V.M.S.-S.); (C.M.B.-N.); (A.G.-C.); (A.H.-G.); (R.R.-N.)
| | - Elvia Mera-Jiménez
- Laboratorio de Cultivo Celular, Neurobiología y Conducta, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico; (E.M.-J.); (M.E.M.-P.)
| | - Martha Edith Macías-Pérez
- Laboratorio de Cultivo Celular, Neurobiología y Conducta, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico; (E.M.-J.); (M.E.M.-P.)
| | - Adriana Hernandez-Guerra
- Laboratorio de Terapia Génica Experimental, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico; (S.A.O.-O.); (V.M.S.-S.); (C.M.B.-N.); (A.G.-C.); (A.H.-G.); (R.R.-N.)
| | - Rodrigo Romero-Nava
- Laboratorio de Terapia Génica Experimental, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico; (S.A.O.-O.); (V.M.S.-S.); (C.M.B.-N.); (A.G.-C.); (A.H.-G.); (R.R.-N.)
| | - Fengyang Huang
- Laboratorio de Investigación en Obesidad y Asma, Hospital Infantil de Mexico “Federico Gómez”, Ciudad de Mexico 06720, Mexico;
| | - Enrique Hong
- Departamento de Neurofarmacobiología, Centro de Investigación y de Estudios Avanzados, Ciudad de Mexico 14330, Mexico;
| | - Santiago Villafaña
- Laboratorio de Terapia Génica Experimental, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico; (S.A.O.-O.); (V.M.S.-S.); (C.M.B.-N.); (A.G.-C.); (A.H.-G.); (R.R.-N.)
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17
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Sun Y, Pang Y, Wu X, Zhu R, Wang L, Tian M, He X, Liu D, Yang X. Landscape of alternative splicing and polyadenylation during growth and development of muscles in pigs. Commun Biol 2024; 7:1607. [PMID: 39627472 PMCID: PMC11614907 DOI: 10.1038/s42003-024-07332-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 11/28/2024] [Indexed: 12/06/2024] Open
Abstract
Alternative polyadenylation (APA) is emerging as a post-transcriptional regulatory mechanism, similar as that of alternative splicing (AS), and plays a prominent role in regulating gene expression and increasing the complexity of the transcriptome and proteome. We use polyadenylation selected long-read isoform sequencing to obtain full-length transcript sequences in porcine muscles at five developmental stages. We identify numerous novel transcripts unannotated in the existing pig genome, including transcripts mapping to known and unknown gene loci, and widespread transcript diversity in porcine muscles. The top 100 most isoformic genes are mainly enriched in Gene Ontology terms related to muscle growth and development. It is revealed that intron retention/exon inclusion and the usage of distal polyadenylation site (PAS) are associated with ageing through analyzing changes of AS and PAS during muscle development. We also identify developmental changes in major transcripts and major PASs. Furthermore, genes/transcripts important for muscle development are identified. The results confirm the importance of AS and APA in pig muscles, substantially increasing transcriptional diversity and showing an important mechanism underlying gene regulation in muscles.
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Affiliation(s)
- Yuanlu Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Yu Pang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaoxu Wu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Rongru Zhu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Liang Wang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ming Tian
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xinmiao He
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
| | - Xiuqin Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China.
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18
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Verdejo-Torres O, Klein DC, Novoa-Aponte L, Carrazco-Carrillo J, Bonilla-Pinto D, Rivera A, Bakhshian A, Fitisemanu FM, Jiménez-González ML, Flinn L, Pezacki AT, Lanzirotti A, Ortiz Frade LA, Chang CJ, Navea JG, Blaby-Haas CE, Hainer SJ, Padilla-Benavides T. Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation and metal homeostasis. PLoS Genet 2024; 20:e1011495. [PMID: 39637238 DOI: 10.1371/journal.pgen.1011495] [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: 07/01/2024] [Revised: 12/26/2024] [Accepted: 11/12/2024] [Indexed: 12/07/2024] Open
Abstract
Copper (Cu) is essential for respiration, neurotransmitter synthesis, oxidative stress response, and transcription regulation, with imbalances leading to neurological, cognitive, and muscular disorders. Here we show the role of a novel Cu-binding protein (Cu-BP) in mammalian transcriptional regulation, specifically on skeletal muscle differentiation using murine primary myoblasts. Utilizing synchrotron X-ray fluorescence-mass spectrometry, we identified murine cysteine-rich intestinal protein 2 (mCrip2) as a key Cu-BP abundant in both nuclear and cytosolic fractions. mCrip2 binds two to four Cu+ ions with high affinity and presents limited redox potential. CRISPR/Cas9-mediated deletion of mCrip2 impaired myogenesis, likely due to Cu accumulation in cells. CUT&RUN and transcriptome analyses revealed its association with gene promoters, including MyoD1 and metallothioneins, suggesting a novel Cu-responsive regulatory role for mCrip2. Our work describes the significance of mCrip2 in skeletal muscle differentiation and metal homeostasis, expanding understanding of the Cu-network in myoblasts. Copper (Cu) is essential for various cellular processes, including respiration and stress response, but imbalances can cause serious health issues. This study reveals a new Cu-binding protein (Cu-BP) involved in muscle development in primary myoblasts. Using unbiased metalloproteomic techniques and high throughput sequencing, we identified mCrip2 as a key Cu-BP found in cell nuclei and cytoplasm. mCrip2 binds up to four Cu+ ions and has a limited redox potential. Deleting mCrip2 using CRISPR/Cas9 disrupted muscle formation due to Cu accumulation. Further analyses showed that mCrip2 regulates the expression of genes like MyoD1, essential for muscle differentiation, and metallothioneins in response to copper supplementation. This research highlights the importance of mCrip2 in muscle development and metal homeostasis, providing new insights into the Cu-network in cells.
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Affiliation(s)
- Odette Verdejo-Torres
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, United States of America
| | - David C Klein
- Department of Biological Sciences. University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lorena Novoa-Aponte
- Department of Chemistry and Biochemistry. Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Jaime Carrazco-Carrillo
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, United States of America
| | - Denzel Bonilla-Pinto
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, United States of America
| | - Antonio Rivera
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, United States of America
| | - Arpie Bakhshian
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, United States of America
| | - Fa'alataitaua M Fitisemanu
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, United States of America
| | - Martha L Jiménez-González
- Departamento de Electroquímica, Centro de Investigación y Desarrollo Tecnológico en Electroquímica, Santiago de Querétaro, Querétaro, México
| | - Lyra Flinn
- Chemistry Department. Skidmore College, Saratoga Springs, New York, United States of America
| | - Aidan T Pezacki
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
- Department of Chemistry. University of California, Berkeley, California, United States of America
| | - Antonio Lanzirotti
- Center for Advanced Radiation Sources, The University of Chicago, Lemont, Illinois, United States of America
| | - Luis Antonio Ortiz Frade
- Departamento de Electroquímica, Centro de Investigación y Desarrollo Tecnológico en Electroquímica, Santiago de Querétaro, Querétaro, México
| | - Christopher J Chang
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
- Department of Chemistry. University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology. University of California, Berkeley, California, United States of America
| | - Juan G Navea
- Chemistry Department. Skidmore College, Saratoga Springs, New York, United States of America
| | - Crysten E Blaby-Haas
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California & DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sarah J Hainer
- Department of Biological Sciences. University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvanian United States of America
| | - Teresita Padilla-Benavides
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, United States of America
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19
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Holman AR, Tran S, Destici E, Farah EN, Li T, Nelson AC, Engler AJ, Chi NC. Single-cell multi-modal integrative analyses highlight functional dynamic gene regulatory networks directing human cardiac development. CELL GENOMICS 2024; 4:100680. [PMID: 39437788 PMCID: PMC11605693 DOI: 10.1016/j.xgen.2024.100680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/01/2024] [Accepted: 09/23/2024] [Indexed: 10/25/2024]
Abstract
Illuminating the precise stepwise genetic programs directing cardiac development provides insights into the mechanisms of congenital heart disease and strategies for cardiac regenerative therapies. Here, we integrate in vitro and in vivo human single-cell multi-omic studies with high-throughput functional genomic screening to reveal dynamic, cardiac-specific gene regulatory networks (GRNs) and transcriptional regulators during human cardiomyocyte development. Interrogating developmental trajectories reconstructed from single-cell data unexpectedly reveal divergent cardiomyocyte lineages with distinct gene programs based on developmental signaling pathways. High-throughput functional genomic screens identify key transcription factors from inferred GRNs that are functionally relevant for cardiomyocyte lineages derived from each pathway. Notably, we discover a critical heat shock transcription factor 1 (HSF1)-mediated cardiometabolic GRN controlling cardiac mitochondrial/metabolic function and cell survival, also observed in fetal human cardiomyocytes. Overall, these multi-modal genomic studies enable the systematic discovery and validation of coordinated GRNs and transcriptional regulators controlling the development of distinct human cardiomyocyte populations.
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Affiliation(s)
- Alyssa R Holman
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shaina Tran
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eugin Destici
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elie N Farah
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ting Li
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Aileena C Nelson
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Institute of Engineering Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92093, USA
| | - Neil C Chi
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Institute of Engineering Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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20
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Putman JN, Watson SD, Zhang Z, Khandelwal N, Kulkarni A, Gibson JR, Huber KM. Pre- and Postsynaptic MEF2C Promotes Experience-Dependent, Input-Specific Development of Cortical Layer 4 to Layer 2/3 Excitatory Synapses and Regulates Activity-Dependent Expression of Synaptic Cell Adhesion Molecules. J Neurosci 2024; 44:e0098242024. [PMID: 39317473 PMCID: PMC11551898 DOI: 10.1523/jneurosci.0098-24.2024] [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: 01/12/2024] [Revised: 08/29/2024] [Accepted: 09/13/2024] [Indexed: 09/26/2024] Open
Abstract
Experience- and activity-dependent transcription is a candidate mechanism to mediate development and refinement of specific cortical circuits. Here, we demonstrate that the activity-dependent transcription factor myocyte enhancer factor 2C (MEF2C) is required in both presynaptic layer (L) 4 and postsynaptic L2/3 mouse (male and female) somatosensory (S1) cortical neurons for development of this specific synaptic connection. While postsynaptic deletion of Mef2c weakens L4 synaptic inputs, it has no effect on inputs from local L2/3, contralateral S1, or the ipsilateral frontal/motor cortex. Similarly, homozygous or heterozygous deletion of Mef2c in presynaptic L4 neurons weakens L4 to L2/3 excitatory synaptic inputs by decreasing presynaptic release probability. Postsynaptic MEF2C is specifically required during an early postnatal, experience-dependent, period for L4 to L2/3 synapse function, and expression of transcriptionally active MEF2C (MEF2C-VP16) rescues weak L4 to L2/3 synaptic strength in sensory-deprived mice. Together, these results suggest that experience- and/or activity-dependent transcriptional activation of MEF2C promotes development of L4 to L2/3 synapses. Additionally, MEF2C regulates the expression of many pre- and postsynaptic genes in postnatal cortical neurons. Interestingly, MEF2C was necessary for activity-dependent expression of many presynaptic genes, including those that function in transsynaptic adhesion and neurotransmitter release. This work provides mechanistic insight into the experience-dependent development of specific cortical circuits.
