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Pereira L. And yet another transcription factor-the complex world of fruit ripening. Plant Physiol 2024; 194:2185-2187. [PMID: 38173334 PMCID: PMC10980389 DOI: 10.1093/plphys/kiad673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Lara Pereira
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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202
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Yang F, Sun X, Wu G, He X, Liu W, Wang Y, Sun Q, Zhao Y, Xu D, Dai X, Ma W, Zeng J. Genome-Wide Identification and Expression Profiling of the ABF Transcription Factor Family in Wheat ( Triticum aestivum L.). Int J Mol Sci 2024; 25:3783. [PMID: 38612594 PMCID: PMC11011718 DOI: 10.3390/ijms25073783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Members of the abscisic acid (ABA)-responsive element (ABRE) binding factor (ABF) and ABA-responsive element binding protein (AREB) families play essential roles in the regulation of ABA signaling pathway activity and shape the ability of plants to adapt to a range of stressful environmental conditions. To date, however, systematic genome-wide analyses focused on the ABF/AREB gene family in wheat are lacking. Here, we identified 35 ABF/AREB genes in the wheat genome, designated TaABF1-TaABF35 according to their chromosomal distribution. These genes were further classified, based on their phylogenetic relationships, into three groups (A-C), with the TaABF genes in a given group exhibiting similar motifs and similar numbers of introns/exons. Cis-element analyses of the promoter regions upstream of these TaABFs revealed large numbers of ABREs, with the other predominant elements that were identified differing across these three groups. Patterns of TaABF gene expansion were primarily characterized by allopolyploidization and fragment duplication, with purifying selection having played a significant role in the evolution of this gene family. Further expression profiling indicated that the majority of the TaABF genes from groups A and B were highly expressed in various tissues and upregulated following abiotic stress exposure such as drought, low temperature, low nitrogen, etc., while some of the TaABF genes in group C were specifically expressed in grain tissues. Regulatory network analyses revealed that four of the group A TaABFs (TaABF2, TaABF7, TaABF13, and TaABF19) were centrally located in protein-protein interaction networks, with 13 of these TaABF genes being regulated by 11 known miRNAs, which play important roles in abiotic stress resistance such as drought and salt stress. The two primary upstream transcription factor types found to regulate TaABF gene expression were BBR/BPC and ERF, which have previously been reported to be important in the context of plant abiotic stress responses. Together, these results offer insight into the role that the ABF/AREB genes play in the responses of wheat to abiotic stressors, providing a robust foundation for future functional studies of these genes.
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Affiliation(s)
- Fuhui Yang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xuelian Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Gang Wu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyan He
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenxing Liu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yongmei Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qingyi Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yan Zhao
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Dengan Xu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xuehuan Dai
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Wujun Ma
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
| | - Jianbin Zeng
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
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203
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Venhuizen J, van Bergen MGJM, Bergevoet SM, Gilissen D, Spruijt CG, Wingens L, van den Akker E, Vermeulen M, Jansen JH, Martens JHA, van der Reijden BA. GFI1B and LSD1 repress myeloid traits during megakaryocyte differentiation. Commun Biol 2024; 7:374. [PMID: 38548886 PMCID: PMC10978956 DOI: 10.1038/s42003-024-06090-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/21/2024] [Indexed: 04/01/2024] Open
Abstract
The transcription factor Growth Factor Independence 1B (GFI1B) recruits Lysine Specific Demethylase 1 A (LSD1/KDM1A) to stimulate gene programs relevant for megakaryocyte and platelet biology. Inherited pathogenic GFI1B variants result in thrombocytopenia and bleeding propensities with varying intensity. Whether these affect similar gene programs is unknow. Here we studied transcriptomic effects of four patient-derived GFI1B variants (GFI1BT174N,H181Y,R184P,Q287*) in MEG01 megakaryoblasts. Compared to normal GFI1B, each variant affected different gene programs with GFI1BQ287* uniquely failing to repress myeloid traits. In line with this, single cell RNA-sequencing of induced pluripotent stem cell (iPSC)-derived megakaryocytes revealed a 4.5-fold decrease in the megakaryocyte/myeloid cell ratio in GFI1BQ287* versus normal conditions. Inhibiting the GFI1B-LSD1 interaction with small molecule GSK-LSD1 resulted in activation of myeloid genes in normal iPSC-derived megakaryocytes similar to what was observed for GFI1BQ287* iPSC-derived megakaryocytes. Thus, GFI1B and LSD1 facilitate gene programs relevant for megakaryopoiesis while simultaneously repressing programs that induce myeloid differentiation.
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Affiliation(s)
- Jeron Venhuizen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Maaike G J M van Bergen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Saskia M Bergevoet
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Daan Gilissen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Cornelia G Spruijt
- Department of Molecular Biology, Faculty of Science, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Laura Wingens
- Department of Molecular Developmental Biology, Faculty of Science, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Emile van den Akker
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, Amsterdam, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands.
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204
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Hatton AA, Cheng FF, Lin T, Shen RJ, Chen J, Zheng Z, Qu J, Lyu F, Harris SE, Cox SR, Jin ZB, Martin NG, Fan D, Montgomery GW, Yang J, Wray NR, Marioni RE, Visscher PM, McRae AF. Genetic control of DNA methylation is largely shared across European and East Asian populations. Nat Commun 2024; 15:2713. [PMID: 38548728 PMCID: PMC10978881 DOI: 10.1038/s41467-024-47005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
DNA methylation is an ideal trait to study the extent of the shared genetic control across ancestries, effectively providing hundreds of thousands of model molecular traits with large QTL effect sizes. We investigate cis DNAm QTLs in three European (n = 3701) and two East Asian (n = 2099) cohorts to quantify the similarities and differences in the genetic architecture across populations. We observe 80,394 associated mQTLs (62.2% of DNAm probes with significant mQTL) to be significant in both ancestries, while 28,925 mQTLs (22.4%) are identified in only a single ancestry. mQTL effect sizes are highly conserved across populations, with differences in mQTL discovery likely due to differences in allele frequency of associated variants and differing linkage disequilibrium between causal variants and assayed SNPs. This study highlights the overall similarity of genetic control across ancestries and the value of ancestral diversity in increasing the power to detect associations and enhancing fine mapping resolution.
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Affiliation(s)
- Alesha A Hatton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Fei-Fei Cheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jie Chen
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jia Qu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Fan Lyu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, 4006, Australia
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, 100191, Beijing, China
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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205
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Patel A, Dharap A. An Emerging Role for Enhancer RNAs in Brain Disorders. Neuromolecular Med 2024; 26:7. [PMID: 38546891 DOI: 10.1007/s12017-024-08776-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Noncoding DNA undergoes widespread context-dependent transcription to produce noncoding RNAs. In recent decades, tremendous advances in genomics and transcriptomics have revealed important regulatory roles for noncoding DNA elements and the RNAs that they produce. Enhancers are one such element that are well-established drivers of gene expression changes in response to a variety of factors such as external stimuli, cellular responses, developmental cues, and disease states. They are known to act at long distances, interact with multiple target gene loci simultaneously, synergize with other enhancers, and associate with dynamic chromatin architectures to form a complex regulatory network. Recent advances in enhancer biology have revealed that upon activation, enhancers transcribe long noncoding RNAs, known as enhancer RNAs (eRNAs), that have been shown to play important roles in enhancer-mediated gene regulation and chromatin-modifying activities. In the brain, enhancer dysregulation and eRNA transcription has been reported in numerous disorders from acute injuries to chronic neurodegeneration. Because this is an emerging area, a comprehensive understanding of eRNA function has not yet been achieved in brain disorders; however, the findings to date have illuminated a role for eRNAs in activity-driven gene expression and phenotypic outcomes. In this review, we highlight the breadth of the current literature on eRNA biology in brain health and disease and discuss the challenges as well as focus areas and strategies for future in-depth research on eRNAs in brain health and disease.
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Affiliation(s)
- Ankit Patel
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
- Byrd Alzheimer's Center & Research Institute, USF Health Neuroscience Institute, Tampa, FL, USA
| | - Ashutosh Dharap
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA.
- Byrd Alzheimer's Center & Research Institute, USF Health Neuroscience Institute, Tampa, FL, USA.
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206
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Ito K, Harada I, Martinez C, Sato K, Lee E, Port E, Byerly JH, Nayak A, Tripathi E, Zhu J, Irie HY. MARCH2, a Novel Oncogene-regulated SNAIL E3 Ligase, Suppresses Triple-negative Breast Cancer Metastases. Cancer Research Communications 2024; 4:946-957. [PMID: 38457262 PMCID: PMC10977041 DOI: 10.1158/2767-9764.crc-23-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 01/02/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Epithelial-mesenchymal transition (EMT) in cancer promotes metastasis and chemotherapy resistance. A subset of triple-negative breast cancer (TNBC) exhibits a mesenchymal gene signature that is associated with poor patient outcomes. We previously identified PTK6 tyrosine kinase as an oncogenic driver of EMT in a subset of TNBC. PTK6 induces EMT by stabilizing SNAIL, a key EMT-initiating transcriptional factor. Inhibition of PTK6 activity reverses mesenchymal features of TNBC cells and suppresses their metastases by promoting SNAIL degradation via a novel mechanism. In the current study, we identify membrane-associated RING-CH2 (MARCH2) as a novel PTK6-regulated E3 ligase that promotes the ubiquitination and degradation of SNAIL protein. The MARCH2 RING domain is critical for SNAIL ubiquitination and subsequent degradation. PTK6 inhibition promotes the interaction of MARCH2 with SNAIL. Overexpression of MARCH2 exhibits tumor suppressive properties and phenocopies the effects of SNAIL downregulation and PTK6 inhibition in TNBC cells, such as inhibition of migration, anoikis resistance, and metastasis. Consistent with this, higher levels of MARCH2 expression in breast and other cancers are associated with better prognosis. We have identified MARCH2 as a novel SNAIL E3 ligase that regulates EMT and metastases of mesenchymal TNBC. SIGNIFICANCE EMT is a process directly linked to drug resistance and metastasis of cancer cells. We identified MARCH2 as a novel regulator of SNAIL, a key EMT driver, that promotes SNAIL ubiquitination and degradation in TNBC cells. MARCH2 is oncogene regulated and inhibits growth and metastasis of TNBC. These insights could contribute to novel strategies to therapeutically target TNBC.
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Affiliation(s)
- Koichi Ito
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ibuki Harada
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Criseyda Martinez
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Katsutoshi Sato
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Elisa Port
- Department of Surgery, Mount Sinai Hospital, New York, New York
| | - Jessica H Byerly
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anupma Nayak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ekta Tripathi
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jun Zhu
- Sema4, Stamford, Connecticut
| | - Hanna Y Irie
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
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207
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Tsagiopoulou M, Rashmi S, Aguilar-Fernandez S, Nieto J, Gut IG. Multi-organ single-cell transcriptomics of immune cells uncovered organ-specific gene expression and functions. Sci Data 2024; 11:316. [PMID: 38538617 PMCID: PMC10973478 DOI: 10.1038/s41597-024-03152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
Despite the wealth of publicly available single-cell datasets, our understanding of distinct resident immune cells and their unique features in diverse human organs remains limited. To address this, we compiled a meta-analysis dataset of 114,275 CD45+ immune cells sourced from 14 organs in healthy donors. While the transcriptome of immune cells remains relatively consistent across organs, our analysis has unveiled organ-specific gene expression differences (GTPX3 in kidney, DNTT and ACVR2B in thymus). These alterations are linked to different transcriptional factor activities and pathways including metabolism. TNF-α signaling through the NFkB pathway was found in several organs and immune compartments. The presence of distinct expression profiles for NFkB family genes and their target genes, including cytokines, underscores their pivotal role in cell positioning. Taken together, immune cells serve a dual role: safeguarding the organs and dynamically adjusting to the intricacies of the host organ environment, thereby actively contributing to its functionality and overall homeostasis.
