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Fu Z, Jiang S, Sun Y, Zheng S, Zong L, Li P. Cut&tag: a powerful epigenetic tool for chromatin profiling. Epigenetics 2024; 19:2293411. [PMID: 38105608 PMCID: PMC10730171 DOI: 10.1080/15592294.2023.2293411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Analysis of transcription factors and chromatin modifications at the genome-wide level provides insights into gene regulatory processes, such as transcription, cell differentiation and cellular response. Chromatin immunoprecipitation is the most popular and powerful approach for mapping chromatin, and other enzyme-tethering techniques have recently become available for living cells. Among these, Cleavage Under Targets and Tagmentation (CUT&Tag) is a relatively novel chromatin profiling method that has rapidly gained popularity in the field of epigenetics since 2019. It has also been widely adapted to map chromatin modifications and TFs in different species, illustrating the association of these chromatin epitopes with various physiological and pathological processes. Scalable single-cell CUT&Tag can be combined with distinct platforms to distinguish cellular identity, epigenetic features and even spatial chromatin profiling. In addition, CUT&Tag has been developed as a strategy for joint profiling of the epigenome, transcriptome or proteome on the same sample. In this review, we will mainly consolidate the applications of CUT&Tag and its derivatives on different platforms, give a detailed explanation of the pros and cons of this technique as well as the potential development trends and applications in the future.
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Affiliation(s)
- Zhijun Fu
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Sanjie Jiang
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Yiwen Sun
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Shanqiao Zheng
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Liang Zong
- BGI Tech Solutions Co, Ltd. BGI-Wuhan, Wuhan, China
| | - Peipei Li
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
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2
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Chen EX, Hu SC, Xu JQ, Liu KY, Tang J, Shen XP, Liang X, Xie YL, Ge LX, Luo X, Wang YX, Xiang YL, Ding YB. Suppression of GATA3 promotes epithelial-mesenchymal transition and simultaneous cellular senescence in human extravillous trophoblasts. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119768. [PMID: 38838858 DOI: 10.1016/j.bbamcr.2024.119768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 05/16/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024]
Abstract
The regulatory mechanism of the transcription factor GATA3 in the differentiation and maturation process of extravillous trophoblasts (EVT) in early pregnancy placenta, as well as its relevance to the occurrence of pregnancy disorders, remains poorly understood. This study leveraged single-cell RNA sequencing data from placental organoid models and placental tissue to explore the dynamic changes in GATA3 expression during EVT maturation. The expression pattern exhibited an initial upregulation followed by subsequent downregulation, with aberrant GATA3 localization observed in cases of recurrent miscarriage (RM). By identifying global targets regulated by GATA3 in primary placental EVT cells, JEG3, and HTR8/SVneo cell lines, this study offered insights into its regulatory mechanisms across different EVT cell models. Shared regulatory targets among these cell types and activation of trophoblast cell marker genes emphasized the importance of GATA3 in EVT differentiation and maturation. Knockdown of GATA3 in JEG3 cells led to repression of GATA3-induced epithelial-mesenchymal transition (EMT), as evidenced by changes in marker gene expression levels and enhanced migration ability. Additionally, interference with GATA3 accelerated cellular senescence, as indicated by reduced proliferation rates and increased activity levels for senescence-associated β-galactosidase enzyme, along with elevated expression levels for senescence-associated genes. This study provides comprehensive insights into the dual role of GATA3 in regulating EMT and cellular senescence during EVT differentiation, shedding light on the dynamic changes in GATA3 expression in normal and pathological placental conditions.
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Affiliation(s)
- En-Xiang Chen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China; Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Department of Basic Medical Sciences, Changsha Medical University, Hunan 410219, China
| | - Si-Chen Hu
- Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jia-Qi Xu
- Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Kun-Yan Liu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Jing Tang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Xi-Peng Shen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Xiao Liang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - You-Long Xie
- Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Lu-Xin Ge
- Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China; Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University. Hunan 410219, China
| | - Xin Luo
- Department of Obstetrics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ying-Xiong Wang
- Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China.
| | - Yun-Long Xiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China.
| | - Yu-Bin Ding
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, China; Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China.
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3
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Matsui S, Shiley JR, Buckley M, Lim HW, Hu YC, Mayhew CN, Iwafuchi M. Protocol for establishing inducible CRISPRd system for blocking transcription factor-binding sites in human pluripotent stem cells. STAR Protoc 2024; 5:103233. [PMID: 39133612 PMCID: PMC11357809 DOI: 10.1016/j.xpro.2024.103233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/29/2024] [Accepted: 07/10/2024] [Indexed: 09/01/2024] Open
Abstract
Transcription factor (TF) gene knockout or knockdown experiments provide comprehensive downstream effects on gene regulation. However, distinguishing primary direct effects from secondary effects remains challenging. To assess the direct effect of TF binding events, we present a protocol for establishing a doxycycline (Dox)-inducible CRISPRd system in human pluripotent stem cells (hPSCs). We describe the steps for establishing CRISPRd host hPSCs, designing and preparing single-guide RNA (sgRNA) expression lentivirus vectors, generating CRISPRd hPSCs transduced with sgRNAs, and analyzing CRISPRd TF-block effects by chromatin immunoprecipitation (ChIP)-qPCR. For complete details on the use and execution of this protocol, please refer to Matsui et al.1.
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Affiliation(s)
- Satoshi Matsui
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA.
| | - Joseph R Shiley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Morgan Buckley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA.
| | - Makiko Iwafuchi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA.
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4
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Li M, Na X, Lin F, Liang S, Huang Y, Song J, Xu X, Yang C. DMF-ChIP-seq for Highly Sensitive and Integrated Epigenomic Profiling of Low-Input Cells. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39303213 DOI: 10.1021/acsami.4c11280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Mapping genome-wide DNA-protein interactions (DPIs) provides insights into the epigenetic landscape of complex biological systems and elucidates the mechanisms of epigenetic regulation in biological progress. However, current technologies in DPI profiling still suffer from high cell demands, low detection sensitivity, and large reagent consumption. To address these problems, we developed DMF-ChIP-seq that builds on digital microfluidic (DMF) technology to profile genome-wide DPIs in a highly efficient, cost-effective, and user-friendly way. The entire workflow including cell pretreatment, antibody recognition, pA-Tn5 tagmentation, fragment enrichment, and PCR amplification is programmatically manipulated on a single chip. Leveraging closed submicroliter reaction volumes and a superhydrophobic interface, DMF-ChIP-seq presented higher sensitivity in peak enrichment than other current methods, with high accuracy (Pearson Correlation Coefficient (PCC) > 0.86) and high repeatability (PCC > 0.92). Furthermore, DMF-ChIP-seq was capable of processing the samples with as few as 8 cells while maintaining a high signal-to-noise ratio. By applying DMF-ChIP-seq, H3K27ac histone modification of early embryonic cells during differentiation was profiled for the investigation of epigenomic landscape dynamics. With the benefits of high efficiency and sensitivity in DPI analysis, the system provides great promise in studying epigenetic regulation during various biological processes.