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Affiliation(s)
- Jennifer N Putman
- Department of Neuroscience, O'Donnell Brain Institute, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Sean D Watson
- Department of Neuroscience, O'Donnell Brain Institute, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Zhe Zhang
- Department of Neuroscience, O'Donnell Brain Institute, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Nitin Khandelwal
- Department of Neuroscience, O'Donnell Brain Institute, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Ashwinikumar Kulkarni
- Department of Neuroscience, O'Donnell Brain Institute, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Jay R Gibson
- Department of Neuroscience, O'Donnell Brain Institute, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Kimberly M Huber
- Department of Neuroscience, O'Donnell Brain Institute, UT Southwestern Medical Center, Dallas, Texas 75390
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21
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Meng S, Xing S, Xu H, Li J, Jiang Y, He H, Cai H, Li M. Integrated analysis of intestinal microbial community and muscle transcriptome profile in rabbits. Anim Biotechnol 2024; 35:2387015. [PMID: 39145993 DOI: 10.1080/10495398.2024.2387015] [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] [Indexed: 08/16/2024]
Abstract
Intestinal microbial community plays an important part in maintaining health and skeletal muscle development in livestock. This study is the first of its kind in the world. In order to better understand the relationship between gut microbiota and gene expression in skeletal muscle of rabbits, caecum contents and longissimus dorsi tissues of rabbits at 0 d (S1), 35 d (S2) and 70d (S3) were collected and subjected for 16S rRNA sequencing and transcriptome sequencing. Our results showed that, among three groups of rabbits, Firmicutes and Bacteroidetes were the dominant phyla at the phylum level, while Akmansia, Bacteroides and Ruminobacter were the dominant genera at the genus level, and the relative abundance of Akmansia and Bacteroides increased firstly and then decreased from 0 d to 70 d. By analyzing the transcriptome sequencing data, we identified 2866, 2446 and 4541 differentially expressed genes (DEGs) in S1 vs S2, S2 vs S3 and S1 vs S3 groups, respectively. Finally, we performed correlation analysis between gut microbiota and the expression levels of muscle development-related genes of rabbits at 0 d and 70 d. Compared with 0 day old rabbits, in 70 day old rabbits Acinetobacter and Cronbacter with decreased abundance, and Ruminococcaceae_UCG-014 and Ruminococcus_1 with increase abundance is beneficial to caecum health in rabbits. These results will lay a foundation for further re-searches about the relationship between caecum microflora and muscle development in rabbits.
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Affiliation(s)
- Shengbo Meng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, P.R. China
| | - Shanshan Xing
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, P.R. China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, P.R. China
| | - Jing Li
- Animal Health Supervision Institute of Biyang, Henan, P.R. China
| | - Yixuan Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, P.R. China
| | - Hui He
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, P.R. China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, P.R. China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, P.R. China
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22
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Li J, Fu S, Tian Y, Zhang X, Meng Y, Zhao X, Liu S, Zhang Y, Sun J. A myogenic regulatory factor is required for myogenesis during limb regeneration in the Chinese mitten crab. Int J Biol Macromol 2024; 279:135024. [PMID: 39208909 DOI: 10.1016/j.ijbiomac.2024.135024] [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: 04/08/2024] [Revised: 08/14/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Myogenic regulatory factors (MRFs) are a group of transcription factors that regulate the activity of skeletal muscle cells during embryonic development and postnatal myogenesis in various vertebrate species. However, the role of MRFs in limb regeneration remains poorly understood in crustaceans. In this study, we identified a full-length cDNA encoding a myogenic regulatory factor from Eriocheir sinensis (EsMRF) and evaluated its mRNA expression profile during muscle development, growth, and regeneration. The expression of EsMRF was found to correlate with the onset of muscle formation during development and with the regeneration process following limb autotomy. To elucidate the function of MRF during limb regeneration in E. sinensis, we assessed regenerative efficiency using RNA interference (RNAi) targeting EsMRF. Our findings revealed that the blockade of MRF delayed limb regeneration by disrupting the proliferation and myogenesis of blastema cells at the basal growth stage. Furthermore, luciferase assays results demonstrated that EsMRF can transcriptionally activate target myogenic genes, either through direct binding to their promoters or by interacting with co-regulators such as EsHEB or EsMEF2. This study identifies a novel MRF in E. sinensis and elucidates its function during limb regeneration, thereby contributing to our understanding of muscle growth and regeneration mechanisms in crustaceans.
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Affiliation(s)
- Ju Li
- College of Life Science, Tianjin Normal University, Tianjin 300387, PR China; Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, PR China.
| | - Simiao Fu
- College of Life Science, Tianjin Normal University, Tianjin 300387, PR China
| | - Yuxin Tian
- College of Life Science, Tianjin Normal University, Tianjin 300387, PR China
| | - Xin Zhang
- College of Life Science, Tianjin Normal University, Tianjin 300387, PR China
| | - Yuxuan Meng
- College of Life Science, Tianjin Normal University, Tianjin 300387, PR China
| | - Xiumei Zhao
- College of Life Science, Tianjin Normal University, Tianjin 300387, PR China
| | - Sidi Liu
- College of Life Science, Tianjin Normal University, Tianjin 300387, PR China
| | - Yuxuan Zhang
- College of Life Science, Tianjin Normal University, Tianjin 300387, PR China
| | - Jinsheng Sun
- College of Life Science, Tianjin Normal University, Tianjin 300387, PR China; Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, PR China.
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23
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Wang X, Zhang J, Su J, Huang T, Lian L, Nie Q, Zhang X, Li J, Wang Y. Genome-wide mapping of the binding sites of myocyte enhancer factor 2A in chicken primary myoblasts. Poult Sci 2024; 103:104097. [PMID: 39094502 PMCID: PMC11345569 DOI: 10.1016/j.psj.2024.104097] [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: 05/03/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024] Open
Abstract
Myocyte enhancer factor 2A (MEF2A) is a transcription factor that plays a critical role in cell proliferation, differentiation and apoptosis. In contrast to the wide characterization of its regulation mechanism in mammalian skeletal muscle, its role in chickens is limited. Especially, its wide target genes remain to be identified. Therefore, we utilized Cleavage Under Targets and Tagmentation (CUT&Tag) technology to reveal the genome-wide binding profile of MEF2A in chicken primary myoblasts thus gaining insights into its potential role in muscle development. Our results revealed that MEF2A binding sites were primarily distributed in intergenic and intronic regions. Within the promoter region, although only 8.87% of MEF2A binding sites were found, these binding sites were concentrated around the transcription start site (TSS). Following peak annotation, a total of 1903 genes were identified as potential targets of MEF2A. Gene Ontology (GO) enrichment analysis further revealed that MEF2A target genes may be involved in the regulation of embryonic development in multiple organ systems, including muscle development, gland development, and visual system development. Moreover, a comparison of the MEF2A target genes identified in chicken primary myoblasts with those in mouse C2C12 cells revealed 388 target genes are conserved across species, 1515 target genes are chicken specific. Among these conserved genes, ankyrin repeat and SOCS box containing 5 (ASB5), transmembrane protein 182 (TMEM182), myomesin 2 (MYOM2), leucyl and cystinyl aminopeptidase (LNPEP), actinin alpha 2 (ACTN2), sorbin and SH3 domain containing 1 (SORBS1), ankyrin 3 (ANK3), sarcoglycan delta (SGCD), and ORAI calcium release-activated calcium modulator 1 (ORAI1) exhibited consistent expression patterns with MEF2A during embryonic muscle development. Finally, TMEM182, as an important negative regulator of muscle development, has been validated to be regulated by MEF2A by dual-luciferase and quantitative real-time PCR (qPCR) assays. In summary, our study for the first time provides a wide landscape of MEF2A target genes in chicken primary myoblasts, which supports the active role of MEF2A in chicken muscle development.
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Affiliation(s)
- Xinglong Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Jiannan Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Jiancheng Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Tianjiao Huang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Ling Lian
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, PR China
| | - Qinghua Nie
- Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou, PR China
| | - Xin Zhang
- Joint Nutrition Center for Animal Feeding of Sichuan University-Shengliyuan Group
| | - Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Joint Nutrition Center for Animal Feeding of Sichuan University-Shengliyuan Group
| | - Yajun Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Joint Nutrition Center for Animal Feeding of Sichuan University-Shengliyuan Group.
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24
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Ali D, Laighneach A, Corley E, Patlola SR, Mahoney R, Holleran L, McKernan DP, Kelly JP, Corvin AP, Hallahan B, McDonald C, Donohoe G, Morris DW. Direct targets of MEF2C are enriched for genes associated with schizophrenia and cognitive function and are involved in neuron development and mitochondrial function. PLoS Genet 2024; 20:e1011093. [PMID: 39259737 PMCID: PMC11419381 DOI: 10.1371/journal.pgen.1011093] [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: 12/06/2023] [Revised: 09/23/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024] Open
Abstract
Myocyte Enhancer Factor 2C (MEF2C) is a transcription factor that plays a crucial role in neurogenesis and synapse development. Genetic studies have identified MEF2C as a gene that influences cognition and risk for neuropsychiatric disorders, including autism spectrum disorder (ASD) and schizophrenia (SCZ). Here, we investigated the involvement of MEF2C in these phenotypes using human-derived neural stem cells (NSCs) and glutamatergic induced neurons (iNs), which represented early and late neurodevelopmental stages. For these cellular models, MEF2C function had previously been disrupted, either by direct or indirect mutation, and gene expression assayed using RNA-seq. We integrated these RNA-seq data with MEF2C ChIP-seq data to identify dysregulated direct target genes of MEF2C in the NSCs and iNs models. Several MEF2C direct target gene-sets were enriched for SNP-based heritability for intelligence, educational attainment and SCZ, as well as being enriched for genes containing rare de novo mutations reported in ASD and/or developmental disorders. These gene-sets are enriched in both excitatory and inhibitory neurons in the prenatal and adult brain and are involved in a wide range of biological processes including neuron generation, differentiation and development, as well as mitochondrial function and energy production. We observed a trans expression quantitative trait locus (eQTL) effect of a single SNP at MEF2C (rs6893807, which is associated with IQ) on the expression of a target gene, BNIP3L. BNIP3L is a prioritized risk gene from the largest genome-wide association study of SCZ and has a function in mitophagy in mitochondria. Overall, our analysis reveals that either direct or indirect disruption of MEF2C dysregulates sets of genes that contain multiple alleles associated with SCZ risk and cognitive function and implicates neuron development and mitochondrial function in the etiology of these phenotypes.