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Affiliation(s)
| | - Sonal Rashmi
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | | | - Juan Nieto
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Ivo G Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain.
- Universitat de Barcelona (UB), Barcelona, Spain.
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208
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Zhang Z, Jin H, Zhang X, Bai M, Zheng K, Tian J, Deng B, Mao L, Qiu P, Huang B. Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression. Front Immunol 2024; 15:1369311. [PMID: 38601162 PMCID: PMC11004287 DOI: 10.3389/fimmu.2024.1369311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Background Coronavirus disease (COVID-19), caused by SARS-CoV-2, has emerged as a infectious disease, coexisting with widespread seasonal and sporadic influenza epidemics globally. Individuals living with HIV, characterized by compromised immune systems, face an elevated risk of severe outcomes and increased mortality when affected by COVID-19. Despite this connection, the molecular intricacies linking COVID-19, influenza, and HIV remain unclear. Our research endeavors to elucidate the shared pathways and molecular markers in individuals with HIV concurrently infected with COVID-19 and influenza. Furthermore, we aim to identify potential medications that may prove beneficial in managing these three interconnected illnesses. Methods Sequencing data for COVID-19 (GSE157103), influenza (GSE185576), and HIV (GSE195434) were retrieved from the GEO database. Commonly expressed differentially expressed genes (DEGs) were identified across the three datasets, followed by immune infiltration analysis and diagnostic ROC analysis on the DEGs. Functional enrichment analysis was performed using GO/KEGG and Gene Set Enrichment Analysis (GSEA). Hub genes were screened through a Protein-Protein Interaction networks (PPIs) analysis among DEGs. Analysis of miRNAs, transcription factors, drug chemicals, diseases, and RNA-binding proteins was conducted based on the identified hub genes. Finally, quantitative PCR (qPCR) expression verification was undertaken for selected hub genes. Results The analysis of the three datasets revealed a total of 22 shared DEGs, with the majority exhibiting an area under the curve value exceeding 0.7. Functional enrichment analysis with GO/KEGG and GSEA primarily highlighted signaling pathways associated with ribosomes and tumors. The ten identified hub genes included IFI44L, IFI44, RSAD2, ISG15, IFIT3, OAS1, EIF2AK2, IFI27, OASL, and EPSTI1. Additionally, five crucial miRNAs (hsa-miR-8060, hsa-miR-6890-5p, hsa-miR-5003-3p, hsa-miR-6893-3p, and hsa-miR-6069), five essential transcription factors (CREB1, CEBPB, EGR1, EP300, and IRF1), and the top ten significant drug chemicals (estradiol, progesterone, tretinoin, calcitriol, fluorouracil, methotrexate, lipopolysaccharide, valproic acid, silicon dioxide, cyclosporine) were identified. Conclusion This research provides valuable insights into shared molecular targets, signaling pathways, drug chemicals, and potential biomarkers for individuals facing the complex intersection of COVID-19, influenza, and HIV. These findings hold promise for enhancing the precision of diagnosis and treatment for individuals with HIV co-infected with COVID-19 and influenza.
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Affiliation(s)
- Zhen Zhang
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Hao Jin
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Xu Zhang
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Mei Bai
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Kexin Zheng
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Jing Tian
- Department of Immunology, School of Basic Medical Science, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Bin Deng
- Laboratory Department, Jinzhou Central Hospital, Jinzhou, Liaoning, China
| | - Lingling Mao
- Institute for Prevention and Control of Infection and Infectious Diseases, Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Pengcheng Qiu
- Thoracic Surgery Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Bo Huang
- Thoracic Surgery Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
- Thoracic Surgery Department, Yingkou Central Hospital, Yingkou, Liaoning, China
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209
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Malekpour SA, Haghverdi L, Sadeghi M. Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms. Brief Bioinform 2024; 25:bbae180. [PMID: 38653489 PMCID: PMC11036345 DOI: 10.1093/bib/bbae180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
There is a growing interest in inferring context specific gene regulatory networks from single-cell RNA sequencing (scRNA-seq) data. This involves identifying the regulatory relationships between transcription factors (TFs) and genes in individual cells, and then characterizing these relationships at the level of specific cell types or cell states. In this study, we introduce scGATE (single-cell gene regulatory gate) as a novel computational tool for inferring TF-gene interaction networks and reconstructing Boolean logic gates involving regulatory TFs using scRNA-seq data. In contrast to current Boolean models, scGATE eliminates the need for individual formulations and likelihood calculations for each Boolean rule (e.g. AND, OR, XOR). By employing a Bayesian framework, scGATE infers the Boolean rule after fitting the model to the data, resulting in significant reductions in time-complexities for logic-based studies. We have applied assay for transposase-accessible chromatin with sequencing (scATAC-seq) data and TF DNA binding motifs to filter out non-relevant TFs in gene regulations. By integrating single-cell clustering with these external cues, scGATE is able to infer context specific networks. The performance of scGATE is evaluated using synthetic and real single-cell multi-omics data from mouse tissues and human blood, demonstrating its superiority over existing tools for reconstructing TF-gene networks. Additionally, scGATE provides a flexible framework for understanding the complex combinatorial and cooperative relationships among TFs regulating target genes by inferring Boolean logic gates among them.
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Affiliation(s)
- Seyed Amir Malekpour
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), 19395-5746, Tehran, Iran
| | - Laleh Haghverdi
- Berlin Institute for Medical Systems Biology, Max Delbrück Center (BIMSB-MDC) in the Helmholtz Association, Berlin, Germany
| | - Mehdi Sadeghi
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, 1497716316, Tehran, Iran
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210
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Hu Q, Xu Y, Song M, Dai Y, Antebi A, Shen Y. BLMP-1 is a critical temporal regulator of dietary-restriction-induced response in Caenorhabditis elegans. Cell Rep 2024; 43:113959. [PMID: 38483903 DOI: 10.1016/j.celrep.2024.113959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 02/07/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024] Open
Abstract
The extrinsic diet and the intrinsic developmental programs are intertwined. Although extensive research has been conducted on how nutrition regulates development, whether and how developmental programs control the timing of nutritional responses remain barely known. Here, we report that a developmental timing regulator, BLMP-1/BLIMP1, governs the temporal response to dietary restriction (DR). At the end of larval development, BLMP-1 is induced and interacts with DR-activated PHA-4/FOXA, a key transcription factor responding to the reduced nutrition. By integrating temporal and nutritional signaling, the DR response regulates many development-related genes, including gska-3/GSK3β, through BLMP-1-PHA-4 at the onset of adulthood. Upon DR, a precocious activation of BLMP-1 in early larval stages impairs neuronal development through gska-3, whereas the increase of gska-3 by BLMP-1-PHA-4 at the last larval stage suppresses WNT signaling in adulthood for DR-induced longevity. Our findings reveal a temporal checkpoint of the DR response that protects larval development and promotes adult health.
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Affiliation(s)
- Qingyuan Hu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunpeng Xu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengjiao Song
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yumin Dai
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany
| | - Yidong Shen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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211
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Ye X, Guerin LN, Chen Z, Rajendren S, Dunker W, Zhao Y, Zhang R, Hodges E, Karijolich J. Enhancer-promoter activation by the Kaposi sarcoma-associated herpesvirus episome maintenance protein LANA. Cell Rep 2024; 43:113888. [PMID: 38416644 PMCID: PMC11005752 DOI: 10.1016/j.celrep.2024.113888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 12/29/2023] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
Higher-order genome structure influences the transcriptional regulation of cellular genes through the juxtaposition of regulatory elements, such as enhancers, close to promoters of target genes. While enhancer activation has emerged as an important facet of Kaposi sarcoma-associated herpesvirus (KSHV) biology, the mechanisms controlling enhancer-target gene expression remain obscure. Here, we discover that the KSHV genome tethering protein latency-associated nuclear antigen (LANA) potentiates enhancer-target gene expression in primary effusion lymphoma (PEL), a highly aggressive B cell lymphoma causally associated with KSHV. Genome-wide analyses demonstrate increased levels of enhancer RNA transcription as well as activating chromatin marks at LANA-bound enhancers. 3D genome conformation analyses identified genes critical for latency and tumorigenesis as targets of LANA-occupied enhancers, and LANA depletion results in their downregulation. These findings reveal a mechanism in enhancer-gene coordination and describe a role through which the main KSHV tethering protein regulates essential gene expression in PEL.
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Affiliation(s)
- Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lindsey N Guerin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Ziche Chen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Suba Rajendren
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - William Dunker
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yang Zhao
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Ruilin Zhang
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, TN 37232, USA; Vanderbilt Center for Immunobiology, Nashville, TN 37232, USA.
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212
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King HO, Owusu-Boaitey KE, Fincher CT, Reddien PW. A transcription factor atlas of stem cell fate in planarians. Cell Rep 2024; 43:113843. [PMID: 38401119 DOI: 10.1016/j.celrep.2024.113843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 12/05/2023] [Accepted: 02/06/2024] [Indexed: 02/26/2024] Open
Abstract
Whole-body regeneration requires the ability to produce the full repertoire of adult cell types. The planarian Schmidtea mediterranea contains over 125 cell types, which can be regenerated from a stem cell population called neoblasts. Neoblast fate choice can be regulated by the expression of fate-specific transcription factors (FSTFs). How fate choices are made and distributed across neoblasts versus their post-mitotic progeny remains unclear. We used single-cell RNA sequencing to systematically map fate choices made in S/G2/M neoblasts and, separately, in their post-mitotic progeny that serve as progenitors for all adult cell types. We defined transcription factor expression signatures associated with all detected fates, identifying numerous new progenitor classes and FSTFs that regulate them. Our work generates an atlas of stem cell fates with associated transcription factor signatures for most cell types in a complete adult organism.
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Affiliation(s)
- Hunter O King
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kwadwo E Owusu-Boaitey
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
| | - Christopher T Fincher
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter W Reddien
- Howard Hughes Medical Institute, Chevy Chase, MD, USA; Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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213
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Smith JJ, Taylor SR, Blum JA, Feng W, Collings R, Gitler AD, Miller DM, Kratsios P. A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes. Cell Rep 2024; 43:113857. [PMID: 38421866 DOI: 10.1016/j.celrep.2024.113857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Motor neurons (MNs) constitute an ancient cell type targeted by multiple adult-onset diseases. It is therefore important to define the molecular makeup of adult MNs in animal models and extract organizing principles. Here, we generate a comprehensive molecular atlas of adult Caenorhabditis elegans MNs and a searchable database. Single-cell RNA sequencing of 13,200 cells reveals that ventral nerve cord MNs cluster into 29 molecularly distinct subclasses. Extending C. elegans Neuronal Gene Expression Map and Network (CeNGEN) findings, all MN subclasses are delineated by distinct expression codes of either neuropeptide or transcription factor gene families. Strikingly, combinatorial codes of homeodomain transcription factor genes succinctly delineate adult MN diversity in both C. elegans and mice. Further, molecularly defined MN subclasses in C. elegans display distinct patterns of connectivity. Hence, our study couples the connectivity map of the C. elegans motor circuit with a molecular atlas of its constituent MNs and uncovers organizing principles and conserved molecular codes of adult MN diversity.