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Affiliation(s)
- Mingyin Li
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xing Na
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fanghe Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shanshan Liang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuehan Huang
- School of International Education, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jia Song
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Xing Xu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Technology for Precision Medicine, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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5
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Yao W, Hu X, Wang X. Crossing epigenetic frontiers: the intersection of novel histone modifications and diseases. Signal Transduct Target Ther 2024; 9:232. [PMID: 39278916 PMCID: PMC11403012 DOI: 10.1038/s41392-024-01918-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/11/2024] [Accepted: 06/30/2024] [Indexed: 09/18/2024] Open
Abstract
Histone post-translational modifications (HPTMs), as one of the core mechanisms of epigenetic regulation, are garnering increasing attention due to their close association with the onset and progression of diseases and their potential as targeted therapeutic agents. Advances in high-throughput molecular tools and the abundance of bioinformatics data have led to the discovery of novel HPTMs which similarly affect gene expression, metabolism, and chromatin structure. Furthermore, a growing body of research has demonstrated that novel histone modifications also play crucial roles in the development and progression of various diseases, including various cancers, cardiovascular diseases, infectious diseases, psychiatric disorders, and reproductive system diseases. This review defines nine novel histone modifications: lactylation, citrullination, crotonylation, succinylation, SUMOylation, propionylation, butyrylation, 2-hydroxyisobutyrylation, and 2-hydroxybutyrylation. It comprehensively introduces the modification processes of these nine novel HPTMs, their roles in transcription, replication, DNA repair and recombination, metabolism, and chromatin structure, as well as their involvement in promoting the occurrence and development of various diseases and their clinical applications as therapeutic targets and potential biomarkers. Moreover, this review provides a detailed overview of novel HPTM inhibitors targeting various targets and their emerging strategies in the treatment of multiple diseases while offering insights into their future development prospects and challenges. Additionally, we briefly introduce novel epigenetic research techniques and their applications in the field of novel HPTM research.
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Affiliation(s)
- Weiyi Yao
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Xinting Hu
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Taishan Scholars Program of Shandong Province, Jinan, Shandong, 250021, China.
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6
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Liu J, Lei F, Yan B, Cui N, Sharma J, Correa V, Roach L, Nicolaou S, Pitts K, Chodosh J, Maidana DE, Vavvas D, Margeta MA, Zhang H, Weitz D, Mostoslavsky R, Paschalis EI. Epigenetic adaptation drives monocyte differentiation into microglia-like cells upon engraftment into the retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612126. [PMID: 39314467 PMCID: PMC11419019 DOI: 10.1101/2024.09.09.612126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
The identification of specific markers for microglia has been a long-standing challenge. Recently, markers such as P2ry12, TMEM119, and Fcrls have been proposed as microglia-specific and widely used to explore microglial functions within various central nervous system (CNS) contexts. The specificity of these markers was based on the assumption that circulating monocytes retain their distinct signatures even after infiltrating the CNS. However, recent findings reveal that infiltrating monocytes can adopt microglia-like characteristics while maintaining a pro-inflammatory profile upon permanent engraftment in the CNS.In this study, we utilize bone marrow chimeras, single-cell RNA sequencing, ATAC-seq, flow cytometry, and immunohistochemistry to demonstrate that engrafted monocytes acquire expression of established microglia markers-P2ry12, TMEM119, Fcrls-and the pan-myeloid marker Iba1, which has been commonly mischaracterized as microglia-specific. These changes are accompanied by alterations in chromatin accessibility and shifts in chromatin binding motifs that are indicative of microglial identity. Moreover, we show that engrafted monocytes dynamically regulate the expression of CX3CR1, CCR2, Ly6C, and transcription factors PU.1, CTCF, RUNX, AP-1, CEBP, and IRF2, all of which are crucial for shaping microglial identity. This study is the first to illustrate that engrafted monocytes in the retina undergo both epigenetic and transcriptional changes, enabling them to express microglia-like signatures. These findings highlight the need for future research to account for these changes when assessing the roles of monocytes and microglia in CNS pathology. Significance Statement Monocytes can express putative microglia markers P2ry12, TMEM119, and Fcrls upon engraftment into the retina. Given their involvement in neuroinflammation, it is crucial to consider this overlap when utilizing these markers for experimental analysis.
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7
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Peeters JGC, Silveria S, Ozdemir M, Ramachandran S, DuPage M. Hyperactivating EZH2 to augment H3K27me3 levels in regulatory T cells enhances immune suppression by driving early effector differentiation. Cell Rep 2024; 43:114724. [PMID: 39264807 DOI: 10.1016/j.celrep.2024.114724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/17/2024] [Accepted: 08/21/2024] [Indexed: 09/14/2024] Open
Abstract
The immunosuppressive function of regulatory T (Treg) cells is essential for maintaining immune homeostasis. Enhancer of zeste homolog 2 (EZH2), a histone H3 lysine 27 (H3K27) methyltransferase, plays a key role in maintaining Treg cell function upon CD28 co-stimulation, and Ezh2 deletion in Treg cells causes autoimmunity. Here, we assess whether increasing H3K27me3 levels, by using an Ezh2Y641F gain-of-function mutation, will improve Treg cell function. We find that Treg cells expressing Ezh2Y641F display an effector Treg phenotype, are poised for improved homing to organ tissues, and can accelerate remission from autoimmunity. The H3K27me3 landscape and transcriptome of naive Ezh2Y641F Treg cells exhibit a redistribution of H3K27me3 modifications that recapitulates the gene expression profile of activated Ezh2WT Treg cells after CD28 co-stimulation. Altogether, increased H3K27me3 levels promote the differentiation of effector Treg cells that can better suppress autoimmunity.