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Affiliation(s)
- Deema Ali
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Ireland
| | - Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Ireland
| | - Emma Corley
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Psychology, University of Galway, Ireland
| | - Saahithh Redddi Patlola
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- Discipline of Pharmacology & Therapeutics, School of Medicine, University of Galway, Ireland
| | - Rebecca Mahoney
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Ireland
| | - Laurena Holleran
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Psychology, University of Galway, Ireland
| | - Declan P. McKernan
- Discipline of Pharmacology & Therapeutics, School of Medicine, University of Galway, Ireland
| | - John P. Kelly
- Discipline of Pharmacology & Therapeutics, School of Medicine, University of Galway, Ireland
| | - Aiden P. Corvin
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Ireland
| | - Brian Hallahan
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- Discipline of Psychiatry, School of Medicine, University of Galway, Ireland
| | - Colm McDonald
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- Discipline of Psychiatry, School of Medicine, University of Galway, Ireland
| | - Gary Donohoe
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Psychology, University of Galway, Ireland
| | - Derek W. Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), University of Galway, Ireland
- School of Biological and Chemical Sciences, University of Galway, Ireland
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25
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Yu Z, Ai N, Xu X, Zhang P, Jin Z, Li X, Ma H. Exploring the Molecular Mechanism of Skeletal Muscle Development in Ningxiang Pig by Weighted Gene Co-Expression Network Analysis. Int J Mol Sci 2024; 25:9089. [PMID: 39201775 PMCID: PMC11354759 DOI: 10.3390/ijms25169089] [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: 07/05/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
With the continuous improvement in living standards, people's demand for high-quality meat is increasing. Ningxiang pig has delicious meat of high nutritional value, and is loved by consumers. However, its slow growth and low meat yield seriously restrict its efficient utilization. Gene expression is the internal driving force of life activities, so in order to fundamentally improve its growth rate, it is key to explore the molecular mechanism of skeletal muscle development in Ningxiang pigs. In this paper, Ningxiang boars were selected in four growth stages (30 days: weaning period, 90 days: nursing period, 150 days: early fattening period, and 210 days: late fattening period), and the longissimus dorsi (LD) muscle was taken from three boars in each stage. The fatty acid content, amino acid content, muscle fiber diameter density and type of LD were detected by gas chromatography, acidolysis, hematoxylin eosin (HE) staining and immunofluorescence (IF) staining. After transcription sequencing, weighted gene co-expression network analysis (WGCNA) combined with the phenotype of the LD was used to explore the key genes and signaling pathways affecting muscle development. The results showed that 10 modules were identified by WGCNA, including 5 modules related to muscle development stage, module characteristics of muscle fiber density, 5 modules characteristic of muscle fiber diameter, and a module characteristic of palmitoleic acid (C16:1) and linoleic acid (C18:2n6C). Gene ontology (GO) enrichment analysis found that 52 transcripts relating to muscle development were enriched in these modules, including 44 known genes and 8 novel genes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these genes were enriched in the auxin, estrogen and cyclic guanosine monophosphate-protein kinase G (cGMP-PKG) pathways. Twelve of these genes were transcription factors, there were interactions among 20 genes, and the interactions among 11 proteins in human, pig and mouse were stable. To sum up, through the integrated analysis of phenotype and transcriptome, this paper analyzed the key genes and possible regulatory networks of skeletal muscle development in Ningxiang pigs at various stages, to provide a reference for the in-depth study of skeletal muscle development.
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Affiliation(s)
| | | | | | | | | | | | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Z.Y.); (N.A.); (X.X.); (P.Z.); (Z.J.); (X.L.)
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26
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Yu C, Shen Q, Holmes AB, Mo T, Tosato A, Soni RK, Corinaldesi C, Koul S, Pasqualucci L, Hussein S, Forouhar F, Dalla-Favera R, Basso K. MEF2B C-terminal mutations enhance transcriptional activity and stability to drive B cell lymphomagenesis. Nat Commun 2024; 15:7195. [PMID: 39179580 PMCID: PMC11343756 DOI: 10.1038/s41467-024-51644-8] [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: 07/14/2023] [Accepted: 08/14/2024] [Indexed: 08/26/2024] Open
Abstract
The myocyte enhancer factor 2B (MEF2B) transcription factor is frequently mutated in germinal center (GC)-derived B-cell lymphomas. Its ammino (N)-terminal mutations drive lymphomagenesis by escaping interaction with transcriptional repressors, while the function of carboxy (C)-terminal mutations remains to be elucidated. Here, we show that MEF2B C-tail is physiologically phosphorylated at specific residues and phosphorylation at serine (S)324 is impaired by lymphoma-associated mutations. Lack of phosphorylation at S324 enhances the interaction of MEF2B with the SWI/SNF chromatin remodeling complex, leading to higher transcriptional activity. In addition, these mutants show an increased protein stability due to impaired interaction with the CUL3/KLHL12 ubiquitin complex. Mice expressing a phosphorylation-deficient lymphoma-associated MEF2B mutant display GC enlargement and develop GC-derived lymphomas, when crossed with Bcl2 transgenic mice. These results unveil converging mechanisms of action for a diverse spectrum of MEF2B mutations, all leading to its dysregulation and GC B-cell lymphomagenesis.
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Affiliation(s)
- Chuanjiang Yu
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Qiong Shen
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Tongwei Mo
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Anna Tosato
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY, USA
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Sanjay Koul
- Department of Biological Sciences & Geology, Queensborough Community College, City University of New York, Bayside, New York, NY, USA
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Shafinaz Hussein
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Farhad Forouhar
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY, USA
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA.
- Departments of Microbiology & Immunology, Genetics & Development, Columbia University, New York, NY, USA.
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA.
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27
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Li M, Lv W, Zhao Y, Huang W, Yuan Q, Yang H, Wang A, Zhou W, Li M. Effects of Substituting Tenebrio molitor and Elodea nuttallii as Feed on Growth, Flesh Quality and Intestinal Microbiota of Red Swamp Crayfish ( Procambarus clarkii). Foods 2024; 13:2292. [PMID: 39063375 PMCID: PMC11275352 DOI: 10.3390/foods13142292] [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: 06/12/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
This study aimed to evaluate the impact of substituting a portion of feed with Tenebrio molitor (TM) and Elodea nuttallii (EN) on crayfish culture. A total of 270 crayfish (5.1 ± 0.4 g) were fed three different diet combinations (A: 100% feed; B: 80% feed + 10% TM + 10% EN; C: 75% feed + 15% TM + 10% EN) for 12 weeks. The findings demonstrated that group C had an important beneficial impact on the growth performance of crayfish. This was evidenced by a rise in digestive enzyme activity (trypsin, lipase, and cellulase) in the intestinal and hepatopancreas, as well as an upregulation in the expression of growth-related genes (ghsr, igfbp7, mhc, mlc1, mef2, and pax7) in the muscle. Furthermore, the assessment of the flesh quality of crayfish muscle in group C was conducted. The findings indicated a significant increase (p < 0.05) in the energy value (moisture, crude protein, and crude lipid) within the muscle. The levels of delicious amino acids (Glu, Ala, Ser, Gly, and Tyr) and polyunsaturated fatty acids (ARA, DHA) were enhanced, resulting in an improved nutritional profile and flavor of the muscle while maintaining the Σn-3/Σn-6 ratio. The remodeling of the intestinal microbiota (abundance of Proteobacteria and ratio of Firmicutes/Bacteroidota bacteria) also revealed improved growth performance. Additional research is necessary to ascertain whether excessive use of TM or EN feed substitution can have negative effects on crayfish culture.
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Affiliation(s)
- Muyan Li
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (M.L.); (Y.Z.)
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (W.H.); (Q.Y.); (H.Y.)
| | - Weiwei Lv
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (W.H.); (Q.Y.); (H.Y.)
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yifan Zhao
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (M.L.); (Y.Z.)
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (W.H.); (Q.Y.); (H.Y.)
| | - Weiwei Huang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (W.H.); (Q.Y.); (H.Y.)
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Quan Yuan
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (W.H.); (Q.Y.); (H.Y.)
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Hang Yang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (W.H.); (Q.Y.); (H.Y.)
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Aimin Wang
- College of Marine and Biology Engineering, Yancheng Institute of Technology, Yancheng 224051, China;
| | - Wenzong Zhou
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (W.H.); (Q.Y.); (H.Y.)
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Mingyou Li
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (M.L.); (Y.Z.)
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28
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Szeto AC, Clark PA, Ferreira AC, Heycock M, Griffiths EL, Jou E, Mannion J, Luan SL, Storrar S, Knolle MD, Kozik P, Jolin HE, Fallon PG, McKenzie AN. Mef2d potentiates type-2 immune responses and allergic lung inflammation. Science 2024; 384:eadl0370. [PMID: 38935708 PMCID: PMC7616247 DOI: 10.1126/science.adl0370] [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: 09/25/2023] [Accepted: 05/02/2024] [Indexed: 06/29/2024]
Abstract
Innate lymphoid cells (ILCs) and adaptive T lymphocytes promote tissue homeostasis and protective immune responses. Their production depends on the transcription factor GATA3, which is further elevated specifically in ILC2s and T helper 2 cells to drive type-2 immunity during tissue repair, allergic disorders, and anti-helminth immunity. The control of this crucial up-regulation is poorly understood. Using CRISPR screens in ILCs we identified previously unappreciated myocyte-specific enhancer factor 2d (Mef2d)-mediated regulation of GATA3-dependent type-2 lymphocyte differentiation. Mef2d-deletion from ILC2s and/or T cells specifically protected against an allergen lung challenge. Mef2d repressed Regnase-1 endonuclease expression to enhance IL-33 receptor production and IL-33 signaling and acted downstream of calcium-mediated signaling to translocate NFAT1 to the nucleus to promote type-2 cytokine-mediated immunity.