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Affiliation(s)
- Jayson J Smith
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA
| | - Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA; Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Jacob A Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA
| | - Rebecca Collings
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA; Program in Neuroscience, Vanderbilt University, Nashville, TN 37240, USA.
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA.
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214
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Childs JE, Morabito S, Das S, Santelli C, Pham V, Kusche K, Vera VA, Reese F, Campbell RR, Matheos DP, Swarup V, Wood MA. Relapse to cocaine seeking is regulated by medial habenula NR4A2/NURR1 in mice. Cell Rep 2024; 43:113956. [PMID: 38489267 DOI: 10.1016/j.celrep.2024.113956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 09/11/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Drugs of abuse can persistently change the reward circuit in ways that contribute to relapse behavior, partly via mechanisms that regulate chromatin structure and function. Nuclear orphan receptor subfamily4 groupA member2 (NR4A2, also known as NURR1) is an important effector of histone deacetylase 3 (HDAC3)-dependent mechanisms in persistent memory processes and is highly expressed in the medial habenula (MHb), a region that regulates nicotine-associated behaviors. Here, expressing the Nr4a2 dominant negative (Nurr2c) in the MHb blocks reinstatement of cocaine seeking in mice. We use single-nucleus transcriptomics to characterize the molecular cascade following Nr4a2 manipulation, revealing changes in transcriptional networks related to addiction, neuroplasticity, and GABAergic and glutamatergic signaling. The network controlled by NR4A2 is characterized using a transcription factor regulatory network inference algorithm. These results identify the MHb as a pivotal regulator of relapse behavior and demonstrate the importance of NR4A2 as a key mechanism driving the MHb component of relapse.
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Affiliation(s)
- Jessica E Childs
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Samuel Morabito
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA; Mathematical, Computational, and Systems Biology (MCSB) Program, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Sudeshna Das
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA
| | - Caterina Santelli
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Victoria Pham
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Kelly Kusche
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Vanessa Alizo Vera
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Fairlie Reese
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Rianne R Campbell
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Dina P Matheos
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA.
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA.
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215
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Groiss S, Viertler C, Kap M, Bernhardt G, Mischinger HJ, Sieuwerts A, Verhoef C, Riegman P, Kruhøffer M, Svec D, Sjöback SR, Becker KF, Zatloukal K. Inter-patient heterogeneity in the hepatic ischemia-reperfusion injury transcriptome: Implications for research and diagnostics. N Biotechnol 2024; 79:20-29. [PMID: 38072306 DOI: 10.1016/j.nbt.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024]
Abstract
Cellular responses induced by surgical procedure or ischemia-reperfusion injury (IRI) may severely alter transcriptome profiles and complicate molecular diagnostics. To investigate this effect, we characterized such pre-analytical effects in 143 non-malignant liver samples obtained from 30 patients at different time points of ischemia during surgery from two individual cohorts treated either with the Pringle manoeuvre or total vascular exclusion. Transcriptomics profiles were analyzed by Affymetrix microarrays and expression of selected mRNAs was validated by RT-PCR. We found 179 mutually deregulated genes which point to elevated cytokine signaling with NFκB as a dominant pathway in ischemia responses. In contrast to ischemia, reperfusion induced pro-apoptotic and pro-inflammatory cascades involving TNF, NFκB and MAPK pathways. FOS and JUN were down-regulated in steatosis compared to their up-regulation in normal livers. Surprisingly, molecular signatures of underlying primary and secondary cancers were present in non-tumor tissue. The reported inter-patient variability might reflect differences in individual stress responses and impact of underlying disease conditions. Furthermore, we provide a set of 230 pre-analytically highly robust genes identified from histologically normal livers (<2% covariation across both cohorts) that might serve as reference genes and could be particularly suited for future diagnostic applications.
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Affiliation(s)
- Silvia Groiss
- Diagnostic & Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Christian Viertler
- Diagnostic & Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Marcel Kap
- Pathology Department, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - Gerwin Bernhardt
- Division of General Surgery, Department of Surgery, Medical University of Graz, 8010 Graz, Austria; Department of Orthopedics and Trauma Surgery, Medical University of Graz, 8010 Graz, Austria
| | - Hans-Jörg Mischinger
- Division of General Surgery, Department of Surgery, Medical University of Graz, 8010 Graz, Austria
| | - Anieta Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - Cees Verhoef
- Department of Surgical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - Peter Riegman
- Pathology Department, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | | | - David Svec
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic
| | | | | | - Kurt Zatloukal
- Diagnostic & Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria.
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216
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Okumura T, Raja Xavier JP, Pasternak J, Yang Z, Hang C, Nosirov B, Singh Y, Admard J, Brucker SY, Kommoss S, Takeda S, Staebler A, Lang F, Salker MS. Rel Family Transcription Factor NFAT5 Upregulates COX2 via HIF-1α Activity in Ishikawa and HEC1a Cells. Int J Mol Sci 2024; 25:3666. [PMID: 38612478 PMCID: PMC11012216 DOI: 10.3390/ijms25073666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Nuclear factor of activated T cells 5 (NFAT5) and cyclooxygenase 2 (COX2; PTGS2) both participate in diverse pathologies including cancer progression. However, the biological role of the NFAT5-COX2 signaling pathway in human endometrial cancer has remained elusive. The present study explored whether NFAT5 is expressed in endometrial tumors and if NFAT5 participates in cancer progression. To gain insights into the underlying mechanisms, NFAT5 protein abundance in endometrial cancer tissue was visualized by immunohistochemistry and endometrial cancer cells (Ishikawa and HEC1a) were transfected with NFAT5 or with an empty plasmid. As a result, NFAT5 expression is more abundant in high-grade than in low-grade endometrial cancer tissue. RNA sequencing analysis of NFAT5 overexpression in Ishikawa cells upregulated 37 genes and downregulated 20 genes. Genes affected included cyclooxygenase 2 and hypoxia inducible factor 1α (HIF1A). NFAT5 transfection and/or treatment with HIF-1α stabilizer exerted a strong stimulating effect on HIF-1α promoter activity as well as COX2 expression level and prostaglandin E2 receptor (PGE2) levels. Our findings suggest that activation of NFAT5-HIF-1α-COX2 axis could promote endometrial cancer progression.
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Affiliation(s)
- Toshiyuki Okumura
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo 113-8421, Japan;
| | - Janet P. Raja Xavier
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Jana Pasternak
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Zhiqi Yang
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Cao Hang
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Bakhtiyor Nosirov
- Department of Cancer Research, Luxembourg Institute of Health, L-1210 Luxembourg, Luxembourg
| | - Yogesh Singh
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
- Institute of Medical Genetics and Applied Genomics, Eberhard Karls University, D-72074 Tübingen, Germany;
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, Eberhard Karls University, D-72074 Tübingen, Germany;
| | - Sara Y. Brucker
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Stefan Kommoss
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo 113-8421, Japan;
| | - Annette Staebler
- Institute of Pathology, Eberhard Karls University, D-72074 Tübingen, Germany;
| | - Florian Lang
- Institute of Physiology, Eberhard Karls University, D-72074 Tübingen, Germany;
| | - Madhuri S. Salker
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
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217
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Lazzari E, Rozera G, Gagliardini R, Esvan R, Mondi A, Mazzotta V, Camici M, Girardi E, Antinori A, Maggi F, Abbate I. Human and Viral microRNA Expression in Acute and Chronic HIV Infections. Viruses 2024; 16:496. [PMID: 38675839 PMCID: PMC11054094 DOI: 10.3390/v16040496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/12/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Human and viral microRNAs (miRNAs) are involved in the regulation of gene transcription, and the establishment of their profiles in acute (AHI) and chronic (CHI) HIV infections may shed light on the pathogenetic events related to different phases of HIV disease. Next-generation sequencing (NGS) of miRNA libraries was performed, and the reads were used to analyze miRNA differential expression in the plasma with AHI and CHI. Functional analysis was then undertaken to investigate the biological processes characterizing the two phases of HIV infection. Except for hsa-miR-122-5p, which was found in 3.39% AHI vs. 0.18% CHI, the most represented human miRNAs were similarly represented in AHI and CHI. However, when considering the overall detected miRNAs in AHI and CHI, 15 displayed differential expression (FDR p < 0.05). Functional analysis identified 163 target mRNAs involved in promoting angiogenesis activation in AHI versus CHI through the action of hsa-miR10b-5p, hsa-miR1290, hsa-miR1-3p, and hsa-miR296-5p. The viral miRNAs detected, all belonging to herpesviruses, accounted for only 0.014% of total reads. The present data suggest that AHI patients exhibit strong innate immune activation through the upregulation of hsa-miR-122-5p and early activation of angiogenesis. More specific investigations are needed to study the role of viral miRNAs in HIV pathogenesis.
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Affiliation(s)
- Elisabetta Lazzari
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (E.L.); (F.M.); (I.A.)
| | - Gabriella Rozera
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (E.L.); (F.M.); (I.A.)
| | - Roberta Gagliardini
- Clinical Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (R.G.); (A.M.); (V.M.); (M.C.); (A.A.)
| | - Rozenn Esvan
- AIDS Referral Center, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy;
| | - Annalisa Mondi
- Clinical Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (R.G.); (A.M.); (V.M.); (M.C.); (A.A.)
| | - Valentina Mazzotta
- Clinical Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (R.G.); (A.M.); (V.M.); (M.C.); (A.A.)
| | - Marta Camici
- Clinical Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (R.G.); (A.M.); (V.M.); (M.C.); (A.A.)
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy;
| | - Andrea Antinori
- Clinical Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (R.G.); (A.M.); (V.M.); (M.C.); (A.A.)
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (E.L.); (F.M.); (I.A.)
| | - Isabella Abbate
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (E.L.); (F.M.); (I.A.)
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218
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Abunimye DA, Okafor IM, Okorowo H, Obeagu EI. The role of GATA family transcriptional factors in haematological malignancies: A review. Medicine (Baltimore) 2024; 103:e37487. [PMID: 38518015 PMCID: PMC10956995 DOI: 10.1097/md.0000000000037487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
GATA transcriptional factors are zinc finger DNA binding proteins that regulate transcription during development and cell differentiation. The 3 important GATA transcription factors GATA1, GATA2 and GATA3 play essential role in the development and maintenance of hematopoietic systems. GATA1 is required for the erythroid and Megakaryocytic commitment during hematopoiesis. GATA2 is crucial for the proliferation and survival of early hematopoietic cells, and is also involved in lineage specific transcriptional regulation as the dynamic partner of GATA1. GATA3 plays an essential role in T lymphoid cell development and immune regulation. As a result, mutations in gene encoding the GATA transcription factor or alteration in the protein expression level or their function have been linked to a variety of human haematological malignancies. This review presents a summary of recent understanding of how the disrupted biological function of GATA may contribute to hematologic diseases.