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Affiliation(s)
- Janneke G C Peeters
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stephanie Silveria
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Merve Ozdemir
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Michel DuPage
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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8
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Moon N, Morgan CP, Marx-Rattner R, Jeng A, Johnson RL, Chikezie I, Mannella C, Sammel MD, Epperson CN, Bale TL. Stress increases sperm respiration and motility in mice and men. Nat Commun 2024; 15:7900. [PMID: 39261485 PMCID: PMC11391062 DOI: 10.1038/s41467-024-52319-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 09/02/2024] [Indexed: 09/13/2024] Open
Abstract
Semen quality and fertility has declined over the last 50 years, corresponding to ever-increasing environmental stressors. However, the cellular mechanisms involved and their impact on sperm functions remain unknown. In a repeated sampling human cohort study, we identify a significant effect of prior perceived stress to increase sperm motility 2-3 months following stress, timing that expands upon our previous studies revealing significant stress-associated changes in sperm RNA important for fertility. We mechanistically examine this post-stress timing in mice using an in vitro stress model in the epididymal epithelial cells responsible for sperm maturation and find 7282 differentially H3K27me3 bound DNA regions involving genes critical for mitochondrial and metabolic pathways. Further, prior stress exposure significantly changes the composition and size of epithelial cell-secreted extracellular vesicles that when incubated with mouse sperm, increase mitochondrial respiration and sperm motility, adding to our prior work showing impacts on embryo development. Together, these studies identify a time-dependent, translational signaling pathway that communicates stress experience to sperm, ultimately affecting reproductive functions.
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Affiliation(s)
- Nickole Moon
- Department of Psychiatry, University of Colorado Anschutz Medical Campus School of Medicine, Aurora, CO, 80045, USA
- Department of Pharmacology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Christopher P Morgan
- Department of Pharmacology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Ruth Marx-Rattner
- Department of Pharmacology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Alyssa Jeng
- Department of Psychiatry, University of Colorado Anschutz Medical Campus School of Medicine, Aurora, CO, 80045, USA
| | - Rachel L Johnson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Ijeoma Chikezie
- Department of Pharmacology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Carmen Mannella
- Department of Physiology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Mary D Sammel
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - C Neill Epperson
- Department of Psychiatry, University of Colorado Anschutz Medical Campus School of Medicine, Aurora, CO, 80045, USA
| | - Tracy L Bale
- Department of Psychiatry, University of Colorado Anschutz Medical Campus School of Medicine, Aurora, CO, 80045, USA.
- Department of Pharmacology, University of Maryland Baltimore, Baltimore, MD, 21201, USA.
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9
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Chen L, Cao X, Li Y, Liu M, Liu Y, Guan Y, Ruan J, Mao Z, Wang W, Yang HQ, Guo T. Photoexcited Cryptochrome 1 Interacts With SPCHLESS to Regulate Stomatal Development in Arabidopsis. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39253954 DOI: 10.1111/pce.15123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 09/11/2024]
Abstract
Stomata are epidermal openings that facilitate plant-atmosphere gas and water exchange during photosynthesis, respiration and water evaporation. SPEECHLESS (SPCH) is a master basic helix-loop-helix (bHLH) transcription factor that determines the initiation of stomatal development. It is known that blue light promotes stomatal development through the blue light photoreceptor cryptochromes (CRYs, CRY1 and CRY2). Whether CRYs regulate stomatal development through directly modulating SPCH is unknown. Here, we demonstrate by biochemical studies that CRY1 physically interacts with SPCH in a blue light-dependent manner. Genetic studies show that SPCH acts downstream of CRY1 to promote stomatal development in blue light. Furthermore, we show that CRY1 enhances the DNA-binding activity of SPCH and promotes the expression of its target genes in blue light. These results suggest that the mechanism by which CRY1 promotes stomatal development involves positive regulation of the DNA-binding activity of SPCH, which is likely mediated by blue light-induced CRY1-SPCH interaction. The precise regulation of SPCH DNA-binding activity by CRY1 may allow plants to optimize stomatal density and pattern according to ambient light conditions.
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Affiliation(s)
- Li Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoli Cao
- School of Life Sciences, Fudan University, Shanghai, China
| | - Yupeng Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Minqing Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yao Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yan Guan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jiaqi Ruan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhilei Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenxiu Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hong-Quan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Tongtong Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, China
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10
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Zhang T, Li S, Tan YA, Chen X, Zhang C, Chen Z, Mishra B, Na JH, Choi S, Shin SJ, Damle P, Chougoni KK, Grossman SR, Wang D, Jiang X, Li Y, Hissong E, Chen YT, Xiang JZ, Du YCN. Bcl-xL is translocated to the nucleus via CtBP2 to epigenetically promote metastasis. Cancer Lett 2024; 604:217240. [PMID: 39265800 DOI: 10.1016/j.canlet.2024.217240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/27/2024] [Accepted: 09/06/2024] [Indexed: 09/14/2024]
Abstract
Nuclear Bcl-xL is found to promote cancer metastasis independently of its mitochondria-based anti-apoptotic activity. How Bcl-xL is translocated into the nucleus and how nuclear Bcl-xL regulates histone H3 trimethyl Lys4 (H3K4me3) modification have yet to be understood. Here, we report that C-terminal Binding Protein 2 (CtBP2) binds to Bcl-xL via its N-terminus and translocates Bcl-xL into the nucleus. Knockdown of CtBP2 by shRNA decreases the nuclear portion of Bcl-xL and reverses Bcl-xL-induced invasion and metastasis in mouse models. Furthermore, knockout of CtBP2 not only reduces the nuclear portion of Bcl-xL but also suppresses Bcl-xL transcription. The binding between Bcl-xL and CtBP2 is required for their interaction with MLL1, a histone H3K4 methyltransferase. Pharmacologic inhibition of the MLL1 enzymatic activity reverses Bcl-xL-induced H3K4me3 and TGFβ mRNA upregulation, as well as invasion. Moreover, the cleavage under targets and release using nuclease (CUT&RUN) assay coupled with next-generation sequencing reveals that H3K4me3 modifications are particularly enriched in the promotor regions of genes encoding TGFβ and its signaling pathway members in cancer cells overexpressing Bcl-xL. Altogether, the metastatic function of Bcl-xL is mediated by its interaction with CtBP2 and MLL1 and this study offers new therapeutic strategies to treat Bcl-xL-overexpressing cancer.