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Affiliation(s)
- Aydan C.H. Szeto
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
| | - Paula A. Clark
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
| | - Ana C.F. Ferreira
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
| | - Morgan Heycock
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
| | - Emma L. Griffiths
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
| | - Eric Jou
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
| | - Jonathan Mannion
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
- Cambridge
University Hospitals,
Cambridge, CB2 0QQ, United Kingdom
| | - Shi-Lu Luan
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
| | - Sophie Storrar
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
| | - Martin D. Knolle
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
- Cambridge
University Hospitals,
Cambridge, CB2 0QQ, United Kingdom
| | - Patrycja Kozik
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
| | - Helen E. Jolin
- MRC Laboratory
of Molecular Biology,
Cambridge, CB2 0QH, United Kingdom
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29
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Zubrzycki M, Schramm R, Costard-Jäckle A, Grohmann J, Gummert JF, Zubrzycka M. Cardiac Development and Factors Influencing the Development of Congenital Heart Defects (CHDs): Part I. Int J Mol Sci 2024; 25:7117. [PMID: 39000221 PMCID: PMC11241401 DOI: 10.3390/ijms25137117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
The traditional description of cardiac development involves progression from a cardiac crescent to a linear heart tube, which in the phase of transformation into a mature heart forms a cardiac loop and is divided with the septa into individual cavities. Cardiac morphogenesis involves numerous types of cells originating outside the initial cardiac crescent, including neural crest cells, cells of the second heart field origin, and epicardial progenitor cells. The development of the fetal heart and circulatory system is subject to regulatation by both genetic and environmental processes. The etiology for cases with congenital heart defects (CHDs) is largely unknown, but several genetic anomalies, some maternal illnesses, and prenatal exposures to specific therapeutic and non-therapeutic drugs are generally accepted as risk factors. New techniques for studying heart development have revealed many aspects of cardiac morphogenesis that are important in the development of CHDs, in particular transposition of the great arteries.
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Affiliation(s)
- Marek Zubrzycki
- Department of Surgery for Congenital Heart Defects, Heart and Diabetes Center NRW, University Hospital, Ruhr-University Bochum, Georgstr. 11, 32545 Bad Oeynhausen, Germany;
| | - Rene Schramm
- Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital, Ruhr-University Bochum, Georgstr. 11, 32545 Bad Oeynhausen, Germany; (R.S.); (A.C.-J.); (J.F.G.)
| | - Angelika Costard-Jäckle
- Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital, Ruhr-University Bochum, Georgstr. 11, 32545 Bad Oeynhausen, Germany; (R.S.); (A.C.-J.); (J.F.G.)
| | - Jochen Grohmann
- Department of Congenital Heart Disease/Pediatric Cardiology, Heart and Diabetes Center NRW, University Hospital, Ruhr-University Bochum, Georgstr. 11, 32545 Bad Oeynhausen, Germany;
| | - Jan F. Gummert
- Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital, Ruhr-University Bochum, Georgstr. 11, 32545 Bad Oeynhausen, Germany; (R.S.); (A.C.-J.); (J.F.G.)
| | - Maria Zubrzycka
- Department of Clinical Physiology, Faculty of Medicine, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
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30
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Sun H, Liu Y, Wu C, Ma LQ, Guan D, Hong H, Yu H, Lin H, Huang X, Gao P. Dihalogenated nitrophenols in drinking water: Prevalence, resistance to household treatment, and cardiotoxic impact on zebrafish embryo. ECO-ENVIRONMENT & HEALTH 2024; 3:183-191. [PMID: 38646095 PMCID: PMC11031730 DOI: 10.1016/j.eehl.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/27/2024] [Accepted: 02/03/2024] [Indexed: 04/23/2024]
Abstract
Dihalogenated nitrophenols (2,6-DHNPs), an emerging group of aromatic disinfection byproducts (DBPs) detected in drinking water, have limited available information regarding their persistence and toxicological risks. The present study found that 2,6-DHNPs are resistant to major drinking water treatment processes (sedimentation and filtration) and households methods (boiling, filtration, microwave irradiation, and ultrasonic cleaning). To further assess their health risks, we conducted a series of toxicology studies using zebrafish embryos as the model organism. Our findings reveal that these emerging 2,6-DHNPs showed lethal toxicity 248 times greater than that of the regulated DBP, dichloroacetic acid. Specifically, at sublethal concentrations, exposure to 2,6-DHNPs generated reactive oxygen species (ROS), caused apoptosis, inhibited cardiac looping, and induced cardiac failure in zebrafish. Remarkably, the use of a ROS scavenger, N-acetyl-l-cysteine, considerably mitigated these adverse effects, emphasizing the essential role of ROS in 2,6-DHNP-induced cardiotoxicity. Our findings highlight the cardiotoxic potential of 2,6-DHNPs in drinking water even at low concentrations of 19 μg/L and the beneficial effect of N-acetyl-l-cysteine in alleviating the 2,6-DHNP-induced cardiotoxicity. This study underscores the urgent need for increased scrutiny of these emerging compounds in public health discussions.
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Affiliation(s)
- Hongjie Sun
- Key Laboratory of Watershed Earth Surface Processes and Ecological Security, College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Yingying Liu
- Key Laboratory of Watershed Earth Surface Processes and Ecological Security, College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Chunxiu Wu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Lena Q. Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dongxing Guan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huachang Hong
- Key Laboratory of Watershed Earth Surface Processes and Ecological Security, College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Haiying Yu
- Key Laboratory of Watershed Earth Surface Processes and Ecological Security, College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Hongjun Lin
- Key Laboratory of Watershed Earth Surface Processes and Ecological Security, College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Xianfeng Huang
- National and Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Peng Gao
- Department of Environmental and Occupational Health, and Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, United States
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232, United States
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31
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Avarlaid A, Falkenberg K, Lehe K, Mudò G, Belluardo N, Di Liberto V, Frinchi M, Tuvikene J, Timmusk T. An upstream enhancer and MEF2 transcription factors fine-tune the regulation of the Bdnf gene in cortical and hippocampal neurons. J Biol Chem 2024; 300:107411. [PMID: 38796067 PMCID: PMC11234010 DOI: 10.1016/j.jbc.2024.107411] [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: 01/15/2024] [Revised: 04/30/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024] Open
Abstract
The myocyte enhancer factor (MEF2) family of transcription factors, originally discovered for its pivotal role in muscle development and function, has emerged as an essential regulator in various aspects of brain development and neuronal plasticity. The MEF2 transcription factors are known to regulate numerous important genes in the nervous system, including brain-derived neurotrophic factor (BDNF), a small secreted neurotrophin responsible for promoting the survival, growth, and differentiation of neurons. The expression of the Bdnf gene is spatiotemporally controlled by various transcription factors binding to both its proximal and distal regulatory regions. While previous studies have investigated the connection between MEF2 transcription factors and Bdnf, the endogenous function of MEF2 factors in the transcriptional regulation of Bdnf remains largely unknown. Here, we aimed to deepen the knowledge of MEF2 transcription factors and their role in the regulation of Bdnf comparatively in rat cortical and hippocampal neurons. As a result, we demonstrate that the MEF2 transcription factor-dependent enhancer located at -4.8 kb from the Bdnf gene regulates the endogenous expression of Bdnf in hippocampal neurons. In addition, we confirm neuronal activity-dependent activation of the -4.8 kb enhancer in vivo. Finally, we show that specific MEF2 family transcription factors have unique roles in the regulation of Bdnf, with the specific function varying based on the particular brain region and stimuli. Altogether, we present MEF2 family transcription factors as crucial regulators of Bdnf expression, fine-tuning Bdnf expression through both distal and proximal regulatory regions.
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Affiliation(s)
- Annela Avarlaid
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
| | - Kaisa Falkenberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Karin Lehe
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Giuseppa Mudò
- Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, Palermo, Italy
| | - Natale Belluardo
- Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, Palermo, Italy
| | - Valentina Di Liberto
- Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, Palermo, Italy
| | - Monica Frinchi
- Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, Palermo, Italy
| | - Jürgen Tuvikene
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia; Protobios LLC, Tallinn, Estonia
| | - Tõnis Timmusk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia; Protobios LLC, Tallinn, Estonia.
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32
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Zhu K, He H, Guo H, Liu B, He X, Zhang N, Xian L, Zhang D. Identification of two MEF2s and their role in inhibiting the transcription of the mstn2a gene in the yellowfin seabream, Acanthopagrus latus (Hottuyn, 1782). Gene 2024; 909:148322. [PMID: 38423140 DOI: 10.1016/j.gene.2024.148322] [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: 11/14/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Myocyte-specific enhancer binding factor 2 (MEF2), which belongs to the MADS superfamily, is a pivotal and conserved transcription factor that combines with the E-box motif to control the expression of muscle genes. Myostatin (mstn), a muscle growth inhibitor, is a vital member of the TGF-β superfamily. Currently, an understanding of the mechanisms of A. latus mstn (Almstn) transcriptional regulation mediated by MEF2 in fish muscle development is lacking. In the present study, two AlMEF2s (AlMEF2A and AlMEF2B) and Almstn2a were characterized from Acanthopagrus latus. AlMEF2A and AlMEF2B had 456 and 315 amino acid (aa) residues, respectively. Two typical regions, a MADS-box, MEF2, and transcriptionally activated (TAD) domains, are present in both AlMEF2s. The expression profiles of the two AlMEF2 genes were similar. The AlMEF2 genes were mainly expressed in the brain, white muscle, and liver, while Almstn2a expression was higher in the brain than in other tissues. Moreover, the expression trends of AlMEF2s and Almstn2a were significantly changed after starvation and refeeding in the five groups. Additionally, truncation experiments showed that -987 to +168 and -105 to +168 were core promoters of Almstn2a that responded to AlMEF2A and AlMEF2B, respectively. The point mutation experiment confirmed that Almstn2a transcription relies on the mutation binding sites 1 or 5 (M1/5) and mutation binding sites 4 or 5 (M4/5) for AlMEF2A and AlMEF2B regulation, respectively. The electrophoretic mobile shift assay (EMSA) further verified that M1 (-527 to -512) was a pivotal site where AlMEF2A acted on the Almstn2a gene. Furthermore, a siRNA interference gene expression experiment showed that reduced levels of AlMEF2A or AlMEF2B could prominently increase Almstn2a transcription. These results provide new information about the regulation of Almstn2a transcriptional activity by AlMEF2s and a theoretical basis for the regulatory mechanisms involved in muscle development in fish.