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Affiliation(s)
- Dennis Akongfe Abunimye
- Department of Haematology and Blood Transfusion Science, University of Calabar, Calabar, Nigeria
| | - Ifeyinwa Maryanne Okafor
- Department of Haematology and Blood Transfusion Science, University of Calabar, Calabar, Nigeria
| | - Henshew Okorowo
- Department of Haematology and Blood Transfusion Science, University of Calabar, Calabar, Nigeria
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219
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Migale R, Neumann M, Mitter R, Rafiee MR, Wood S, Olsen J, Lovell-Badge R. FOXL2 interaction with different binding partners regulates the dynamics of ovarian development. Sci Adv 2024; 10:eadl0788. [PMID: 38517962 PMCID: PMC10959415 DOI: 10.1126/sciadv.adl0788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
The transcription factor FOXL2 is required in ovarian somatic cells for female fertility. Differential timing of Foxl2 deletion, in embryonic versus adult mouse ovary, leads to distinctive outcomes, suggesting different roles across development. Here, we comprehensively investigated FOXL2's role through a multi-omics approach to characterize gene expression dynamics and chromatin accessibility changes, coupled with genome-wide identification of FOXL2 targets and on-chromatin interacting partners in somatic cells across ovarian development. We found that FOXL2 regulates more targets postnatally, through interaction with factors regulating primordial follicle formation and steroidogenesis. Deletion of one interactor, ubiquitin-specific protease 7 (Usp7), results in impairment of somatic cell differentiation, germ cell nest breakdown, and ovarian development, leading to sterility. Our datasets constitute a comprehensive resource for exploration of the molecular mechanisms of ovarian development and causes of female infertility.
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Affiliation(s)
- Roberta Migale
- Laboratory of Stem Cell Biology and Developmental Genetics, The Francis Crick Institute, London NW1 1AT, UK
| | - Michelle Neumann
- Laboratory of Stem Cell Biology and Developmental Genetics, The Francis Crick Institute, London NW1 1AT, UK
| | - Richard Mitter
- Bioinformatics core, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mahmoud-Reza Rafiee
- RNA Networks Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sophie Wood
- Genetic Modification Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jessica Olsen
- Genetic Modification Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Robin Lovell-Badge
- Laboratory of Stem Cell Biology and Developmental Genetics, The Francis Crick Institute, London NW1 1AT, UK
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220
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Mindel V, Brodsky S, Cohen A, Manadre W, Jonas F, Carmi M, Barkai N. Intrinsically disordered regions of the Msn2 transcription factor encode multiple functions using interwoven sequence grammars. Nucleic Acids Res 2024; 52:2260-2272. [PMID: 38109289 PMCID: PMC10954448 DOI: 10.1093/nar/gkad1191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/04/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
Intrinsically disordered regions (IDRs) are abundant in eukaryotic proteins, but their sequence-function relationship remains poorly understood. IDRs of transcription factors (TFs) can direct promoter selection and recruit coactivators, as shown for the budding yeast TF Msn2. To examine how IDRs encode both these functions, we compared genomic binding specificity, coactivator recruitment, and gene induction amongst a large set of designed Msn2-IDR mutants. We find that both functions depend on multiple regions across the > 600AA IDR. Yet, transcription activity was readily disrupted by mutations that showed no effect on the Msn2 binding specificity. Our data attribute this differential sensitivity to the integration of a relaxed, composition-based code directing binding specificity with a more stringent, motif-based code controlling the recruitment of coactivators and transcription activity. Therefore, Msn2 utilizes interwoven sequence grammars for encoding multiple functions, suggesting a new IDR design paradigm of potentially general use.
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Affiliation(s)
- Vladimir Mindel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Aileen Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Wajd Manadre
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miri Carmi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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221
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Xiong X, Chen H, Zhang Q, Liu Y, Xu C. Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing. Nucleic Acids Res 2024; 52:e24. [PMID: 38261991 PMCID: PMC10954476 DOI: 10.1093/nar/gkae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
Hemi-methylated cytosine dyads widely occur on mammalian genomic DNA, and can be stably inherited across cell divisions, serving as potential epigenetic marks. Previous identification of hemi-methylation relied on harsh bisulfite treatment, leading to extensive DNA degradation and loss of methylation information. Here we introduce Mhemi-seq, a bisulfite-free strategy, to efficiently resolve methylation status of cytosine dyads into unmethylation, strand-specific hemi-methylation, or full-methylation. Mhemi-seq reproduces methylomes from bisulfite-based sequencing (BS-seq & hpBS-seq), including the asymmetric hemi-methylation enrichment flanking CTCF motifs. By avoiding base conversion, Mhemi-seq resolves allele-specific methylation and associated imprinted gene expression more efficiently than BS-seq. Furthermore, we reveal an inhibitory role of hemi-methylation in gene expression and transcription factor (TF)-DNA binding, and some displays a similar extent of inhibition as full-methylation. Finally, we uncover new hemi-methylation patterns within Alu retrotransposon elements. Collectively, Mhemi-seq can accelerate the identification of DNA hemi-methylation and facilitate its integration into the chromatin environment for future studies.
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Affiliation(s)
- Xiong Xiong
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Hengye Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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222
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Ku J, Lee K, Ku D, Kim S, Lee J, Bang H, Kim N, Do H, Lee H, Lim C, Han J, Lee YS, Kim Y. Alternative polyadenylation determines the functional landscape of inverted Alu repeats. Mol Cell 2024; 84:1062-1077.e9. [PMID: 38309276 DOI: 10.1016/j.molcel.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/27/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
Inverted Alu repeats (IRAlus) are abundantly found in the transcriptome, especially in introns and 3' untranslated regions (UTRs). Yet, the biological significance of IRAlus embedded in 3' UTRs remains largely unknown. Here, we find that 3' UTR IRAlus silences genes involved in essential signaling pathways. We utilize J2 antibody to directly capture and map the double-stranded RNA structure of 3' UTR IRAlus in the transcriptome. Bioinformatic analysis reveals alternative polyadenylation as a major axis of IRAlus-mediated gene regulation. Notably, the expression of mouse double minute 2 (MDM2), an inhibitor of p53, is upregulated by the exclusion of IRAlus during UTR shortening, which is exploited to silence p53 during tumorigenesis. Moreover, the transcriptome-wide UTR lengthening in neural progenitor cells results in the global downregulation of genes associated with neurodegenerative diseases, including amyotrophic lateral sclerosis, via IRAlus inclusion. Our study establishes the functional landscape of 3' UTR IRAlus and its role in human pathophysiology.
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Affiliation(s)
- Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Keonyong Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Doyeong Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sujin Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jongbin Lee
- Research Center for Cellular Identity, KAIST, Daejeon 34141, Korea
| | - Hyunwoo Bang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Namwook Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hyunsu Do
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Korea
| | - Hyeonjung Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Korea
| | - Chunghun Lim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Jinju Han
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Korea; BioMedical Research Center, KAIST, Daejeon 34141, Korea
| | - Young-Suk Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Korea; Graduate School of Engineering Biology, KAIST, Daejeon 34141, Korea.
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; Graduate School of Engineering Biology, KAIST, Daejeon 34141, Korea; KAIST Institute for BioCentury, KAIST, Daejeon 34141, Korea; KAIST Institute for Health Science and Technology (KIHST), KAIST, Daejeon 34141, Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Korea.
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223
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Chong S, Yoshida S. How transcription factor binding controls transcriptional bursting dynamics: A single-molecule view. Mol Cell 2024; 84:997-999. [PMID: 38518750 DOI: 10.1016/j.molcel.2024.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/24/2024]
Abstract
In this issue, Pomp et al.1 simultaneously tracked transcriptional bursts of yeast gene GAL10 and transient binding of transcription factor Gal4 at the gene using novel methods. Dynamic exchange and infrequent long binding of Gal4 together enable prolonged transcriptional bursts of GAL10.
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Affiliation(s)
- Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Shawn Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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224
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Skardžiūtė K, Kvederavičiūtė K, Pečiulienė I, Narmontė M, Gibas P, Ličytė J, Klimašauskas S, Kriukienė E. One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci. Cell Chem Biol 2024; 31:607-621.e9. [PMID: 38154461 PMCID: PMC10962225 DOI: 10.1016/j.chembiol.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
We present a method, named Mx-TOP, for profiling of three epigenetic regulatory layers-chromatin accessibility, general DNA modification, and DNA hydroxymethylation-from a single library. The approach is based on chemo-enzymatic covalent tagging of unmodified CG sites and hydroxymethylated cytosine (5hmC) along with GC sites in chromatin, which are then mapped using tag-selective base-resolution TOP-seq sequencing. Our in-depth validation of the approach revealed its sensitivity and informativity in evaluating chromatin accessibility and DNA modification interactions that drive transcriptional regulation. We employed the technology in a study of chromatin and DNA demethylation dynamics during in vitro neuronal differentiation. The study highlighted the involvement of gene body 5hmC in modulating an extensive decoupling between promoter accessibility and transcription. The importance of 5hmC in chromatin remodeling was further demonstrated by the observed resistance of the developmentally acquired open loci to the global 5hmC erasure in neuronal progenitors.
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Affiliation(s)
- Kotryna Skardžiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Kotryna Kvederavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Inga Pečiulienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Milda Narmontė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Janina Ličytė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania.
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225
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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226
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Pomp W, Meeussen JVW, Lenstra TL. Transcription factor exchange enables prolonged transcriptional bursts. Mol Cell 2024; 84:1036-1048.e9. [PMID: 38377994 PMCID: PMC10962226 DOI: 10.1016/j.molcel.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
Single-molecule imaging inside living cells has revealed that transcription factors (TFs) bind to DNA transiently, but a long-standing question is how this transient binding is related to transcription activation. Here, we devised a microscopy method to simultaneously measure transient TF binding at a single locus and the effect of these binding events on transcription. We show that DNA binding of the yeast TF Gal4 activates transcription of a target gene within a few seconds, with at least ∼20% efficiency and with a high initiation rate of ∼1 RNA/s. Gal4 DNA dissociation decreases transcription rapidly. Moreover, at a gene with multiple binding sites, individual Gal4 molecules only rarely stay bound throughout the entire burst but instead frequently exchange during a burst to increase the transcriptional burst duration. Our results suggest a mechanism for enhancer regulation in more complex eukaryotes, where TF cooperativity and exchange enable robust and responsive transcription regulation.
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Affiliation(s)
- Wim Pomp
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Joseph V W Meeussen
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
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227
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Gerstner M, Heller V, Fechner J, Hermann B, Wang L, Lausen J. Prmt6 represses the pro-adipogenic Ppar-gamma-C/ebp-alpha transcription factor loop. Sci Rep 2024; 14:6656. [PMID: 38509237 PMCID: PMC10954715 DOI: 10.1038/s41598-024-57310-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/17/2024] [Indexed: 03/22/2024] Open
Abstract
The feed-forward loop between the transcription factors Ppar-gamma and C/ebp-alpha is critical for lineage commitment during adipocytic differentiation. Ppar-gamma interacts with epigenetic cofactors to activate C/ebp-alpha and the downstream adipocytic gene expression program. Therefore, knowledge of the epigenetic cofactors associated with Ppar-gamma, is central to understanding adipocyte differentiation in normal differentiation and disease. We found that Prmt6 is present with Ppar-gamma on the Ppar-gamma and C/ebp-alpha promoter. It contributes to the repression of C/ebp-alpha expression, in part through its ability to induce H3R2me2a. During adipocyte differentiation, Prmt6 expression is reduced and the methyltransferase leaves the promoters. As a result, the expression of Ppar-gamma and C/ebp-alpha is upregulated and the adipocytic gene expression program is established. Inhibition of Prmt6 by a small molecule enhances adipogenesis, opening up the possibility of epigenetic manipulation of differentiation. Our data provide detailed information on the molecular mechanism controlling the Ppar-gamma-C/ebp-alpha feed-forward loop. Thus, they advance our understanding of adipogenesis in normal and aberrant adipogenesis.