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Affiliation(s)
- Tiantian Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Sha Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Yingcai Adrian Tan
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Xiang Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Cheryl Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Zhengming Chen
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Bikash Mishra
- Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Joseph HyungJoon Na
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Soyoung Choi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Sandra J Shin
- Department of Pathology, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, 11549, USA
| | - Priyadarshan Damle
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Kranthi Kumar Chougoni
- USC Norris Comprehensive Cancer Center and Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Steven R Grossman
- USC Norris Comprehensive Cancer Center and Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Dunrui Wang
- Laboratory of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xuejun Jiang
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Erika Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Yao-Tseng Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jenny Z Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Yi-Chieh Nancy Du
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
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11
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Malla S, Kumari K, García-Prieto CA, Caroli J, Nordin A, Phan TTT, Bhattarai DP, Martinez-Gamero C, Dorafshan E, Stransky S, Álvarez-Errico D, Saiki PA, Lai W, Lyu C, Lizana L, Gilthorpe JD, Wang H, Sidoli S, Mateus A, Lee DF, Cantù C, Esteller M, Mattevi A, Roman AC, Aguilo F. The scaffolding function of LSD1 controls DNA methylation in mouse ESCs. Nat Commun 2024; 15:7758. [PMID: 39237615 PMCID: PMC11377572 DOI: 10.1038/s41467-024-51966-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/21/2024] [Indexed: 09/07/2024] Open
Abstract
Lysine-specific histone demethylase 1 (LSD1), which demethylates mono- or di- methylated histone H3 on lysine 4 (H3K4me1/2), is essential for early embryogenesis and development. Here we show that LSD1 is dispensable for mouse embryonic stem cell (ESC) self-renewal but is required for mouse ESC growth and differentiation. Reintroduction of a catalytically-impaired LSD1 (LSD1MUT) recovers the proliferation capability of mouse ESCs, yet the enzymatic activity of LSD1 is essential to ensure proper differentiation. Indeed, increased H3K4me1 in Lsd1 knockout (KO) mouse ESCs does not lead to major changes in global gene expression programs related to stemness. However, ablation of LSD1 but not LSD1MUT results in decreased DNMT1 and UHRF1 proteins coupled to global hypomethylation. We show that both LSD1 and LSD1MUT control protein stability of UHRF1 and DNMT1 through interaction with HDAC1 and the ubiquitin-specific peptidase 7 (USP7), consequently, facilitating the deacetylation and deubiquitination of DNMT1 and UHRF1. Our studies elucidate a mechanism by which LSD1 controls DNA methylation in mouse ESCs, independently of its lysine demethylase activity.
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Affiliation(s)
- Sandhya Malla
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Kanchan Kumari
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Carlos A García-Prieto
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Jonatan Caroli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Trinh T T Phan
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Devi Prasad Bhattarai
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Carlos Martinez-Gamero
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Eshagh Dorafshan
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Paulina Avovome Saiki
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Cong Lyu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ludvig Lizana
- Department of Physics, Integrated Science Lab, Umeå University, Umeå, Sweden
| | | | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andre Mateus
- Department of Chemistry, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
- Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Angel-Carlos Roman
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Francesca Aguilo
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.
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12
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Maslan A, Altemose N, Marcus J, Mishra R, Brennan LD, Sundararajan K, Karpen G, Straight AF, Streets A. Mapping protein-DNA interactions with DiMeLo-seq. Nat Protoc 2024:10.1038/s41596-024-01032-9. [PMID: 39237830 DOI: 10.1038/s41596-024-01032-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 06/04/2024] [Indexed: 09/07/2024]
Abstract
We recently developed directed methylation with long-read sequencing (DiMeLo-seq) to map protein-DNA interactions genome wide. DiMeLo-seq is capable of mapping multiple interaction sites on single DNA molecules, profiling protein binding in the context of endogenous DNA methylation, identifying haplotype-specific protein-DNA interactions and mapping protein-DNA interactions in repetitive regions of the genome that are difficult to study with short-read methods. With DiMeLo-seq, adenines in the vicinity of a protein of interest are methylated in situ by tethering the Hia5 methyltransferase to an antibody using protein A. Protein-DNA interactions are then detected by direct readout of adenine methylation with long-read, single-molecule DNA sequencing platforms such as Nanopore sequencing. Here we present a detailed protocol and practical guidance for performing DiMeLo-seq. This protocol can be run on nuclei from fresh, lightly fixed or frozen cells. The protocol requires 1-2 d for performing in situ targeted methylation, 1-5 d for library preparation depending on desired fragment length and 1-3 d for Nanopore sequencing depending on desired sequencing depth. The protocol requires basic molecular biology skills and equipment, as well as access to a Nanopore sequencer. We also provide a Python package, dimelo, for analysis of DiMeLo-seq data.
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Affiliation(s)
- Annie Maslan
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nicolas Altemose
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jeremy Marcus
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Reet Mishra
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Lucy D Brennan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Gary Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of BioEngineering and BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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13
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Stewart KS, Abdusselamoglu MD, Tierney MT, Gola A, Hur YH, Gonzales KAU, Yuan S, Bonny AR, Yang Y, Infarinato NR, Cowley CJ, Levorse JM, Pasolli HA, Ghosh S, Rothlin CV, Fuchs E. Stem cells tightly regulate dead cell clearance to maintain tissue fitness. Nature 2024; 633:407-416. [PMID: 39169186 PMCID: PMC11390485 DOI: 10.1038/s41586-024-07855-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/19/2024] [Indexed: 08/23/2024]
Abstract
Billions of cells are eliminated daily from our bodies1-4. Although macrophages and dendritic cells are dedicated to migrating and engulfing dying cells and debris, many epithelial and mesenchymal tissue cells can digest nearby apoptotic corpses1-4. How these non-motile, non-professional phagocytes sense and eliminate dying cells while maintaining their normal tissue functions is unclear. Here we explore the mechanisms that underlie their multifunctionality by exploiting the cyclical bouts of tissue regeneration and degeneration during hair cycling. We show that hair follicle stem cells transiently unleash phagocytosis at the correct time and place through local molecular triggers that depend on both lipids released by neighbouring apoptotic corpses and retinoids released by healthy counterparts. We trace the heart of this dual ligand requirement to RARγ-RXRα, whose activation enables tight regulation of apoptotic cell clearance genes and provides an effective, tunable mechanism to offset phagocytic duties against the primary stem cell function of preserving tissue integrity during homeostasis. Finally, we provide functional evidence that hair follicle stem cell-mediated phagocytosis is not simply redundant with professional phagocytes but rather has clear benefits to tissue fitness. Our findings have broad implications for other non-motile tissue stem or progenitor cells that encounter cell death in an immune-privileged niche.