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Affiliation(s)
- Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China
| | - Hongxi He
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China
| | - Huayang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China
| | - Baosuo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China
| | - Xin He
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China
| | - Lin Xian
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China
| | - Dianchang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China.
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Li SY, Wang YZ, Chen W, Ma LX, Zhang JM, Zhang YL, Zeng YQ. Integrated analysis of the DNA methylome and RNA transcriptome during the development of skeletal muscle in Duroc pigs. BMC Genomics 2024; 25:504. [PMID: 38778260 PMCID: PMC11110227 DOI: 10.1186/s12864-024-10404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Skeletal muscle development plays a crucial role in yield and quality of pork; however, this process is influenced by various factors. In this study, we employed whole-genome bisulfite sequencing (WGBS) and transcriptome sequencing to comprehensively investigate the longissimus dorsi muscle (LDM), aiming to identify key genes that impact the growth and development of Duroc pigs with different average daily gains (ADGs). RESULTS Eight pigs were selected and divided into two groups based on ADGs: H (774.89 g) group and L (658.77 g) group. Each pair of the H and L groups were half-siblings. The results of methylation sequencing revealed 2631 differentially methylated genes (DMGs) involved in metabolic processes, signalling, insulin secretion, and other biological activities. Furthermore, a joint analysis was conducted on these DMGs and the differentially expressed genes (DEGs) obtained from transcriptome sequencing of the same individual. This analysis identified 316 differentially methylated and differentially expressed genes (DMEGs), including 18 DMEGs in promoter regions and 294 DMEGs in gene body regions. Finally, LPAR1 and MEF2C were selected as candidate genes associated with muscle development. Bisulfite sequencing PCR (BSP) and quantitative real-time PCR (qRT-PCR) revealed that the promoter region of LPAR1 exhibited significantly lower methylation levels (P < 0.05) and greater expression levels (P < 0.05) in the H group than in the L group. Additionally, hypermethylation was observed in the gene body region of MEF2C, as was a low expression level, in the H group (P < 0.05). CONCLUSIONS These results suggest that the differences in the ADGs of Duroc pigs fed the same diet may be influenced by the methylation levels and expression levels of genes related to skeletal muscle development.
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Affiliation(s)
- Shi-Yin Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Street, Taian, 271018, Shandong, China
| | - Yun-Zhou Wang
- Shandong Vocational Animal Science and Veterinary College, Weifang, 261061, Shandong, China
| | - Wei Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Street, Taian, 271018, Shandong, China
| | - Li-Xia Ma
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Street, Taian, 271018, Shandong, China
| | - Jian-Min Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Street, Taian, 271018, Shandong, China
| | - Yu-Lun Zhang
- Department, Shandong Ding Tai Animal Husbandry Co. Ltd., Jinan, 250300, Shandong, China
| | - Yong-Qing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Street, Taian, 271018, Shandong, China.
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Wang X, Shen H, Chen Y, Zhang Y, Wang J, Liu S, Xu B, Wang H, Frangou C, Zhang J. MEF2D Functions as a Tumor Suppressor in Breast Cancer. Int J Mol Sci 2024; 25:5207. [PMID: 38791246 PMCID: PMC11121549 DOI: 10.3390/ijms25105207] [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: 03/19/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The myocyte enhancer factor 2 (MEF2) gene family play fundamental roles in the genetic programs that control cell differentiation, morphogenesis, proliferation, and survival in a wide range of cell types. More recently, these genes have also been implicated as drivers of carcinogenesis, by acting as oncogenes or tumor suppressors depending on the biological context. Nonetheless, the molecular programs they regulate and their roles in tumor development and progression remain incompletely understood. The present study evaluated whether the MEF2D transcription factor functions as a tumor suppressor in breast cancer. The knockout of the MEF2D gene in mouse mammary epithelial cells resulted in phenotypic changes characteristic of neoplastic transformation. These changes included enhanced cell proliferation, a loss of contact inhibition, and anchorage-independent growth in soft agar, as well as the capacity for tumor development in mice. Mechanistically, the knockout of MEF2D induced the epithelial-to-mesenchymal transition (EMT) and activated several oncogenic signaling pathways, including AKT, ERK, and Hippo-YAP. Correspondingly, a reduced expression of MEF2D was observed in human triple-negative breast cancer cell lines, and a low MEF2D expression in tissue samples was found to be correlated with a worse overall survival and relapse-free survival in breast cancer patients. MEF2D may, thus, be a putative tumor suppressor, acting through selective gene regulatory programs that have clinical and therapeutic significance.
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Affiliation(s)
- Xiaoxia Wang
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
| | - He Shen
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
| | - Yanmin Chen
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
| | - Yali Zhang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (Y.Z.); (J.W.); (S.L.)
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (Y.Z.); (J.W.); (S.L.)
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (Y.Z.); (J.W.); (S.L.)
| | - Bo Xu
- Department of Pathology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA;
| | - Hai Wang
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA;
| | - Costa Frangou
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA;
| | - Jianmin Zhang
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
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Verdejo-Torres O, Klein DC, Novoa-Aponte L, Carrazco-Carrillo J, Bonilla-Pinto D, Rivera A, Fitisemanu F, Jiménez-González ML, Flinn L, Pezacki AT, Lanzirotti A, Ortiz-Frade LA, Chang CJ, Navea JG, Blaby-Haas C, Hainer SJ, Padilla-Benavides T. Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592485. [PMID: 38746126 PMCID: PMC11092763 DOI: 10.1101/2024.05.03.592485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Copper (Cu) is an essential trace element required for respiration, neurotransmitter synthesis, oxidative stress response, and transcriptional regulation. Imbalance in Cu homeostasis can lead to several pathological conditions, affecting neuronal, cognitive, and muscular development. Mechanistically, Cu and Cu-binding proteins (Cu-BPs) have an important but underappreciated role in transcription regulation in mammalian cells. In this context, our lab investigates the contributions of novel Cu-BPs in skeletal muscle differentiation using murine primary myoblasts. Through an unbiased synchrotron X-ray fluorescence-mass spectrometry (XRF/MS) metalloproteomic approach, we identified the murine cysteine rich intestinal protein 2 (mCrip2) in a sample that showed enriched Cu signal, which was isolated from differentiating primary myoblasts derived from mouse satellite cells. Immunolocalization analyses showed that mCrip2 is abundant in both nuclear and cytosolic fractions. Thus, we hypothesized that mCrip2 might have differential roles depending on its cellular localization in the skeletal muscle lineage. mCrip2 is a LIM-family protein with 4 conserved Zn2+-binding sites. Homology and phylogenetic analyses showed that mammalian Crip2 possesses histidine residues near two of the Zn2+-binding sites (CX2C-HX2C) which are potentially implicated in Cu+-binding and competition with Zn2+. Biochemical characterization of recombinant human hsCRIP2 revealed a high Cu+-binding affinity for two and four Cu+ ions and limited redox potential. Functional characterization using CRISPR/Cas9-mediated deletion of mCrip2 in primary myoblasts did not impact proliferation, but impaired myogenesis by decreasing the expression of differentiation markers, possibly attributed to Cu accumulation. Transcriptome analyses of proliferating and differentiating mCrip2 KO myoblasts showed alterations in mRNA processing, protein translation, ribosome synthesis, and chromatin organization. CUT&RUN analyses showed that mCrip2 associates with a select set of gene promoters, including MyoD1 and metallothioneins, acting as a novel Cu-responsive or Cu-regulating protein. Our work demonstrates novel regulatory functions of mCrip2 that mediate skeletal muscle differentiation, presenting new features of the Cu-network in myoblasts.
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Affiliation(s)
- Odette Verdejo-Torres
- Department of Molecular Biology and Biochemistry, Wesleyan University, CT, 06459. USA
| | - David C. Klein
- Department of Biological Sciences. University of Pittsburgh, Pittsburgh, PA. 15207. USA
| | - Lorena Novoa-Aponte
- Present address: Genetics and Metabolism Section, Liver Diseases Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD. USA
| | | | - Denzel Bonilla-Pinto
- Department of Molecular Biology and Biochemistry, Wesleyan University, CT, 06459. USA
| | - Antonio Rivera
- Department of Molecular Biology and Biochemistry, Wesleyan University, CT, 06459. USA
| | | | | | - Lyra Flinn
- Chemistry Department. Skidmore College, Saratoga Springs New York, 12866. USA
| | - Aidan T. Pezacki
- Department of Chemistry. University of California, Berkeley, California, 94720. USA
| | - Antonio Lanzirotti
- Center for Advanced Radiation Sources, The University of Chicago, Lemont, IL 60439. USA
| | | | - Christopher J. Chang
- Department of Chemistry. University of California, Berkeley, California, 94720. USA
- Department of Molecular and Cell Biology. University of California, Berkeley, California, 94720. USA
| | - Juan G. Navea
- Chemistry Department. Skidmore College, Saratoga Springs New York, 12866. USA
| | - Crysten Blaby-Haas
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA & DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA. USA
| | - Sarah J. Hainer
- Department of Biological Sciences. University of Pittsburgh, Pittsburgh, PA. 15207. USA
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36
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Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A. Folding of Class IIa HDAC Derived Peptides into α-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA. J Mol Biol 2024; 436:168541. [PMID: 38492719 DOI: 10.1016/j.jmb.2024.168541] [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: 10/15/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Interaction of transcription factor myocyte enhancer factor-2 (MEF2) family members with class IIa histone deacetylases (HDACs) has been implicated in a wide variety of diseases. Though considerable knowledge on this topic has been accumulated over the years, a high resolution and detailed analysis of the binding mode of multiple class IIa HDAC derived peptides with MEF2D is still lacking. To fulfil this gap, we report here the crystal structure of MEF2D in complex with double strand DNA and four different class IIa HDAC derived peptides, namely HDAC4, HDAC5, HDAC7 and HDAC9. All class IIa HDAC derived peptides form extended amphipathic α-helix structures that fit snugly in the hydrophobic groove of MEF2D domain. Binding mode of class IIa HDAC derived peptides to MEF2D is very similar and occur primarily through nonpolar interactions mediated by highly conserved branched hydrophobic amino acids. Further studies revealed that class IIa HDAC derived peptides are unstructured in solution and appear to adopt a folded α-helix structure only upon binding to MEF2D. Comparison of our peptide-protein complexes with previously characterized structures of MEF2 bound to different co-activators and co-repressors, highlighted both differences and similarities, and revealed the adaptability of MEF2 in protein-protein interactions. The elucidation of the three-dimensional structure of MEF2D in complex with multiple class IIa HDAC derived peptides provide not only a better understanding of the molecular basis of their interactions but also have implications for the development of novel antagonist.