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Affiliation(s)
- Mirjam Gerstner
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Vivien Heller
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Johannes Fechner
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Benedikt Hermann
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Lei Wang
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Joern Lausen
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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228
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Felício D, Alves-Ferreira M, Santos M, Quintas M, Lopes AM, Lemos C, Pinto N, Martins S. Integrating functional scoring and regulatory data to predict the effect of non-coding SNPs in a complex neurological disease. Brief Funct Genomics 2024; 23:138-149. [PMID: 37254524 DOI: 10.1093/bfgp/elad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/13/2023] [Accepted: 05/09/2023] [Indexed: 06/01/2023] Open
Abstract
Most SNPs associated with complex diseases seem to lie in non-coding regions of the genome; however, their contribution to gene expression and disease phenotype remains poorly understood. Here, we established a workflow to provide assistance in prioritising the functional relevance of non-coding SNPs of candidate genes as susceptibility loci in polygenic neurological disorders. To illustrate the applicability of our workflow, we considered the multifactorial disorder migraine as a model to follow our step-by-step approach. We annotated the overlap of selected SNPs with regulatory elements and assessed their potential impact on gene expression based on publicly available prediction algorithms and functional genomics information. Some migraine risk loci have been hypothesised to reside in non-coding regions and to be implicated in the neurotransmission pathway. In this study, we used a set of 22 non-coding SNPs from neurotransmission and synaptic machinery-related genes previously suggested to be involved in migraine susceptibility based on our candidate gene association studies. After prioritising these SNPs, we focused on non-reported ones that demonstrated high regulatory potential: (1) VAMP2_rs1150 (3' UTR) was predicted as a target of hsa-mir-5010-3p miRNA, possibly disrupting its own gene expression; (2) STX1A_rs6951030 (proximal enhancer) may affect the binding affinity of zinc-finger transcription factors (namely ZNF423) and disturb TBL2 gene expression; and (3) SNAP25_rs2327264 (distal enhancer) expected to be in a binding site of ONECUT2 transcription factor. This study demonstrated the applicability of our practical workflow to facilitate the prioritisation of potentially relevant non-coding SNPs and predict their functional impact in multifactorial neurological diseases.
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Affiliation(s)
- Daniela Felício
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto 4200-135, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto 4050-313, Portugal
| | - Miguel Alves-Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto 4050-313, Portugal
- Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
- Centre for Predictive and Preventive Genetics (CGPP), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
| | - Mariana Santos
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
| | - Marlene Quintas
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto 4050-313, Portugal
- Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
| | - Alexandra M Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto 4200-135, Portugal
- Centre for Predictive and Preventive Genetics (CGPP), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
| | - Carolina Lemos
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto 4050-313, Portugal
- Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
| | - Nádia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto 4200-135, Portugal
- Centro de Matemática da Universidade do Porto (CMUP), Porto 4169-007, Portugal
| | - Sandra Martins
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto 4200-135, Portugal
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Liu Y, Niu J, Ye F, Solberg T, Lu B, Wang C, Nowacki M, Gao S. Dynamic DNA N 6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus. Genome Res 2024; 34:256-271. [PMID: 38471739 PMCID: PMC10984389 DOI: 10.1101/gr.278796.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
The formation of resting cysts commonly found in unicellular eukaryotes is a complex and highly regulated survival strategy against environmental stress that involves drastic physiological and biochemical changes. Although most studies have focused on the morphology and structure of cysts, little is known about the molecular mechanisms that control this process. Recent studies indicate that DNA N 6-adenine methylation (6mA) could be dynamically changing in response to external stimuli; however, its potential role in the regulation of cyst formation remains unknown. We used the ciliate Pseudocohnilembus persalinus, which can be easily induced to form cysts to investigate the dynamic pattern of 6mA in trophonts and cysts. Single-molecule real-time (SMRT) sequencing reveals high levels of 6mA in trophonts that decrease in cysts, along with a conversion of symmetric 6mA to asymmetric 6mA. Further analysis shows that 6mA, a mark of active transcription, is involved in altering the expression of encystment-related genes through changes in 6mA levels and 6mA symmetric-to-asymmetric conversion. Most importantly, we show that reducing 6mA levels by knocking down the DNA 6mA methyltransferase PpAMT1 accelerates cyst formation. Taken together, we characterize the genome-wide 6mA landscape in P. persalinus and provide insights into the role of 6mA in gene regulation under environmental stress in eukaryotes. We propose that 6mA acts as a mark of active transcription to regulate the encystment process along with symmetric-to-asymmetric conversion, providing important information for understanding the molecular response to environmental cues from the perspective of 6mA modification.
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Affiliation(s)
- Yongqiang Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Junhua Niu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Fei Ye
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Therese Solberg
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
- Department of Molecular Biology, Keio University School of Medicine, 160-8582 Tokyo, Japan
- Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio University, 108-8345 Tokyo, Japan
| | - Borong Lu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Chundi Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Shan Gao
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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Chan WS, Ng CF, Pang BPS, Hang M, Tse MCL, Iu ECY, Ooi XC, Yang X, Kim JK, Lee CW, Chan CB. Exercise-induced BDNF promotes PPARδ-dependent reprogramming of lipid metabolism in skeletal muscle during exercise recovery. Sci Signal 2024; 17:eadh2783. [PMID: 38502732 PMCID: PMC11022078 DOI: 10.1126/scisignal.adh2783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
Post-exercise recovery is essential to resolve metabolic perturbations and promote long-term cellular remodeling in response to exercise. Here, we report that muscle-generated brain-derived neurotrophic factor (BDNF) elicits post-exercise recovery and metabolic reprogramming in skeletal muscle. BDNF increased the post-exercise expression of the gene encoding PPARδ (peroxisome proliferator-activated receptor δ), a transcription factor that is a master regulator of lipid metabolism. After exercise, mice with muscle-specific Bdnf knockout (MBKO) exhibited impairments in PPARδ-regulated metabolic gene expression, decreased intramuscular lipid content, reduced β-oxidation, and dysregulated mitochondrial dynamics. Moreover, MBKO mice required a longer period to recover from a bout of exercise and did not show increases in exercise-induced endurance capacity. Feeding naïve mice with the bioavailable BDNF mimetic 7,8-dihydroxyflavone resulted in effects that mimicked exercise-induced adaptations, including improved exercise capacity. Together, our findings reveal that BDNF is an essential myokine for exercise-induced metabolic recovery and remodeling in skeletal muscle.
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Affiliation(s)
- Wing Suen Chan
- School of Biological Sciences, the University of Hong Kong, 5N10 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Chun Fai Ng
- School of Biological Sciences, the University of Hong Kong, 5N10 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Brian Pak Shing Pang
- School of Biological Sciences, the University of Hong Kong, 5N10 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Miaojia Hang
- School of Biological Sciences, the University of Hong Kong, 5N10 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Margaret Chui Ling Tse
- School of Biological Sciences, the University of Hong Kong, 5N10 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Elsie Chit Yu Iu
- School of Biological Sciences, the University of Hong Kong, 5N10 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Xin Ci Ooi
- School of Biological Sciences, the University of Hong Kong, 5N10 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Xiuying Yang
- Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, Beijing 101399, China
| | - Jason K. Kim
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Chi Wai Lee
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Chi Bun Chan
- School of Biological Sciences, the University of Hong Kong, 5N10 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, China
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231
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Cao H. Lipopolysaccharide regulation of antiinflammatory tristetraprolin family and proinflammatory gene expression in mouse macrophages. BMC Res Notes 2024; 17:82. [PMID: 38504371 PMCID: PMC10949775 DOI: 10.1186/s13104-024-06743-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/08/2024] [Indexed: 03/21/2024] Open
Abstract
OBJECTIVE Tristetraprolin (TTP/ZFP36) family proteins exhibit antiinflammatory effects by destabilizing proinflammatory mRNAs. Previous studies showed that bacterial endotoxin lipopolysaccharides (LPS) stimulated TTP and tumor necrosis factor (TNF) gene expression, but less was known about LPS effects on TTP homologues and other proinflammatory gene expression in macrophages. The objective was to investigate LPS regulation of TTP family gene and TTP-targeted gene expression in mouse RAW264.7 macrophages using much higher concentrations of LPS and much longer treatment time than previous studies. RESULTS MTT assay showed that LPS was not toxic to the cells under LPS treatment up to 1000 ng/mL for 2-24 h. LPS mildly affected the soluble protein content in the cells. qPCR assay showed that LPS stimulated TTP mRNA rapidly but not sustainably with 40, 10, and 3 fold of the DMSO control after 2, 8 and 24 h treatment, respectively. Immunoblotting confirmed qPCR results on LPS stimulation of TTP gene expression in the mouse macrophages. LPS exhibited minimal effects on ZFP36L1, ZFP36L2 and ZFP36L3 mRNA levels. LPS increased mRNA levels of TNF, COX2, GM-CSF, INFγ and IL12b up to 311, 418, 11, 9 and 4 fold, respectively. This study demonstrated that LPS did not affect macrophage viability, dramatically increased antiinflammatory TTP gene expression as well as proinflammatory TNF and COX2 gene expression but had only mild effects on TTP homologues and other proinflammatory cytokine gene expression in the mouse macrophages.
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Affiliation(s)
- Heping Cao
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, 1100 Allen Toussaint Blvd, New Orleans, LA, 70124, USA.
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232
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Jiogo H, Crist C. Navigating translational control of gene expression in satellite cells. Curr Top Dev Biol 2024; 158:253-277. [PMID: 38670709 DOI: 10.1016/bs.ctdb.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Satellite cells, named for their satellite position around the sarcolemma of the myofibre, are responsible for skeletal muscle regeneration. Satellite cells normally reside in a quiescent state, but rapidly activate the myogenic program and the cell cycle in response to injury. Translational control of gene expression has emerged as an important regulator of satellite cell activity. Quiescent satellite cells maintain low levels of protein synthesis and selectively translate specific mRNAs to conserve limited energy. Activated satellite cells rapidly restore global protein synthesis to meet the demands of proliferating myogenic progenitors that participate in muscle repair. We propose a model by which translational control enables rapid protein level changes in response to injury-induced environmental shifts, serving as both a brake mechanism during quiescence and an accelerator for injury response. In this Chapter, we navigate the processing, translation and metabolism of newly transcribed mRNAs. We review the modifications of mRNA that occur during mRNA processing in the nucleus of satellite cells, and illustrate how these modifications impact the translation and stability of mRNAs. In the cytoplasm, we review how pathways work in concert to regulate protein synthesis globally, while trans acting microRNAs and RNA binding proteins modify specific mRNA translation within a context of tightly regulated protein synthesis. While navigating translational control of gene expression in satellite cells, this chapter reveals that despite significant progress, the field remains nascent in the broader scope of translational control in cell biology. We propose that future investigations will benefit from incorporating emerging global analyses to study translational control of gene expression in rare satellite cells, and we pose unanswered questions that warrant future exploration.