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Affiliation(s)
- Katherine S Stewart
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
| | - Merve Deniz Abdusselamoglu
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Matthew T Tierney
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Anita Gola
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Yun Ha Hur
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kevin A U Gonzales
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Department of Discovery Technology and Genomics, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Shaopeng Yuan
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Altos Labs, Cambridge Institute of Science, Granta Park, Cambridge, UK
| | - Alain R Bonny
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Yihao Yang
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Altos Labs, San Diego, CA, USA
| | - Nicole R Infarinato
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- PrecisionScienta, Yardley, PA, USA
| | - Christopher J Cowley
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John M Levorse
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Cardiovascular Research Group, Temple University, Philadelphia, PA, USA
| | - Hilda Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Sourav Ghosh
- Departments of Neurology and Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Carla V Rothlin
- Departments of Immunobiology and Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
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14
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Pandiloski N, Horváth V, Karlsson O, Koutounidou S, Dorazehi F, Christoforidou G, Matas-Fuentes J, Gerdes P, Garza R, Jönsson ME, Adami A, Atacho DAM, Johansson JG, Englund E, Kokaia Z, Jakobsson J, Douse CH. DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor. Nat Commun 2024; 15:7534. [PMID: 39214989 PMCID: PMC11364546 DOI: 10.1038/s41467-024-50765-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. How HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains largely unknown. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding, and simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric α-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.
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Affiliation(s)
- Ninoslav Pandiloski
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Vivien Horváth
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Ofelia Karlsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Symela Koutounidou
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Fereshteh Dorazehi
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Georgia Christoforidou
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jon Matas-Fuentes
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
| | - Patricia Gerdes
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Anita Adami
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Diahann A M Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jenny G Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
| | - Elisabet Englund
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Zaal Kokaia
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Laboratory of Stem Cells and Restorative Neurology, Department of Clinical Sciences, BMC B10, Lund University, Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Christopher H Douse
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden.
- Lund Stem Cell Center, Lund University, Lund, Sweden.
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15
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Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C. Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch. SCIENCE ADVANCES 2024; 10:eadp0975. [PMID: 39196936 PMCID: PMC11352909 DOI: 10.1126/sciadv.adp0975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 07/24/2024] [Indexed: 08/30/2024]
Abstract
During tumor development, promoter CpG islands that are normally silenced by Polycomb repressive complexes (PRCs) become DNA-hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) [DNMT(s)] catalyze CpG methylation at PRC-regulated regions remains unclear. Here, we report a cryo-electron microscopy structure of the DNMT3A long isoform (DNMT3A1) amino-terminal region in complex with a nucleosome carrying PRC1-mediated histone H2A lysine-119 monoubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 amino terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Further, aberrant redistribution of DNMT3A1 to Polycomb target genes recapitulates the cancer-associated DNA hypermethylation signature and inhibits their transcriptional activation during cell differentiation. This effect is rescued by disruption of the DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for mediating promoter CpG island DNA hypermethylation, a major molecular hallmark of cancer.
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Affiliation(s)
- Kristjan H. Gretarsson
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Stephen Abini-Agbomson
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | | | - Daniel N. Weinberg
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | - Varun Sahu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rachel Lee
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Xinjing Xu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Natalie Lipieta
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel Flashner
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY 10032, USA
| | | | | | | | | | | | | | | | - Hiroshi Nakagawa
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY 10032, USA
| | | | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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16
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Simats A, Zhang S, Messerer D, Chong F, Beşkardeş S, Chivukula AS, Cao J, Besson-Girard S, Montellano FA, Morbach C, Carofiglio O, Ricci A, Roth S, Llovera G, Singh R, Chen Y, Filser S, Plesnila N, Braun C, Spitzer H, Gokce O, Dichgans M, Heuschmann PU, Hatakeyama K, Beltrán E, Clauss S, Bonev B, Schulz C, Liesz A. Innate immune memory after brain injury drives inflammatory cardiac dysfunction. Cell 2024; 187:4637-4655.e26. [PMID: 39043180 DOI: 10.1016/j.cell.2024.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 04/22/2024] [Accepted: 06/21/2024] [Indexed: 07/25/2024]
Abstract
The medical burden of stroke extends beyond the brain injury itself and is largely determined by chronic comorbidities that develop secondarily. We hypothesized that these comorbidities might share a common immunological cause, yet chronic effects post-stroke on systemic immunity are underexplored. Here, we identify myeloid innate immune memory as a cause of remote organ dysfunction after stroke. Single-cell sequencing revealed persistent pro-inflammatory changes in monocytes/macrophages in multiple organs up to 3 months after brain injury, notably in the heart, leading to cardiac fibrosis and dysfunction in both mice and stroke patients. IL-1β was identified as a key driver of epigenetic changes in innate immune memory. These changes could be transplanted to naive mice, inducing cardiac dysfunction. By neutralizing post-stroke IL-1β or blocking pro-inflammatory monocyte trafficking with a CCR2/5 inhibitor, we prevented post-stroke cardiac dysfunction. Such immune-targeted therapies could potentially prevent various IL-1β-mediated comorbidities, offering a framework for secondary prevention immunotherapy.