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Affiliation(s)
- Monica Chinellato
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy
| | - Stefano Perin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
| | - Alberto Carli
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy
| | - Luana Lastella
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
| | - Giuseppe Borsato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
| | - Eros Di Giorgio
- Department of Medicine, Università Degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medicine, Università Degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Laura Cendron
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy.
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy; European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy.
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37
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Hoang NM, Liu Y, Bates PD, Heaton AR, Lopez AF, Liu P, Zhu F, Chen R, Kondapelli A, Zhang X, Selberg PE, Ngo VN, Skala MC, Capitini CM, Rui L. Targeting DNMT3A-mediated oxidative phosphorylation to overcome ibrutinib resistance in mantle cell lymphoma. Cell Rep Med 2024; 5:101484. [PMID: 38554704 PMCID: PMC11031386 DOI: 10.1016/j.xcrm.2024.101484] [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: 04/11/2023] [Revised: 11/21/2023] [Accepted: 03/04/2024] [Indexed: 04/02/2024]
Abstract
The use of Bruton tyrosine kinase (BTK) inhibitors such as ibrutinib achieves a remarkable clinical response in mantle cell lymphoma (MCL). Acquired drug resistance, however, is significant and affects long-term survival of MCL patients. Here, we demonstrate that DNA methyltransferase 3A (DNMT3A) is involved in ibrutinib resistance. We find that DNMT3A expression is upregulated upon ibrutinib treatment in ibrutinib-resistant MCL cells. Genetic and pharmacological analyses reveal that DNMT3A mediates ibrutinib resistance independent of its DNA-methylation function. Mechanistically, DNMT3A induces the expression of MYC target genes through interaction with the transcription factors MEF2B and MYC, thus mediating metabolic reprogramming to oxidative phosphorylation (OXPHOS). Targeting DNMT3A with low-dose decitabine inhibits the growth of ibrutinib-resistant lymphoma cells both in vitro and in a patient-derived xenograft mouse model. These findings suggest that targeting DNMT3A-mediated metabolic reprogramming to OXPHOS with decitabine provides a potential therapeutic strategy to overcome ibrutinib resistance in relapsed/refractory MCL.
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Affiliation(s)
- Nguyet-Minh Hoang
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Yunxia Liu
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Paul D Bates
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Alexa R Heaton
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Angelica F Lopez
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Biomedical Engineering, University of Wisconsin-Madison College of Engineering, Madison, WI 53706, USA
| | - Peng Liu
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Fen Zhu
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Ruoyu Chen
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Apoorv Kondapelli
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Xiyu Zhang
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Paul E Selberg
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Vu N Ngo
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Melissa C Skala
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Biomedical Engineering, University of Wisconsin-Madison College of Engineering, Madison, WI 53706, USA
| | - Christian M Capitini
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Lixin Rui
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA.
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38
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Kuang R, Xu Z, Zhou H, Zhang Z, Peng H, Wang D, Xu X, Zhao S, Zhao Y, Zhu M. H3K27ac modification and transcription characteristics of adipose and muscle tissues in Chuxiang Black pig. Anim Genet 2024; 55:217-229. [PMID: 38296601 DOI: 10.1111/age.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 12/25/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
The establishment of high-quality pork breeds for improving meat quality in the pig industry is needed. The Chuxiang Black (CX) pig is a new breed developed from Chinese local pigs and Western lean pigs that has a high proportion of lean meat and excellent meat quality. However, the characteristics of cis-regulatory elements in CX pigs are still unknown. In this study, cis-regulatory elements of muscle and adipose tissues in CX pigs were investigated using ChIP-seq and RNA sequencing. Compared with the reported cis-regulatory elements of muscle and adipose tissues, 1768 and 1012 highly activated enhancers and 433 and 275 highly activated promoters in CX muscle and adipose tissues were identified, respectively. Motif analysis showed that transcription factors, such as MEF2A and MEF2C, were core regulators of highly activated enhancers and promoters in muscle. Similarly, the transcription factors JUNB and CUX1 were identified as essential for highly activated enhancers and promoters in CX adipose tissue. These results enrich the resources for the analysis of cis-regulatory elements in the pig genome and provide new basic data for further meat quality improvement through breeding in pigs.
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Affiliation(s)
- Renzhuo Kuang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Zhixiang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Honghong Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Zhao Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Hao Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Daoyuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yunxia Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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39
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Alamin M, Humaira Sultana M, Babarinde IA, Azad AKM, Moni MA, Xu H. Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs). Brief Bioinform 2024; 25:bbae230. [PMID: 38739758 PMCID: PMC11089419 DOI: 10.1093/bib/bbae230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/07/2024] [Accepted: 04/27/2024] [Indexed: 05/16/2024] Open
Abstract
The complicated process of neuronal development is initiated early in life, with the genetic mechanisms governing this process yet to be fully elucidated. Single-cell RNA sequencing (scRNA-seq) is a potent instrument for pinpointing biomarkers that exhibit differential expression across various cell types and developmental stages. By employing scRNA-seq on human embryonic stem cells, we aim to identify differentially expressed genes (DEGs) crucial for early-stage neuronal development. Our focus extends beyond simply identifying DEGs. We strive to investigate the functional roles of these genes through enrichment analysis and construct gene regulatory networks to understand their interactions. Ultimately, this comprehensive approach aspires to illuminate the molecular mechanisms and transcriptional dynamics governing early human brain development. By uncovering potential links between these DEGs and intelligence, mental disorders, and neurodevelopmental disorders, we hope to shed light on human neurological health and disease. In this study, we have used scRNA-seq to identify DEGs involved in early-stage neuronal development in hESCs. The scRNA-seq data, collected on days 26 (D26) and 54 (D54), of the in vitro differentiation of hESCs to neurons were analyzed. Our analysis identified 539 DEGs between D26 and D54. Functional enrichment of those DEG biomarkers indicated that the up-regulated DEGs participated in neurogenesis, while the down-regulated DEGs were linked to synapse regulation. The Reactome pathway analysis revealed that down-regulated DEGs were involved in the interactions between proteins located in synapse pathways. We also discovered interactions between DEGs and miRNA, transcriptional factors (TFs) and DEGs, and between TF and miRNA. Our study identified 20 significant transcription factors, shedding light on early brain development genetics. The identified DEGs and gene regulatory networks are valuable resources for future research into human brain development and neurodevelopmental disorders.
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Affiliation(s)
- Md Alamin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | | | - Isaac Adeyemi Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - A K M Azad
- Department of Mathematics and Statistics, College of Science, Imam Muhammad Ibn Saud Islamic University, Riyadh 11432, Saudi Arabia
| | - Mohammad Ali Moni
- Artificial Intelligence and Cyber Futures Institute, Charles Sturt University, Bathurst, NSW 2795, Australia
| | - Haiming Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
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40
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Dai S, Guo L, Dey R, Guo M, Zhang X, Bates D, Cayford J, Jiang L, Wei H, Chen Z, Zhang Y, Chen L, Chen Y. Structural insights into the HDAC4-MEF2A-DNA complex and its implication in long-range transcriptional regulation. Nucleic Acids Res 2024; 52:2711-2723. [PMID: 38281192 PMCID: PMC10954479 DOI: 10.1093/nar/gkae036] [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: 07/27/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
Class IIa Histone deacetylases (HDACs), including HDAC4, 5, 7 and 9, play key roles in multiple important developmental and differentiation processes. Recent studies have shown that class IIa HDACs exert their transcriptional repressive function by interacting with tissue-specific transcription factors, such as members of the myocyte enhancer factor 2 (MEF2) family of transcription factors. However, the molecular mechanism is not well understood. In this study, we determined the crystal structure of an HDAC4-MEF2A-DNA complex. This complex adopts a dumbbell-shaped overall architecture, with a 2:4:2 stoichiometry of HDAC4, MEF2A and DNA molecules. In the complex, two HDAC4 molecules form a dimer through the interaction of their glutamine-rich domain (GRD) to form the stem of the 'dumbbell'; while two MEF2A dimers and their cognate DNA molecules are bridged by the HDAC4 dimer. Our structural observations were then validated using biochemical and mutagenesis assays. Further cell-based luciferase reporter gene assays revealed that the dimerization of HDAC4 is crucial in its ability to repress the transcriptional activities of MEF2 proteins. Taken together, our findings not only provide the structural basis for the assembly of the HDAC4-MEF2A-DNA complex but also shed light on the molecular mechanism of HDAC4-mediated long-range gene regulation.
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Affiliation(s)
- Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410078, China
| | - Liang Guo
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
| | - Raja Dey
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiangqian Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Darren Bates
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
| | - Justin Cayford
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Longying Jiang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhuchu Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ye Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lin Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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Steiman S, Miyake T, McDermott JC. FoxP1 Represses MEF2A in Striated Muscle. Mol Cell Biol 2024; 44:57-71. [PMID: 38483114 PMCID: PMC10950271 DOI: 10.1080/10985549.2024.2323959] [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: 09/06/2023] [Revised: 12/14/2023] [Accepted: 01/23/2024] [Indexed: 03/19/2024] Open
Abstract
Myocyte enhancer factor 2 (MEF2) proteins are involved in multiple developmental, physiological, and pathological processes in vertebrates. Protein-protein interactions underlie the plethora of biological processes impacted by MEF2A, necessitating a detailed characterization of the MEF2A interactome. A nanobody based affinity-purification/mass spectrometry strategy was employed to achieve this goal. Specifically, the MEF2A protein complexes were captured from myogenic lysates using a GFP-tagged MEF2A protein immobilized with a GBP-nanobody followed by LC-MS/MS proteomic analysis to identify MEF2A interactors. After bioinformatic analysis, we further characterized the interaction of MEF2A with a transcriptional repressor, FOXP1. FOXP1 coprecipitated with MEF2A in proliferating myogenic cells which diminished upon differentiation (myotube formation). Ectopic expression of FOXP1 inhibited MEF2A driven myogenic reporter genes (derived from the creatine kinase muscle and myogenin genes) and delayed induction of endogenous myogenin during differentiation. Conversely, FOXP1 depletion enhanced MEF2A transactivation properties and myogenin expression. The FoxP1:MEF2A interaction is also preserved in cardiomyocytes and FoxP1 depletion enhanced cardiomyocyte hypertrophy. FOXP1 prevented MEF2A phosphorylation and activation by the p38MAPK pathway. Overall, these data implicate FOXP1 in restricting MEF2A function in order to avoid premature differentiation in myogenic progenitors and also to possibly prevent re-activation of embryonic gene expression in cardiomyocyte hypertrophy.