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Affiliation(s)
- Holly Jiogo
- Department of Human Genetics, McGill University, Montreal, QC, Canada; Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Colin Crist
- Department of Human Genetics, McGill University, Montreal, QC, Canada; Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.
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233
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Li Y, Hirano S, Sato K, Osawa M, Nagaoka H. Assessing Interferon Regulatory Factor 4 Complex Formation: Differential Behavior of Homocomplexes Versus Heterocomplexes Induced by Mutations. Biochemistry 2024; 63:767-776. [PMID: 38439718 DOI: 10.1021/acs.biochem.3c00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Interferon regulatory factor 4 (IRF4) is a crucial transcription factor that plays a vital role in lymphocyte development, including in the fate-determining steps in terminal differentiation. It is also implicated in the development of lymphoid tumors such as multiple myeloma and adult T-cell leukemia. IRF4 can form a homodimer and multiple heterocomplexes with other transcription factors such as purine-rich box1 and activator protein 1. Each protein complex binds to specific DNA sequences to regulate a distinct set of genes. However, the precise relationship among these complex formations remains unclear. Herein, we investigated the abilities of IRF4 proteins with functional mutations in the IRF-association domain and autoinhibitory region to form complexes using luciferase reporter assays. The assays allowed us to selectively assess the activity of each complex. Our results revealed that certain IRF-association domain mutants, previously known to have impaired heterocomplex formation, maintained or even enhanced homodimer activity. This discrepancy suggests that the mutated amino acid residues selectively influence homodimer activity. Conversely, a phosphomimetic serine mutation in the autoinhibitory region displayed strong activating effects in all complexes. Furthermore, we observed that partner proteins involved in heterocomplex formation could disrupt the activity of the homodimer, suggesting a potential competition between homocomplexes and heterocomplexes. Our findings provide new insights into the mechanistic function of IRF4.
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Affiliation(s)
- Yupeng Li
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Setoka Hirano
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Katsuya Sato
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Masatake Osawa
- Department of Regeneration and Applied Biomedical Sciences, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Hitoshi Nagaoka
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
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234
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Penner-Goeke S, Binder EB. Linking environmental factors and gene regulation. eLife 2024; 13:e96710. [PMID: 38497535 PMCID: PMC10948141 DOI: 10.7554/elife.96710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
A technique called mSTARR-seq sheds light on how DNA methylation may shape responses to external stimuli by altering the activity of sequences that control gene expression.
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Affiliation(s)
- Signe Penner-Goeke
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Elisabeth B Binder
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
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235
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Buson F, Gao Y, Wang B. Genetic Parts and Enabling Tools for Biocircuit Design. ACS Synth Biol 2024; 13:697-713. [PMID: 38427821 DOI: 10.1021/acssynbio.3c00691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Synthetic biology aims to engineer biological systems for customized tasks through the bottom-up assembly of fundamental building blocks, which requires high-quality libraries of reliable, modular, and standardized genetic parts. To establish sets of parts that work well together, synthetic biologists created standardized part libraries in which every component is analyzed in the same metrics and context. Here we present a state-of-the-art review of the currently available part libraries for designing biocircuits and their gene expression regulation paradigms at transcriptional, translational, and post-translational levels in Escherichia coli. We discuss the necessary facets to integrate these parts into complex devices and systems along with the current efforts to catalogue and standardize measurement data. To better display the range of available parts and to facilitate part selection in synthetic biology workflows, we established biopartsDB, a curated database of well-characterized and useful genetic part and device libraries with detailed quantitative data validated by the published literature.
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Affiliation(s)
- Felipe Buson
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
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236
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Liu D, Gou L, Sun T, Liu J, Fan TP, Deng H, Cai Y. Characterization and Application of a Stationary Phase Promoter Library from Serratia marcescens. ACS Synth Biol 2024; 13:969-972. [PMID: 38340070 DOI: 10.1021/acssynbio.3c00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Serratia marcescens has garnered increasing attention as a promising host for valuable compound production. However, the lack of an efficient gene regulation toolkit severely hampers its applications. Here, a library of stationary phase promoters was screened in S. marcescens HBA7 using RNA-seq and RT-qPCR, revealing a 43-fold regulatory range with the red fluorescent protein mKate2 as the reporter. The β-galactosidase was employed to demonstrate the universality in driving the expression of different proteins. The wide-ranging utility of these promoters in different hosts was demonstrated in Escherichia coli. Moreover, to assess their potential application, the strongest promoter, P2, was employed to express the swrW gene, resulting in a roughly 20-fold increase in serrawettin W1 production in S. marcescens HBQA7ΔswrW. In summary, this study successfully constructed a gradient-strength stationary phase promoter library, providing an effective toolkit for gene regulation and secondary metabolite production in diverse prokaryotes, including S. marcescens and E. coli.
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Affiliation(s)
- Di Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Linbo Gou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Tingting Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1TN, U.K
| | - Huaxiang Deng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
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237
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Couasnay G, Garcia H, Elefteriou F. A comparative analysis of TonEBP conditional knockout mouse models reveals inter-dependency between compartments of the intervertebral disc. Development 2024; 151:dev202354. [PMID: 38421307 PMCID: PMC11006390 DOI: 10.1242/dev.202354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Interactions between notochord and sclerotome are required for normal embryonic spine patterning, but whether the postnatal derivatives of these tissues also require interactions for postnatal intervertebral disc (IVD) growth and maintenance is less established. We report here the comparative analysis of four conditional knockout mice deficient for TonEBP, a transcription factor known to allow cells to adapt to changes in extracellular osmotic pressure, in specific compartments of the IVD. We show that TonEBP deletion in nucleus pulposus (NP) cells does not affect their survival or aggrecan expression, but promoted cell proliferation in the NP and in adjacent vertebral growth plates (GPs). In cartilage end plates/GPs, TonEBP deletion induced cell death, but also structural alterations in the adjacent NP cells and vertebral bodies. Embryonic or postnatal TonEBP loss generated similar IVD changes. In addition to demonstrating the requirement of TonEBP in the different compartments of the IVD, this comparative analysis uncovers the in vivo interdependency of the different IVD compartments during the growth of the postnatal IVD-vertebral units.
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Affiliation(s)
- Greig Couasnay
- Department of Orthopedic Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haley Garcia
- Department of Orthopedic Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Florent Elefteriou
- Department of Orthopedic Surgery, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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238
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Herr LA, Fiala GJ, Sagar, Schaffer AM, Hummel JF, Zintchenko M, Raute K, Velasco Cárdenas RMH, Heizmann B, Ebert K, Fehrenbach K, Janowska I, Chan S, Tanriver Y, Minguet S, Schamel WW. Kidins220 and Aiolos promote thymic iNKT cell development by reducing TCR signals. Sci Adv 2024; 10:eadj2802. [PMID: 38489359 PMCID: PMC10942104 DOI: 10.1126/sciadv.adj2802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
Development of T cells is controlled by the signal strength of the TCR. The scaffold protein kinase D-interacting substrate of 220 kilodalton (Kidins220) binds to the TCR; however, its role in T cell development was unknown. Here, we show that T cell-specific Kidins220 knockout (T-KO) mice have strongly reduced invariant natural killer T (iNKT) cell numbers and modest decreases in conventional T cells. Enhanced apoptosis due to increased TCR signaling in T-KO iNKT thymocytes of developmental stages 2 and 3 shows that Kidins220 down-regulates TCR signaling at these stages. scRNA-seq indicated that the transcription factor Aiolos is down-regulated in Kidins220-deficient iNKT cells. Analysis of an Aiolos KO demonstrated that Aiolos is a downstream effector of Kidins220 during iNKT cell development. In the periphery, T-KO iNKT cells show reduced TCR signaling upon stimulation with α-galactosylceramide, suggesting that Kidins220 promotes TCR signaling in peripheral iNKT cells. Thus, Kidins220 reduces or promotes signaling dependent on the iNKT cell developmental stage.
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Affiliation(s)
- Laurenz A. Herr
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Gina J. Fiala
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Sagar
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anna-Maria Schaffer
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Jonas F. Hummel
- Institute of Medical Microbiology and Hygiene, Medical Center, University of Freiburg, Germany
| | - Marina Zintchenko
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Katrin Raute
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Rubí M.-H. Velasco Cárdenas
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Beate Heizmann
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS UMR7104, Université de Strasbourg, Illkirch, France
| | - Karolina Ebert
- Institute of Medical Microbiology and Hygiene, Medical Center, University of Freiburg, Germany
| | - Kerstin Fehrenbach
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Iga Janowska
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS UMR7104, Université de Strasbourg, Illkirch, France
| | - Yakup Tanriver
- Institute of Medical Microbiology and Hygiene, Medical Center, University of Freiburg, Germany
- Department of Medicine IV: Nephrology and Primary Care, Medical Center, University of Freiburg, Freiburg, Germany
| | - Susana Minguet
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Wolfgang W. Schamel
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
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239
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Jiang Y, Ye Y, Zhang X, Yu Y, Huang L, Bao X, Xu X. Identification and characterization of CHD4-associated eRNA as a novel modulator of fetal hemoglobin levels in β-thalassemia. Biochem Biophys Res Commun 2024; 701:149555. [PMID: 38325179 DOI: 10.1016/j.bbrc.2024.149555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/09/2024]
Abstract
Fetal-to-adult hemoglobin switching is controlled by programmed silencing of γ-globin while the re-activation of fetal hemoglobin (HbF) is an effective strategy for ameliorating the clinical severity of β-thalassemia and sickle cell disease. The identification of enhancer RNAs (eRNAs) related to the fetal (α2γ2) to adult hemoglobin (α2β2) switching remains incomplete. In this study, the transcriptomes of GYPA+ cells from six β-thalassemia patients with extreme HbF levels were sequenced to identify differences in patterns of noncoding RNA expression. It is interesting that an enhancer upstream of CHD4, an HbF-related core subunit of the NuRD complex, was differentially transcribed. We found a significantly positive correlation of eRNA-CHD4 enhancer-gene interaction using the public database of FANTOM5. Specifically, the eRNA-CHD4 expression was found to be significantly higher in both CD34+ HSPCs and HUDEP-2 than those in K562 cells which commonly expressed high level of HbF, suggesting a correlation between eRNA and HbF expression. Furthermore, prediction of transcription binding sites of cis-eQTLs and the CHD4 genomic region revealed a putative interaction site between rs73264846 and ZNF410, a known transcription factor regulating HbF expression. Moreover, in-vitro validation showed that the inhibition of eRNA could reduce the expression of HBG expression in HUDEP-2 cells. Taken together, the findings of this study demonstrate that a distal enhancer contributes to stage-specific silencing of γ-globin genes through direct modulation of CHD4 expression and provide insights into the epigenetic mechanisms of NuRD-mediated hemoglobin switching.
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Affiliation(s)
- Yida Jiang
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Key Chip Laboratory, Guangzhou, Guangdong, China
| | - Yuhua Ye
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Key Chip Laboratory, Guangzhou, Guangdong, China
| | - Xinhua Zhang
- Department of Hematology, 923rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Yanping Yu
- Department of Pediatric, 923rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Liping Huang
- Department of Pediatric, 923rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Xiuqin Bao
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Xiangmin Xu
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Key Chip Laboratory, Guangzhou, Guangdong, China.