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Affiliation(s)
- Alba Simats
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; Cerebrovascular Research Laboratory, Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Sijia Zhang
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Denise Messerer
- Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, Munich, Germany
| | - Faye Chong
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Sude Beşkardeş
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Jiayu Cao
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Simon Besson-Girard
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Felipe A Montellano
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany; Institute of Clinical Epidemiology and Biometry, Julius-Maximilian-University Würzburg, Würzburg, Germany
| | - Caroline Morbach
- Department Clinical Research & Epidemiology, Comprehensive Heart Failure Center, and Department Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Olga Carofiglio
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Alessio Ricci
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Stefan Roth
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Gemma Llovera
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Rashween Singh
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Yiming Chen
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Severin Filser
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Nikolaus Plesnila
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Christian Braun
- Institute of Legal Medicine, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Hannah Spitzer
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Ozgun Gokce
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Partner Sites Munich and Bonn, Germany; Department of Old Age Psychiatry and cognitive Disorders, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Partner Sites Munich and Bonn, Germany
| | - Peter U Heuschmann
- Institute of Clinical Epidemiology and Biometry, Julius-Maximilian-University Würzburg, Würzburg, Germany; Institute for Medical Data Sciences, University Hospital Würzburg, Würzburg, Germany; Clinical Trial Centre Würzburg, University Hospital Würzburg, Würzburg, Germany
| | - Kinta Hatakeyama
- Department of Pathology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Eduardo Beltrán
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany; Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Sebastian Clauss
- Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, Munich, Germany; Institute of Surgical Research at the Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer (ICONLMU), LMU Munich, Munich, Germany
| | - Boyan Bonev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany; Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Schulz
- Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, Munich, Germany; Institute of Surgical Research at the Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Department of Immunopharmacology, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Arthur Liesz
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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17
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Ochoa Bernal MA, Song Y, Joshi N, Burns GW, Paul EN, Vegter E, Hrbek S, Sempere LF, Fazleabas AT. The Regulation of MicroRNA-21 by Interleukin-6 and Its Role in the Development of Fibrosis in Endometriotic Lesions. Int J Mol Sci 2024; 25:8994. [PMID: 39201680 PMCID: PMC11354763 DOI: 10.3390/ijms25168994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Endometriosis is one of the most common causes of chronic pelvic pain and infertility that affects 10% of women of reproductive age. It is currently defined as the presence of endometrial epithelial and stromal cells at ectopic sites; however, advances in endometriosis research have some authors believing that endometriosis should be re-defined as "a fibrotic condition in which endometrial stroma and epithelium can be identified". microRNAs (miRNAs) are regulatory molecules that potentially play a role in endometriotic lesion development. There is evidence that suggests that miRNAs, including microRNA-21 (miR-21), participate in fibrotic processes in different organs, including the heart, kidney, liver and lungs. The objective of this study was to understand the role of miR-21 and the mechanisms that can contribute to the development of fibrosis by determining how IL-6 regulates miR-21 expression and how this miRNA regulates the transforming growth factor beta (TGF-β) signaling pathway to promote fibrosis. We investigated the expression of miR-21 in the baboon and mouse model of endometriosis and its correlation with fibrosis. We demonstrated that inflammation and fibrosis are present at a very early stage of endometriosis and that the inflammatory environment in the peritoneal cavity, which includes interleukin 6 (IL-6), can regulate the expression of miR-21 in vitro and in vivo.
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Affiliation(s)
- Maria Ariadna Ochoa Bernal
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, MI 49503, USA; (M.A.O.B.); (Y.S.); (N.J.); (G.W.B.); (E.N.P.); (E.V.); (S.H.)
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Yong Song
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, MI 49503, USA; (M.A.O.B.); (Y.S.); (N.J.); (G.W.B.); (E.N.P.); (E.V.); (S.H.)
| | - Niraj Joshi
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, MI 49503, USA; (M.A.O.B.); (Y.S.); (N.J.); (G.W.B.); (E.N.P.); (E.V.); (S.H.)
| | - Gregory W. Burns
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, MI 49503, USA; (M.A.O.B.); (Y.S.); (N.J.); (G.W.B.); (E.N.P.); (E.V.); (S.H.)
| | - Emmanuel N. Paul
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, MI 49503, USA; (M.A.O.B.); (Y.S.); (N.J.); (G.W.B.); (E.N.P.); (E.V.); (S.H.)
| | - Erin Vegter
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, MI 49503, USA; (M.A.O.B.); (Y.S.); (N.J.); (G.W.B.); (E.N.P.); (E.V.); (S.H.)
| | - Samantha Hrbek
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, MI 49503, USA; (M.A.O.B.); (Y.S.); (N.J.); (G.W.B.); (E.N.P.); (E.V.); (S.H.)
| | - Lorenzo F. Sempere
- Precision Health Program and Department of Radiology Michigan State University, East Lansing, MI 48824, USA;
| | - Asgerally T. Fazleabas
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, MI 49503, USA; (M.A.O.B.); (Y.S.); (N.J.); (G.W.B.); (E.N.P.); (E.V.); (S.H.)
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18
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Häußermann L, Singh A, Swart EC. Two paralogous PHD finger proteins participate in natural genome editing in Paramecium tetraurelia. J Cell Sci 2024; 137:jcs261979. [PMID: 39212120 PMCID: PMC11385659 DOI: 10.1242/jcs.261979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/28/2024] [Indexed: 09/04/2024] Open
Abstract
The unicellular eukaryote Paramecium tetraurelia contains functionally distinct nuclei: germline micronuclei (MICs) and a somatic macronucleus (MAC). During sex, the MIC genome is reorganized into a new MAC genome and the old MAC is lost. Almost 45,000 unique internal eliminated sequences (IESs) distributed throughout the genome require precise excision to guarantee a functional new MAC genome. Here, we characterize a pair of paralogous PHD finger proteins involved in DNA elimination. DevPF1, the early-expressed paralog, is present in only some of the gametic and post-zygotic nuclei during meiosis. Both DevPF1 and DevPF2 localize in the new developing MACs, where IES excision occurs. Upon DevPF2 knockdown (KD), long IESs are preferentially retained and late-expressed small RNAs decrease; no length preference for retained IESs was observed in DevPF1-KD and development-specific small RNAs were abolished. The expression of at least two genes from the new MAC with roles in genome reorganization seems to be influenced by DevPF1- and DevPF2-KD. Thus, both PHD fingers are crucial for new MAC genome development, with distinct functions, potentially via regulation of non-coding and coding transcription in the MICs and new MACs.
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Affiliation(s)
- Lilia Häußermann
- Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Aditi Singh
- Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Estienne C Swart
- Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
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19
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Roth GV, Gengaro IR, Qi LS. Precision epigenetic editing: Technological advances, enduring challenges, and therapeutic applications. Cell Chem Biol 2024:S2451-9456(24)00309-X. [PMID: 39137782 DOI: 10.1016/j.chembiol.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/31/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024]
Abstract
The epigenome is a complex framework through which gene expression is precisely and flexibly modulated to incorporate heritable memory and responses to environmental stimuli. It governs diverse cellular processes, including cell fate, disease, and aging. The need to understand this system and precisely control gene expression outputs for therapeutic purposes has precipitated the development of a diverse set of epigenetic editing tools. Here, we review the existing toolbox for targeted epigenetic editing, technical considerations of the current technologies, and opportunities for future development. We describe applications of therapeutic epigenetic editing and their potential for treating disease, with a discussion of ongoing delivery challenges that impede certain clinical interventions, particularly in the brain. With simultaneous advancements in available engineering tools and appropriate delivery technologies, we predict that epigenetic editing will increasingly cement itself as a powerful approach for safely treating a wide range of disorders in all tissues of the body.