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Affiliation(s)
- Sydney Steiman
- Department of Biology, York University, Toronto, ON, Canada
- Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada
- Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada
| | - Tetsuaki Miyake
- Department of Biology, York University, Toronto, ON, Canada
- Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada
- Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada
| | - John C. McDermott
- Department of Biology, York University, Toronto, ON, Canada
- Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada
- Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada
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Xia L, Nie T, Lu F, Huang L, Shi X, Ren D, Lu J, Li X, Xu T, Cui B, Wang Q, Gao G, Yang Q. Direct regulation of FNIP1 and FNIP2 by MEF2 sustains MTORC1 activation and tumor progression in pancreatic cancer. Autophagy 2024; 20:505-524. [PMID: 37772772 PMCID: PMC10936626 DOI: 10.1080/15548627.2023.2259735] [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: 01/12/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023] Open
Abstract
MTOR (mechanistic target of rapamycin kinase) complex 1 (MTORC1) orchestrates diverse environmental signals to facilitate cell growth and is frequently activated in cancer. Translocation of MTORC1 from the cytosol to the lysosomal surface by the RRAG GTPases is the key step in MTORC1 activation. Here, we demonstrated that transcription factors MEF2A and MEF2D synergistically regulated MTORC1 activation via modulating its cyto-lysosome shutting. Mechanically, MEF2A and MEF2D controlled the transcription of FNIP1 and FNIP2, the components of the FLCN-FNIP1 or FNIP2 complex that acts as a RRAGC-RRAGD GTPase-activating element to promote the recruitment of MTORC1 to lysosome and its activation. Furthermore, we determined that the pro-oncogenic protein kinase SRC/c-Src directly phosphorylated MEF2D at three conserved tyrosine residues. The tyrosine phosphorylation enhanced MEF2D transcriptional activity and was indispensable for MTORC1 activation. Finally, both the protein and tyrosine phosphorylation levels of MEF2D are elevated in human pancreatic cancers, positively correlating with MTORC1 activity. Depletion of both MEF2A and MEF2D or expressing the unphosphorylatable MEF2D mutant suppressed tumor cell growth. Thus, our study revealed a transcriptional regulatory mechanism of MTORC1 that promoted cell anabolism and proliferation and uncovered its critical role in pancreatic cancer progression.Abbreviation: ACTB: actin beta; ChIP: chromatin immunoprecipitation; EGF: epidermal growth factor; EIF4EBP1: eukaryotic translation initiation factor 4E binding protein 1; FLCN: folliculin; FNIP1: folliculin interacting protein 1; FNIP2: folliculin interacting protein 2; GAP: GTPase activator protein; GEF: guanine nucleotide exchange factors; GTPase: guanosine triphosphatase; LAMP2: lysosomal associated membrane protein 2; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MEF2: myocyte enhancer factor 2; MEF2A: myocyte enhancer factor 2A; MEF2D: myocyte enhancer factor 2D; MEF2D-3YF: Y131F, Y333F, Y337F mutant; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; NR4A1: nuclear receptor subfamily 4 group A member 1; RPTOR: regulatory associated protein of MTOR complex 1; RHEB: Ras homolog, mTORC1 binding; RPS6KB1: ribosomal protein S6 kinase B1; RRAG: Ras related GTP binding; RT-qPCR: real time-quantitative PCR; SRC: SRC proto-oncogene, non-receptor tyrosine kinase; TMEM192: transmembrane protein 192; WT: wild-type.
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Affiliation(s)
- Li Xia
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Tiejian Nie
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Fangfang Lu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Lu Huang
- Department of Anesthesiology, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiaolong Shi
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Dongni Ren
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jianjun Lu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiaobin Li
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Tuo Xu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Bozhou Cui
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Qing Wang
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Guodong Gao
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Qian Yang
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
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Cho JY, Rumschlag JA, Tsvetkov E, Proper DS, Lang H, Berto S, Assali A, Cowan CW. MEF2C Hypofunction in GABAergic Cells Alters Sociability and Prefrontal Cortex Inhibitory Synaptic Transmission in a Sex-Dependent Manner. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:100289. [PMID: 38390348 PMCID: PMC10881314 DOI: 10.1016/j.bpsgos.2024.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 02/24/2024] Open
Abstract
Background Heterozygous mutations or deletions of MEF2C cause a neurodevelopmental disorder termed MEF2C haploinsufficiency syndrome (MCHS), characterized by autism spectrum disorder and neurological symptoms. In mice, global Mef2c heterozygosity has produced multiple MCHS-like phenotypes. MEF2C is highly expressed in multiple cell types of the developing brain, including GABAergic (gamma-aminobutyric acidergic) inhibitory neurons, but the influence of MEF2C hypofunction in GABAergic neurons on MCHS-like phenotypes remains unclear. Methods We employed GABAergic cell type-specific manipulations to study mouse Mef2c heterozygosity in a battery of MCHS-like behaviors. We also performed electroencephalography, single-cell transcriptomics, and patch-clamp electrophysiology and optogenetics to assess the impact of Mef2c haploinsufficiency on gene expression and prefrontal cortex microcircuits. Results Mef2c heterozygosity in developing GABAergic cells produced female-specific deficits in social preference and altered approach-avoidance behavior. In female, but not male, mice, we observed that Mef2c heterozygosity in developing GABAergic cells produced 1) differentially expressed genes in multiple cell types, including parvalbumin-expressing GABAergic neurons, 2) baseline and social-related frontocortical network activity alterations, and 3) reductions in parvalbumin cell intrinsic excitability and inhibitory synaptic transmission onto deep-layer pyramidal neurons. Conclusions MEF2C hypofunction in female, but not male, developing GABAergic cells is important for typical sociability and approach-avoidance behaviors and normal parvalbumin inhibitory neuron function in the prefrontal cortex of mice. While there is no apparent sex bias in autism spectrum disorder symptoms of MCHS, our findings suggest that GABAergic cell-specific dysfunction in females with MCHS may contribute disproportionately to sociability symptoms.
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Affiliation(s)
- Jennifer Y. Cho
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
- Medical Scientist Training Program, Medical University of South Carolina, Charleston, South Carolina
| | - Jeffrey A. Rumschlag
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Evgeny Tsvetkov
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
| | - Divya S. Proper
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
| | - Hainan Lang
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Stefano Berto
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
| | - Ahlem Assali
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
| | - Christopher W. Cowan
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina
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Ferguson CA, Firulli BA, Zoia M, Osterwalder M, Firulli AB. Identification and characterization of Hand2 upstream genomic enhancers active in developing stomach and limbs. Dev Dyn 2024; 253:215-232. [PMID: 37551791 PMCID: PMC11365009 DOI: 10.1002/dvdy.646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The bHLH transcription factor HAND2 plays important roles in the development of the embryonic heart, face, limbs, and sympathetic and enteric nervous systems. To define how and when HAND2 regulates these developmental systems, requires understanding the transcriptional regulation of Hand2. RESULTS Remarkably, Hand2 is flanked by an extensive upstream gene desert containing a potentially diverse enhancer landscape. Here, we screened the regulatory interval 200 kb proximal to Hand2 for putative enhancers using evolutionary conservation and histone marks in Hand2-expressing tissues. H3K27ac signatures across embryonic tissues pointed to only two putative enhancer regions showing deep sequence conservation. Assessment of the transcriptional enhancer potential of these elements using transgenic reporter lines uncovered distinct in vivo enhancer activities in embryonic stomach and limb mesenchyme, respectively. Activity of the identified stomach enhancer was restricted to the developing antrum and showed expression within the smooth muscle and enteric neurons. Surprisingly, the activity pattern of the limb enhancer did not overlap Hand2 mRNA but consistently yielded a defined subectodermal anterior expression pattern within multiple transgenic lines. CONCLUSIONS Together, these results start to uncover the diverse regulatory potential inherent to the Hand2 upstream regulatory interval.
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Affiliation(s)
- Chloe A. Ferguson
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN 46202-5225, USA
| | - Beth A. Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN 46202-5225, USA
| | - Matteo Zoia
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Marco Osterwalder
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Anthony B. Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN 46202-5225, USA
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Chengcheng L, Raza SHA, Zhimei Y, Sihu W, Shengchen Y, Aloufi BH, Bingzhi L, Zan L. Bta-miR-181d and Bta-miR-196a mediated proliferation, differentiation, and apoptosis in Bovine Myogenic Cells. J Anim Sci 2024; 102:skae142. [PMID: 38766769 PMCID: PMC11161902 DOI: 10.1093/jas/skae142] [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: 11/21/2023] [Accepted: 05/17/2024] [Indexed: 05/22/2024] Open
Abstract
Skeletal muscle is an important component of livestock and poultry organisms. The proliferation and differentiation of myoblasts are highly coordinated processes, which rely on the regulation of miRNA. MiRNAs are widely present in organisms and play roles in various biological processes, including cell proliferation, differentiation, and apoptosis. MiR-181d and miR-196a, identified as tumor suppressors, have been found to be involved in cell proliferation, apoptosis, directed differentiation, and cancer cell invasion. However, their role in beef cattle skeletal muscle metabolism remains unclear. In this study, we discovered that overexpression of bta-miR-181d and bta-miR-196a in Qinchuan cattle myoblasts inhibited proliferation and apoptosis while promoting myogenic differentiation through EDU staining, flow cytometry analysis, immunofluorescence staining, and Western blotting. RNA-seq analysis of differential gene expression revealed that after overexpression of bta-miR-181d and bta-miR-196a, the differentially expressed genes were mainly enriched in the PI3K-Akt and MAPK signaling pathways. Furthermore, the phosphorylation levels of key proteins p-AKT in the PI3K signaling pathway and p-MAPK in the MAPK signaling pathway were significantly decreased after overexpression of bta-miR-181d and bta-miR-196a. Overall, this study provides preliminary evidence that bta-miR-181d and bta-miR-196a may regulate proliferation, apoptosis, and differentiation processes in Qinchuan cattle myoblasts by affecting the phosphorylation status of key proteins in PI3K-Akt and MAPK-ERK signaling pathways.