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240
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Le TNY, Nguyen TA. High-throughput protocol for studying pri-miRNA processing using randomized sequences. STAR Protoc 2024; 5:102782. [PMID: 38103193 PMCID: PMC10770632 DOI: 10.1016/j.xpro.2023.102782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/07/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
The Microprocessor complex is crucial in microRNA (miRNA) biogenesis, as it processes primary miRNAs (pri-miRNAs) into precursor miRNAs. Here, we present a high-throughput, radioisotope-free protocol for studying pri-miRNA processing using randomized sequences. We describe steps for randomized substrate preparation, protein purification, processing assays, and DNA library construction for sequencing. This technique explores pri-miRNA processing, uncovers key RNA elements, and illuminates gene expression regulation. However, its efficacy may be constrained by data analysis complexity and the requirement for specialized equipment. For complete details on the use and execution of this protocol, please refer to Nguyen et al. (2023).1.
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Affiliation(s)
- Thi Nhu-Y Le
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China.
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241
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Chen S, Liu Y, Wang Z, Qi C, Yu Y, Xu L, Hou T, Sheng R. Identification of 3-aryl-5-methyl-isoxazole-4-carboxamide derivatives and analogs as novel HIF-2α agonists through docking-based virtual screening and structural modification. Eur J Med Chem 2024; 268:116227. [PMID: 38387335 DOI: 10.1016/j.ejmech.2024.116227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Hypoxia-inducible factor-2 (HIF-2) serves as the pivotal transcription factor in cellular responses to low oxygen levels, particularly concerning the regulation of erythropoietin (EPO) production. A docking-based virtual screening on crystal structures of HIF-2α inhibitors unexpectedly identified 3-phenyl-5-methyl-isoxazole-4-carboxamide derivative v19 as a hit of HIF-2α agonist. Further structural optimizations of compound v19 led to the discovery of a series of HIF-2α agonists with novel scaffolds. The most promising compounds 12g and 14d exhibited potent HIF-2α agonistic activities in vitro with EC50 values of 2.29 μM and 1.78 μM, respectively. Molecular dynamics simulations have revealed their capacity to allosterically enhance HIF-2 dimerization, which shed light on their mechanism of action. Moreover, compound 14d demonstrated a favorable pharmacokinetic (PK) profile, boasting an impressive oral bioavailability value of 68.71 %. These findings strongly suggest that compound 14d is an auspicious lead compound for the treatment of renal anemia.
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Affiliation(s)
- Siyuan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yao Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengcheng Qi
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanzhen Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Rong Sheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Jinhua Institute of Zhejiang University, Zhejiang University, Jinhua, 321036, China.
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242
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Yu M, Tang TS, Ghamsari L, Yuen G, Scuoppo C, Rotolo JA, Kappel BJ, Mason JM. Exponential Combination of a and e/g Intracellular Peptide Libraries Identifies a Selective ATF3 Inhibitor. ACS Chem Biol 2024; 19:753-762. [PMID: 38412264 PMCID: PMC10949195 DOI: 10.1021/acschembio.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/19/2024] [Accepted: 02/07/2024] [Indexed: 02/29/2024]
Abstract
Activating transcription factor 3 (ATF3) is an activation transcription factor/cyclic adenosine monophosphate (cAMP) responsive element-binding (CREB) protein family member. It is recognized as an important regulator of cancer progression by repressing expression of key inflammatory factors such as interferon-γ and chemokine (C-C motif) ligand 4 (CCL4). Here, we describe a novel library screening approach that probes individual leucine zipper components before combining them to search exponentially larger sequence spaces not normally accessible to intracellular screening. To do so, we employ two individual semirational library design approaches and screen using a protein-fragment complementation assay (PCA). First, a 248,832-member library explored 12 amino acid positions at all five a positions to identify those that provided improved binding, with all e/g positions fixed as Q, placing selection pressure onto the library options provided. Next, a 59,049-member library probed all ten e/g positions with 3 options. Similarly, during e/g library screening, a positions were locked into a generically bindable sequence pattern (AIAIA), weakly favoring leucine zipper formation, while placing selection pressure onto e/g options provided. The combined a/e/g library represents ∼14.7 billion members, with the resulting peptide, ATF3W_aeg, binding ATF3 with high affinity (Tm = 60 °C; Kd = 151 nM) while strongly disfavoring homodimerization. Moreover, ATF3W_aeg is notably improved over component PCA hits, with target specificity found to be driven predominantly by electrostatic interactions. The combined a/e/g exponential library screening approach provides a robust, accelerated platform for exploring larger peptide libraries, toward derivation of potent yet selective antagonists that avoid homoassociation to provide new insight into rational peptide design.
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Affiliation(s)
- Miao Yu
- Department
of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - T.M. Simon Tang
- Department
of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Lila Ghamsari
- Sapience
Therapeutics, Inc. 500
Mamaroneck Ave. Suite 320, Tarrytown, New York 10591, United States
| | - Graham Yuen
- Sapience
Therapeutics, Inc. 500
Mamaroneck Ave. Suite 320, Tarrytown, New York 10591, United States
| | - Claudio Scuoppo
- Sapience
Therapeutics, Inc. 500
Mamaroneck Ave. Suite 320, Tarrytown, New York 10591, United States
| | - Jim A. Rotolo
- Sapience
Therapeutics, Inc. 500
Mamaroneck Ave. Suite 320, Tarrytown, New York 10591, United States
| | - Barry J. Kappel
- Sapience
Therapeutics, Inc. 500
Mamaroneck Ave. Suite 320, Tarrytown, New York 10591, United States
| | - Jody M. Mason
- Department
of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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243
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Emerson FJ, Chiu C, Lin LY, Riedel CG, Zhu M, Lee SS. The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans. Nat Commun 2024; 15:2320. [PMID: 38485937 PMCID: PMC10940595 DOI: 10.1038/s41467-024-46510-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
SET-26, HCF-1, and HDA-1 are highly conserved chromatin factors with key roles in development and aging. Here we present mechanistic insights into how these factors regulate gene expression and modulate longevity in C. elegans. We show that SET-26 and HCF-1 cooperate to regulate a common set of genes, and both antagonize the histone deacetylase HDA-1 to limit longevity. HCF-1 localization at chromatin is largely dependent on functional SET-26, whereas SET-26 is only minorly affected by loss of HCF-1, suggesting that SET-26 could recruit HCF-1 to chromatin. HDA-1 opposes SET-26 and HCF-1 on the regulation of a subset of their common target genes and in longevity. Our findings suggest that SET-26, HCF-1, and HDA-1 comprise a mechanism to fine-tune gene expression and longevity and likely have important implications for the mechanistic understanding of how these factors function in diverse organisms, particularly in aging biology.
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Affiliation(s)
- Felicity J Emerson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Caitlin Chiu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Laura Y Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Christian G Riedel
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ming Zhu
- National Institute of Biological Sciences, Beijing, China
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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244
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Yu YC, Tong ZJ, Liang XT, Wu JZ, Xu YJ, Wang JJ, Zhang MY, Wei TH, Yang J, Wang YB, Wang QX, Li QQ, Wang Z, Leng X, Ding N, Xue X, Sun SL, Li NG, Wang XL. Discovery of RORγ Allosteric Fluorescent Probes and Their Application: Fluorescence Polarization, Screening, and Bioimaging. J Med Chem 2024; 67:4194-4224. [PMID: 38442261 DOI: 10.1021/acs.jmedchem.4c00058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Retinoic acid receptor-related orphan receptor γ (RORγ) acts as a crucial transcription factor in Th17 cells and is involved in diverse autoimmune disorders. RORγ allosteric inhibitors have gained significant research focus as a novel strategy to inhibit RORγ transcriptional activity. Leveraging the high affinity and selectivity of RORγ allosteric inhibitor MRL-871 (1), this study presents the design, synthesis, and characterization of 11 allosteric fluorescent probes. Utilizing the preferred probe 12h, we established an efficient and cost-effective fluorescence polarization-based affinity assay for screening RORγ allosteric binders. By employing virtual screening in conjunction with this assay, 10 novel RORγ allosteric inhibitors were identified. The initial SAR studies focusing on the hit compound G381-0087 are also presented. The encouraging outcomes indicate that probe 12h possesses the potential to function as a powerful tool in facilitating the exploration of RORγ allosteric inhibitors and furthering understanding of RORγ function.
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Affiliation(s)
- Yan-Cheng Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Zhen-Jiang Tong
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Xiao-Ting Liang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Jia-Zhen Wu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Yu-Jing Xu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Jing-Jing Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Meng-Yuan Zhang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Tian-Hua Wei
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Jin Yang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Yi-Bo Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Qing-Xin Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Qing-Qing Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Zixuan Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - XueJiao Leng
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Xiao-Long Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
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245
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Lin W, Wall JD, Li G, Newman D, Yang Y, Abney M, VandeBerg JL, Olivier M, Gilad Y, Cox LA. Genetic regulatory effects in response to a high-cholesterol, high-fat diet in baboons. Cell Genom 2024; 4:100509. [PMID: 38430910 PMCID: PMC10943580 DOI: 10.1016/j.xgen.2024.100509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/20/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Abstract
Steady-state expression quantitative trait loci (eQTLs) explain only a fraction of disease-associated loci identified through genome-wide association studies (GWASs), while eQTLs involved in gene-by-environment (GxE) interactions have rarely been characterized in humans due to experimental challenges. Using a baboon model, we found hundreds of eQTLs that emerge in adipose, liver, and muscle after prolonged exposure to high dietary fat and cholesterol. Diet-responsive eQTLs exhibit genomic localization and genic features that are distinct from steady-state eQTLs. Furthermore, the human orthologs associated with diet-responsive eQTLs are enriched for GWAS genes associated with human metabolic traits, suggesting that context-responsive eQTLs with more complex regulatory effects are likely to explain GWAS hits that do not seem to overlap with standard eQTLs. Our results highlight the complexity of genetic regulatory effects and the potential of eQTLs with disease-relevant GxE interactions in enhancing the understanding of GWAS signals for human complex disease using non-human primate models.
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Affiliation(s)
- Wenhe Lin
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ge Li
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Deborah Newman
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78229, USA
| | - Yunqi Yang
- Committee on Genetics, Genomics and System Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Mark Abney
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - John L VandeBerg
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Yoav Gilad
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL 60637, USA.
| | - Laura A Cox
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78229, USA.
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246
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Dong X, Zhan Y, Li S, Yang M, Gao Y. MKRN1 regulates the expression profiles and transcription factor activity in HeLa cells inhibition suppresses cervical cancer cell progression. Sci Rep 2024; 14:6129. [PMID: 38480859 PMCID: PMC10937657 DOI: 10.1038/s41598-024-56830-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/12/2024] [Indexed: 03/17/2024] Open
Abstract
Cervical cancer is one of the most common gynecologic malignancies worldwide, necessitating the identification of novel biomarkers and therapeutic targets. This study aimed to investigate the significance of MKRN1 in cervical cancer and explore its potential as a diagnostic marker and therapeutic target. The results indicated that MKRN1 expression was up-regulated in cervical cancer tissues and correlated with advanced tumor stage, higher grade, and poor patient survival. Functional studies demonstrated that targeting MKRN1 effectively inhibited cell proliferation, migration, and invasion, highlighting its critical role in tumor progression and metastasis. Moreover, the knockdown of MKRN1 resulted in altered expression patterns of six transcription factor-encoding genes, revealing its involvement in gene regulation. Co-expression network analysis unveiled complex regulatory mechanisms underlying the effects of MKRN1 knockdown on gene expression. Furthermore, the results suggested that MKRN1 might serve as a diagnostic marker for personalized treatment strategies and a therapeutic target to inhibit tumor growth, metastasis, and overcome drug resistance. The development of MKRN1-targeted interventions might hold promise for advancing personalized medicine approaches in cervical cancer treatment. Further research is warranted to validate these findings, elucidate underlying mechanisms, and translate these insights into improved management and outcomes for cervical cancer patients.