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Affiliation(s)
- Goldie V Roth
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Isabella R Gengaro
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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20
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Bailey JK, Ma D, Clegg DO. Initial Characterization of WDR5B Reveals a Role in the Proliferation of Retinal Pigment Epithelial Cells. Cells 2024; 13:1189. [PMID: 39056772 PMCID: PMC11275010 DOI: 10.3390/cells13141189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
The chromatin-associated protein WDR5 has been widely studied due to its role in histone modification and its potential as a pharmacological target for the treatment of cancer. In humans, the protein with highest sequence homology to WDR5 is encoded by the retrogene WDR5B, which remains unexplored. Here, we used CRISPR-Cas9 genome editing to generate WDR5B knockout and WDR5B-FLAG knock-in cell lines for further characterization. In contrast to WDR5, WDR5B exhibits low expression in pluripotent cells and is upregulated upon neural differentiation. Loss or shRNA depletion of WDR5B impairs cell growth and increases the fraction of non-viable cells in proliferating retinal pigment epithelial (RPE) cultures. CUT&RUN chromatin profiling in RPE and neural progenitors indicates minimal WDR5B enrichment at established WDR5 binding sites. These results suggest that WDR5 and WDR5B exhibit several divergent biological properties despite sharing a high degree of sequence homology.
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Affiliation(s)
- Jeffrey K. Bailey
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Dennis O. Clegg
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
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21
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Kumar RP, Kumar R, Ganguly A, Ghosh A, Ray S, Islam MR, Saha A, Roy N, Dasgupta P, Knowles T, Niloy AJ, Marsh C, Paul S. METTL3 shapes m6A epitranscriptomic landscape for successful human placentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603294. [PMID: 39026770 PMCID: PMC11257629 DOI: 10.1101/2024.07.12.603294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Methyltransferase-like 3 (METTL3), the catalytic enzyme of methyltransferase complex for m6A methylation of RNA, is essential for mammalian development. However, the importance of METTL3 in human placentation remains largely unexplored. Here, we show that a fine balance of METTL3 function in trophoblast cells is essential for successful human placentation. Both loss-of and gain-in METTL3 functions are associated with adverse human pregnancies. A subset of recurrent pregnancy losses and preterm pregnancies are often associated with loss of METTL3 expression in trophoblast progenitors. In contrast, METTL3 is induced in pregnancies associated with fetal growth restriction (FGR). Our loss of function analyses showed that METTL3 is essential for the maintenance of human TSC self-renewal and their differentiation to extravillous trophoblast cells (EVTs). In contrast, loss of METTL3 in human TSCs promotes syncytiotrophoblast (STB) development. Global analyses of RNA m6A modification and METTL3-RNA interaction in human TSCs showed that METTL3 regulates m6A modifications on the mRNA molecules of critical trophoblast regulators, including GATA2, GATA3, TEAD1, TEAD4, WWTR1, YAP1, TFAP2C and ASCL2, and loss of METTL3 leads to depletion of mRNA molecules of these critical regulators. Importantly, conditional deletion of Mettl3 in trophoblast progenitors of an early post-implantation mouse embryo also leads to arrested self-renewal. Hence, our findings indicate that METLL3 is a conserved epitranscriptomic governor in trophoblast progenitors and ensures successful placentation by regulating their self-renewal and dictating their differentiation fate.
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Affiliation(s)
- Ram Parikshan Kumar
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
- Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Rajnish Kumar
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
| | - Avishek Ganguly
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
| | - Ananya Ghosh
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
| | - Soma Ray
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
| | - Md. Rashedul Islam
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
| | - Abhik Saha
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
| | - Namrata Roy
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
| | - Purbasa Dasgupta
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
| | - Taylor Knowles
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
| | - Asef Jawad Niloy
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
| | - Courtney Marsh
- Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Soumen Paul
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center Kansas City, KS 66160, USA
- Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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22
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Marin H, Simental E, Allen C, Martin E, Panning B, Al-Sady B, Buchwalter A. The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602542. [PMID: 39026839 PMCID: PMC11257442 DOI: 10.1101/2024.07.08.602542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Heterochromatic loci marked by histone H3 lysine 9 dimethylation (H3K9me2) are enriched at the nuclear periphery in metazoans, but the effect of spatial position on heterochromatin function has not been defined. Here, we remove three nuclear lamins and lamin B receptor (LBR) in mouse embryonic stem cells (mESCs) and show that heterochromatin detaches from the nuclear periphery. Mutant mESCs sustain naïve pluripotency and maintain H3K9me2 across the genome but cannot repress H3K9me2-marked genes or transposons. Further, mutant cells fail to differentiate into epiblast-like cells (EpiLCs), a transition that requires the expansion of H3K9me2 across the genome. Mutant EpiLCs can silence naïve pluripotency genes and activate epiblast-stage genes. However, H3K9me2 cannot repress markers of alternative fates, including primitive endoderm. We conclude that the nuclear periphery controls the spatial position, dynamic remodeling, and repressive capacity of H3K9me2-marked heterochromatin to shape cell fate decisions.