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Affiliation(s)
- Liang Chengcheng
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan 464000, P.R. China
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Yang Zhimei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Wang Sihu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Yu Shengchen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Bandar Hamad Aloufi
- Biology Department, Faculty of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Li Bingzhi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- National Beef Cattle Improvement Center, Northwest A&F University, Yangling, 712100, China
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Payne S, Neal A, De Val S. Transcription factors regulating vasculogenesis and angiogenesis. Dev Dyn 2024; 253:28-58. [PMID: 36795082 PMCID: PMC10952167 DOI: 10.1002/dvdy.575] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Transcription factors (TFs) play a crucial role in regulating the dynamic and precise patterns of gene expression required for the initial specification of endothelial cells (ECs), and during endothelial growth and differentiation. While sharing many core features, ECs can be highly heterogeneous. Differential gene expression between ECs is essential to pattern the hierarchical vascular network into arteries, veins and capillaries, to drive angiogenic growth of new vessels, and to direct specialization in response to local signals. Unlike many other cell types, ECs have no single master regulator, instead relying on differing combinations of a necessarily limited repertoire of TFs to achieve tight spatial and temporal activation and repression of gene expression. Here, we will discuss the cohort of TFs known to be involved in directing gene expression during different stages of mammalian vasculogenesis and angiogenesis, with a primary focus on development.
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Affiliation(s)
- Sophie Payne
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Alice Neal
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Sarah De Val
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
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Grunert M, Dorn C, Rickert-Sperling S. Cardiac Transcription Factors and Regulatory Networks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:295-311. [PMID: 38884718 DOI: 10.1007/978-3-031-44087-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Cardiac development is a fine-tuned process governed by complex transcriptional networks, in which transcription factors (TFs) interact with other regulatory layers. In this chapter, we introduce the core cardiac TFs including Gata, Hand, Nkx2, Mef2, Srf, and Tbx. These factors regulate each other's expression and can also act in a combinatorial manner on their downstream targets. Their disruption leads to various cardiac phenotypes in mice, and mutations in humans have been associated with congenital heart defects. In the second part of the chapter, we discuss different levels of regulation including cis-regulatory elements, chromatin structure, and microRNAs, which can interact with transcription factors, modulate their function, or are downstream targets. Finally, examples of disturbances of the cardiac regulatory network leading to congenital heart diseases in human are provided.
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Affiliation(s)
- Marcel Grunert
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Cornelia Dorn
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
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Zhang P, Lu R. The Molecular and Biological Function of MEF2D in Leukemia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:379-403. [PMID: 39017853 DOI: 10.1007/978-3-031-62731-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Myocyte enhancer factor 2 (MEF2) is a key transcription factor (TF) in skeletal, cardiac, and neural tissue development and includes four isoforms: MEF2A, MEF2B, MEF2C, and MEF2D. These isoforms significantly affect embryonic development, nervous system regulation, muscle cell differentiation, B- and T-cell development, thymocyte selection, and effects on tumorigenesis and leukemia. This chapter describes the multifaceted roles of MEF2 family proteins, covering embryonic development, nervous system regulation, and muscle cell differentiation. It further elucidates the contribution of MEF2 to various blood and immune cell functions. Specifically, in B-cell precursor acute lymphoblastic leukemia (BCP-ALL), MEF2D is aberrantly expressed and forms a fusion protein with BCL9, CSF1R, DAZAP1, HNRNPUL1, and SS18. These fusion proteins are closely related to the pathogenesis of leukemia. In addition, it specifically introduces the regulatory effect of MEF2D fusion protein on the proliferation and growth of B-cell acute lymphoblastic leukemia (B-ALL) cells. Finally, we detail the positive feedback loop between MEF2D and IRF8 that significantly promotes the progression of acute myeloid leukemia (AML) and the importance of the ZMYND8-BRD4 interaction in regulating the IRF8 and MYC transcriptional programs. The MEF2D-CEBPE axis is highlighted as a key transcriptional mechanism controlling the block of leukemic cell self-renewal and differentiation in AML. This chapter starts with the structure and function of MEF2 family proteins, specifically summarizing and analyzing the role of MEF2D in B-ALL and AML, mediating the complex molecular mechanisms of transcriptional regulation and exploring their implications for human health and disease.
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Affiliation(s)
- Pengcheng Zhang
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Rui Lu
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA.
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de Barros JW, Joule Pierre K, Kempinas WDG, Tremblay JJ. Ethylene dimethanesulfonate effects on gene promoter activities related to the endocrine function of immortalized Leydig cell lines R2C and MA-10. Curr Res Toxicol 2023; 6:100147. [PMID: 38234696 PMCID: PMC10792691 DOI: 10.1016/j.crtox.2023.100147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024] Open
Abstract
Ethylene dimethanesulfonate (EDS) is a molecule with known selective cytotoxicity on adult Leydig cells. A single intraperitoneal injection in rats but not mice, leads to male androgen deprivation and infertility. In vitro studies using rat and mouse immortalized Leydig cell lines, showed similar effects of cell death promoted by EDS in rat cells as seen in vivo, and suggest that EDS affects gene transcription, which could firstly compromise steroidogenesis before the apoptosis process. Using gene reporter assay, this study aimed to investigate EDS effects on the promoter activity of genes important for endocrine function (Star, Insl3) and response to toxic agents (Gsta3) in immortalized Leydig cell lines (rat R2C and mouse MA-10 cells), as well as identify possible EDS-responsive elements in the Star gene promoter. EDS exposure of R2C and MA-10 Leydig cells increased Gsta3 promoter activity after 4 h of treatment and decreased Insl3 promoter activity only in R2C cells after 24 h of treatment. EDS also decreased Star promoter activity in both Leydig cell lines. Using R2C cells, the EDS-responsive region in the Star promoter was located between -400 and -195 bp. This suggests that this region and the associated transcription factors, which include MEF2, might be targeted by EDS. Additional somatic gonadal cell lines expressing Star were used and EDS did not affect Star promoter activity in DC3 granulosa cells while Star promoter activity was increased in MSC-1 Sertoli cells after 24 h of treatment. This study contributes to the knowledge regarding the mechanism of EDS action in Leydig cells, and in other gonadal cell lineages, and brings new light regarding the rats and mice differential susceptibility to EDS effects, in addition to providing new avenues for experimental approaches to better understand Leydig cell function and dynamics in different rodent species.
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Affiliation(s)
- Jorge W.F. de Barros
- Laboratory of Reproductive and Developmental Biology and Toxicology, São Paulo State University (Unesp), Department of Structural and Functional Biology, Institute of Biosciences, Botucatu, SP, Brazil
- Reproduction, Mother and Child Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec – Université Laval, Québec City, Canada
| | - Kenley Joule Pierre
- Reproduction, Mother and Child Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec – Université Laval, Québec City, Canada
| | - Wilma De G. Kempinas
- Laboratory of Reproductive and Developmental Biology and Toxicology, São Paulo State University (Unesp), Department of Structural and Functional Biology, Institute of Biosciences, Botucatu, SP, Brazil
| | - Jacques J. Tremblay
- Reproduction, Mother and Child Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec – Université Laval, Québec City, Canada
- Department of Obstetrics, Gynecology, and Reproduction, Faculty of Medicine, Centre for Research in Reproduction, Development and Intergenerational Health, Université Laval, Québec City, Canada
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Hu J, Zhang X, Ma F, Huang C, Jiang Y. LncRNA CASC2 Alleviates Renal Interstitial Inflammation and Fibrosis through MEF2C Downregulation-Induced Hinderance of M1 Macrophage Polarization. Nephron Clin Pract 2023; 148:245-263. [PMID: 38142674 DOI: 10.1159/000531919] [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: 08/18/2022] [Accepted: 05/25/2023] [Indexed: 12/26/2023] Open
Abstract
INTRODUCTION Long noncoding RNA (lncRNA) cancer susceptibility candidate 2 (CASC2) alleviates the progression of diabetic nephropathy by inhibiting inflammation and fibrosis. This study investigated how CASC2 impacts renal interstitial fibrosis (RIF) through regulating M1 macrophage (M1) polarization. METHOD Nine-week-old mice underwent unilateral ureteral obstruction (UUO) establishment. Macrophages were induced toward M1 polarization using lipopolysaccharide (LPS) in vitro and cocultured with fibroblasts to examine how M1 polarization influences RIF. LnCeCell predicted that CASC2 interacted with myocyte enhancer factor 2 C (MEF2C), which was validated by dual-luciferase reporter assay. CASC2/MEF2C overexpression was achieved by lentivirus-expressing lncRNA CASC2 injection in vivo or CASC2 and MEF2C transfection in vitro. Renal injury was evaluated through biochemical analysis and hematoxylin-eosin/Masson staining. Macrophage infiltration and M1 polarization in the kidney and/or macrophages were detected by immunofluorescence, flow cytometry, and/or quantitative reverse transcription polymerase chain reaction (qRT-PCR). Expressions of CASC2, MEF2C, and markers related to inflammation/M1/fibrosis in the kidney/macrophages/fibroblasts were analyzed by qRT-PCR, fluorescence in situ hybridization, enzyme-linked immunosorbent assay, and/or Western blot. RESULT In the kidneys of mice, CASC2 was downregulated and macrophage infiltration was promoted time-dependently from days 3 to 14 post-UUO induction; CASC2 overexpression alleviated renal histological abnormalities, hindered macrophage infiltration and M1 polarization, downregulated renal function markers serum creatinine and blood urea nitrogen and inflammation/M1/fibrosis-related makers, and offset UUO-induced MEF2C upregulation. LncRNA CASC2 overexpression inhibited fibroblast fibrosis and M1 polarization in cocultured fibroblasts with LPS-activated macrophages. Also, CASC2 bound to MEF2C and inhibited its expression in LPS-activated macrophages. Furthermore, MEF2C reversed the inhibitory effects of lncRNA CASC2 overexpression. CONCLUSION CASC2 alleviates RIF by inhibiting M1 polarization through directly downregulating MEF2C expression. CASC2 might represent a promising value of future investigations on treatment for RIF.
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Affiliation(s)
- Jinping Hu
- Department of Nephrology, HongHui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Xiaoyan Zhang
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Feng Ma
- Department of Nephrology, HongHui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Chen Huang
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yali Jiang
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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