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Affiliation(s)
- Xiang Dong
- School of Life Science, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, Anhui, China
- Research Center of Clinical Laboratory Science, School of Laboratory Medicine, Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Yuling Zhan
- School of Life Science, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, Anhui, China
- Research Center of Clinical Laboratory Science, School of Laboratory Medicine, Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Suwan Li
- School of Life Science, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, Anhui, China
- Research Center of Clinical Laboratory Science, School of Laboratory Medicine, Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Minghui Yang
- Research Center of Clinical Laboratory Science, School of Laboratory Medicine, Bengbu Medical College, Bengbu, 233030, Anhui, China
- School of Basic Courses, Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Yu Gao
- School of Life Science, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, Anhui, China.
- Laboratory Animal Center, Bengbu Medical College, Bengbu, 233030, Anhui, China.
- Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Bengbu, 233030, Anhui, China.
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247
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Feng AC, Thomas BJ, Purbey PK, de Melo FM, Liu X, Daly AE, Sun F, Lo JHH, Cheng L, Carey MF, Scumpia PO, Smale ST. The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling. Immunity 2024; 57:462-477.e9. [PMID: 38430908 PMCID: PMC10984581 DOI: 10.1016/j.immuni.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 11/26/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024]
Abstract
Inducible nucleosome remodeling at hundreds of latent enhancers and several promoters shapes the transcriptional response to Toll-like receptor 4 (TLR4) signaling in macrophages. We aimed to define the identities of the transcription factors that promote TLR-induced remodeling. An analysis strategy based on ATAC-seq and single-cell ATAC-seq that enriched for genomic regions most likely to undergo remodeling revealed that the transcription factor nuclear factor κB (NF-κB) bound to all high-confidence peaks marking remodeling during the primary response to the TLR4 ligand, lipid A. Deletion of NF-κB subunits RelA and c-Rel resulted in the loss of remodeling at high-confidence ATAC-seq peaks, and CRISPR-Cas9 mutagenesis of NF-κB-binding motifs impaired remodeling. Remodeling selectivity at defined regions was conferred by collaboration with other inducible factors, including IRF3- and MAP-kinase-induced factors. Thus, NF-κB is unique among TLR4-activated transcription factors in its broad contribution to inducible nucleosome remodeling, alongside its ability to activate poised enhancers and promoters assembled into open chromatin.
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Affiliation(s)
- An-Chieh Feng
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Brandon J Thomas
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Behavioral Science, University of Washington, Seattle, WA 98195, USA
| | - Prabhat K Purbey
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Filipe Menegatti de Melo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xin Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Allison E Daly
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fei Sun
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jerry Hung-Hao Lo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lijing Cheng
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael F Carey
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Philip O Scumpia
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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248
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Jiang Y, Gruszka D, Zeng C, Swindell WR, Gaskill C, Sorensen C, Brown W, Gangwar RS, Tsoi LC, Webster J, Sigurðardóttir SL, Sarkar MK, Uppala R, Kidder A, Xing X, Plazyo O, Xing E, Billi AC, Maverakis E, Kahlenberg JM, Gudjonsson JE, Ward NL. Suppression of TCF4 promotes a ZC3H12A-mediated self-sustaining inflammatory feedback cycle involving IL-17RA/IL-17RE epidermal signaling. JCI Insight 2024; 9:e172764. [PMID: 38470486 DOI: 10.1172/jci.insight.172764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/05/2024] [Indexed: 03/13/2024] Open
Abstract
IL-17C is an epithelial cell-derived proinflammatory cytokine whose transcriptional regulation remains unclear. Analysis of the IL17C promoter region identified TCF4 as putative regulator, and siRNA knockdown of TCF4 in human keratinocytes (KCs) increased IL17C. IL-17C stimulation of KCs (along with IL-17A and TNF-α stimulation) decreased TCF4 and increased NFKBIZ and ZC3H12A expression in an IL-17RA/RE-dependent manner, thus creating a feedback loop. ZC3H12A (MCPIP1/Regnase-1), a transcriptional immune-response regulator, also increased following TCF4 siRNA knockdown, and siRNA knockdown of ZC3H12A decreased NFKBIZ, IL1B, IL36G, CCL20, and CXCL1, revealing a proinflammatory role for ZC3H12A. Examination of lesional skin from the KC-Tie2 inflammatory dermatitis mouse model identified decreases in TCF4 protein concomitant with increases in IL-17C and Zc3h12a that reversed following the genetic elimination of Il17c, Il17ra, and Il17re and improvement in the skin phenotype. Conversely, interference with Tcf4 in KC-Tie2 mouse skin increased Il17c and exacerbated the inflammatory skin phenotype. Together, these findings identify a role for TCF4 in the negative regulation of IL-17C, which, alone and with TNF-α and IL-17A, feed back to decrease TCF4 in an IL-17RA/RE-dependent manner. This loop is further amplified by IL-17C-TCF4 autocrine regulation of ZC3H12A and IL-17C regulation of NFKBIZ to promote self-sustaining skin inflammation.
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Affiliation(s)
- Yanyun Jiang
- Department of Dermatology, Ann Arbor, Michigan, USA
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dennis Gruszka
- Departments of Nutrition and Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Chang Zeng
- Department of Dermatology, Ann Arbor, Michigan, USA
| | - William R Swindell
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Christa Gaskill
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christian Sorensen
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Whitney Brown
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Roopesh Singh Gangwar
- Departments of Nutrition and Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Lam C Tsoi
- Department of Dermatology, Ann Arbor, Michigan, USA
| | - Joshua Webster
- Departments of Nutrition and Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | | | | | | | | | | | | | - Enze Xing
- Department of Dermatology, Ann Arbor, Michigan, USA
| | | | - Emanual Maverakis
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, California, USA
| | - J Michelle Kahlenberg
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Nicole L Ward
- Departments of Nutrition and Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation (VI4) and Vanderbilt Center for Immunobiology (VCI), Vanderbilt University Medical Center, Nashville, Tennessee, USA
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249
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Strenkert D, Schmollinger S, Paruthiyil S, Brown BC, Green S, Shafer CM, Salomé P, Nelson H, Blaby-Haas CE, Moseley JL, Merchant SS. Distinct function of Chlamydomonas CTRA-CTR transporters in Cu assimilation and intracellular mobilization. Metallomics 2024; 16:mfae013. [PMID: 38439674 PMCID: PMC10959442 DOI: 10.1093/mtomcs/mfae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/02/2024] [Indexed: 03/06/2024]
Abstract
Successful acclimation to copper (Cu) deficiency involves a fine balance between Cu import and export. In the green alga Chlamydomonas reinhardtii, Cu import is dependent on a transcription factor, Copper Response Regulator 1 (CRR1), responsible for activating genes in Cu-deficient cells. Among CRR1 target genes are two Cu transporters belonging to the CTR/COPT gene family (CTR1 and CTR2) and a related soluble protein (CTR3). The ancestor of these green algal proteins was likely acquired from an ancient chytrid and contained conserved cysteine-rich domains (named the CTR-associated domains, CTRA) that are predicted to be involved in Cu acquisition. We show by reverse genetics that Chlamydomonas CTR1 and CTR2 are canonical Cu importers albeit with distinct affinities, while loss of CTR3 did not result in an observable phenotype under the conditions tested. Mutation of CTR1, but not CTR2, recapitulates the poor growth of crr1 in Cu-deficient medium, consistent with a dominant role for CTR1 in high-affinity Cu(I) uptake. On the other hand, the overaccumulation of Cu(I) (20 times the quota) in zinc (Zn) deficiency depends on CRR1 and both CTR1 and CTR2. CRR1-dependent activation of CTR gene expression needed for Cu over-accumulation can be bypassed by the provision of excess Cu in the growth medium. Over-accumulated Cu is sequestered into the acidocalcisome but can become remobilized by restoring Zn nutrition. This mobilization is also CRR1-dependent, and requires activation of CTR2 expression, again distinguishing CTR2 from CTR1 and consistent with the lower substrate affinity of CTR2. ONE SENTENCE SUMMARY Regulation of Cu uptake and sequestration by members of the CTR family of proteins in Chlamydomonas.
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Affiliation(s)
- Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Srinand Paruthiyil
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Bonnie C Brown
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Sydnee Green
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Catherine M Shafer
- Molecular Toxicology Inter-departmental Ph.D. program, University of California, Los Angeles, CA 90095, USA
| | - Patrice Salomé
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Hosea Nelson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Crysten E Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jeffrey L Moseley
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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250
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Gilbert CJ, Rabolli CP, Golubeva VA, Sattler KM, Wang M, Ketabforoush A, Arnold WD, Lepper C, Accornero F. YTHDF2 governs muscle size through a targeted modulation of proteostasis. Nat Commun 2024; 15:2176. [PMID: 38467649 PMCID: PMC10928198 DOI: 10.1038/s41467-024-46546-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 02/28/2024] [Indexed: 03/13/2024] Open
Abstract
The regulation of proteostasis is fundamental for maintenance of muscle mass and function. Activation of the TGF-β pathway drives wasting and premature aging by favoring the proteasomal degradation of structural muscle proteins. Yet, how this critical post-translational mechanism is kept in check to preserve muscle health remains unclear. Here, we reveal the molecular link between the post-transcriptional regulation of m6A-modified mRNA and the modulation of SMAD-dependent TGF-β signaling. We show that the m6A-binding protein YTHDF2 is essential to determining postnatal muscle size. Indeed, muscle-specific genetic deletion of YTHDF2 impairs skeletal muscle growth and abrogates the response to hypertrophic stimuli. We report that YTHDF2 controls the mRNA stability of the ubiquitin ligase ASB2 with consequences on anti-growth gene program activation through SMAD3. Our study identifies a post-transcriptional to post-translational mechanism for the coordination of gene expression in muscle.
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Affiliation(s)
- Christopher J Gilbert
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Charles P Rabolli
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Volha A Golubeva
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Kristina M Sattler
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Meifang Wang
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
- Department of Physical Medicine and Rehabilitation, University of Missouri, Columbia, MO, USA
| | - Arsh Ketabforoush
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
- Department of Physical Medicine and Rehabilitation, University of Missouri, Columbia, MO, USA
| | - W David Arnold
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
- Department of Physical Medicine and Rehabilitation, University of Missouri, Columbia, MO, USA
- Department of Neurology, University of Missouri, Columbia, MO, USA
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO, USA
- Division of Neuromuscular Disorders, Department of Neurology, The Ohio State University, Columbus, OH, USA
- Department of Physical Medicine and Rehabilitation, The Ohio State University, Columbus, OH, USA
| | - Christoph Lepper
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Federica Accornero
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.
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