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Affiliation(s)
- Harold Marin
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Eric Simental
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Department of Biochemistry, University of California, San Francisco, CA, USA
| | - Charlie Allen
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Eric Martin
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Barbara Panning
- Department of Biochemistry, University of California, San Francisco, CA, USA
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Physiology, University of California, San Francisco, CA, USA
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23
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Ishikawa T, Masuda T, Hachiya T, Dina C, Simonet F, Nagata Y, Tanck MWT, Sonehara K, Glinge C, Tadros R, Khongphatthanayothin A, Lu TP, Higuchi C, Nakajima T, Hayashi K, Aizawa Y, Nakano Y, Nogami A, Morita H, Ohno S, Aiba T, Krijger Juárez C, Mauleekoonphairoj J, Poovorawan Y, Gourraud JB, Shimizu W, Probst V, Horie M, Wilde AAM, Redon R, Juang JMJ, Nademanee K, Bezzina CR, Barc J, Tanaka T, Okada Y, Schott JJ, Makita N. Brugada syndrome in Japan and Europe: a genome-wide association study reveals shared genetic architecture and new risk loci. Eur Heart J 2024; 45:2320-2332. [PMID: 38747976 DOI: 10.1093/eurheartj/ehae251] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/02/2024] [Accepted: 04/08/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND AND AIMS Brugada syndrome (BrS) is an inherited arrhythmia with a higher disease prevalence and more lethal arrhythmic events in Asians than in Europeans. Genome-wide association studies (GWAS) have revealed its polygenic architecture mainly in European populations. The aim of this study was to identify novel BrS-associated loci and to compare allelic effects across ancestries. METHODS A GWAS was conducted in Japanese participants, involving 940 cases and 1634 controls, followed by a cross-ancestry meta-analysis of Japanese and European GWAS (total of 3760 cases and 11 635 controls). The novel loci were characterized by fine-mapping, gene expression, and splicing quantitative trait associations in the human heart. RESULTS The Japanese-specific GWAS identified one novel locus near ZSCAN20 (P = 1.0 × 10-8), and the cross-ancestry meta-analysis identified 17 association signals, including six novel loci. The effect directions of the 17 lead variants were consistent (94.1%; P for sign test = 2.7 × 10-4), and their allelic effects were highly correlated across ancestries (Pearson's R = .91; P = 2.9 × 10-7). The genetic risk score derived from the BrS GWAS of European ancestry was significantly associated with the risk of BrS in the Japanese population [odds ratio 2.12 (95% confidence interval 1.94-2.31); P = 1.2 × 10-61], suggesting a shared genetic architecture across ancestries. Functional characterization revealed that a lead variant in CAMK2D promotes alternative splicing, resulting in an isoform switch of calmodulin kinase II-δ, favouring a pro-inflammatory/pro-death pathway. CONCLUSIONS This study demonstrates novel susceptibility loci implicating potentially novel pathogenesis underlying BrS. Despite differences in clinical expressivity and epidemiology, the polygenic architecture of BrS was substantially shared across ancestries.
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Affiliation(s)
- Taisuke Ishikawa
- Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Tatsuo Masuda
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- StemRIM Institute of Regeneration-Inducing Medicine, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tsuyoshi Hachiya
- Institute for Biomedical Sciences, Iwate Medical University, Iwate, Japan
| | - Christian Dina
- L'institut du thorax, Nantes Université, CHU Nantes, CNRS, INSERM, Nantes, France
| | - Floriane Simonet
- L'institut du thorax, Nantes Université, CHU Nantes, CNRS, INSERM, Nantes, France
| | - Yuki Nagata
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Human Genetics and Disease Diversity, Tokyo Medical and Dental University, Tokyo, Japan
| | - Michael W T Tanck
- Epidemiology and Data Science, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Charlotte Glinge
- Department of Experimental Cardiology, Amsterdam UMC location University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
- Heart Failure & Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART https://guardheart.ern-net.eu)
| | - Rafik Tadros
- Department of Experimental Cardiology, Amsterdam UMC location University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
- Heart Failure & Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
- Montreal Heart Institute, Universite de Montreal, Cardiovascular Genetics Centre, Montreal, Quebec, Canada
| | - Apichai Khongphatthanayothin
- Department of Medicine, Center of Excellence in Arrhythmia Research Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Pediatrics, Division of Cardiology Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Cardiology, Bangkok Hospital, Bangkok, Thailand
| | - Tzu-Pin Lu
- Department of Public Health, Institute of Health Data Analytics and Statistics, National Taiwan University, Taipei, Taiwan
| | - Chihiro Higuchi
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Settsu, Japan
| | - Tadashi Nakajima
- Department of Cardiovascular Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kenshi Hayashi
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Yoshiyasu Aizawa
- Department of Cardiovascular Medicine, International University of Health and Welfare, Narita, Japan
| | - Yukiko Nakano
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Akihiko Nogami
- Department of Cardiology, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Morita
- Department of Cardiovascular Therapeutics, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Seiko Ohno
- Medical Genome Center, National Cerebral and Cardiovascular Center, Suita, Japan
- Department of Cardiovascular Medicine, Shiga University of Medical Sciences, Otsu, Japan
| | - Takeshi Aiba
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Christian Krijger Juárez
- Department of Experimental Cardiology, Amsterdam UMC location University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
- Heart Failure & Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - John Mauleekoonphairoj
- Department of Medicine, Center of Excellence in Arrhythmia Research Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jean-Baptiste Gourraud
- L'institut du thorax, Nantes Université, CHU Nantes, CNRS, INSERM, Nantes, France
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART https://guardheart.ern-net.eu)
| | - Wataru Shimizu
- Department of Cardiovascular Medicine, Nippon Medical School, Tokyo, Japan
| | - Vincent Probst
- L'institut du thorax, Nantes Université, CHU Nantes, CNRS, INSERM, Nantes, France
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART https://guardheart.ern-net.eu)
| | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Sciences, Otsu, Japan
| | - Arthur A M Wilde
- Heart Failure & Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART https://guardheart.ern-net.eu)
- Department of Cardiology, Amsterdam UMC location University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
| | - Richard Redon
- L'institut du thorax, Nantes Université, CHU Nantes, CNRS, INSERM, Nantes, France
| | - Jyh-Ming Jimmy Juang
- Cardiovascular Center, Heart Failure Center and Department of Internal Medicine, Division of Cardiology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Koonlawee Nademanee
- Department of Medicine, Center of Excellence in Arrhythmia Research Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Pacific Rim Electrophysiology Research Institute, Bumrungrad International Hospital, Bangkok, Thailand
| | - Connie R Bezzina
- Department of Experimental Cardiology, Amsterdam UMC location University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
- Heart Failure & Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART https://guardheart.ern-net.eu)
| | - Julien Barc
- L'institut du thorax, Nantes Université, CHU Nantes, CNRS, INSERM, Nantes, France
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART https://guardheart.ern-net.eu)
| | - Toshihiro Tanaka
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Human Genetics and Disease Diversity, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Jean-Jacques Schott
- L'institut du thorax, Nantes Université, CHU Nantes, CNRS, INSERM, Nantes, France
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART https://guardheart.ern-net.eu)
| | - Naomasa Makita
- Department of Cardiology, Sapporo Teishinkai Hospital, N33, E1, Sapporo 065-0033, Japan
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, 6-1, Kishibe Shimmachi, 564-8565 Suita, Japan
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24
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Liu M, Hemba-Waduge RUS, Li X, Huang X, Liu TH, Han X, Wang Y, Ji JY. Wnt/Wingless signaling promotes lipid mobilization through signal-induced transcriptional repression. Proc Natl Acad Sci U S A 2024; 121:e2322066121. [PMID: 38968125 PMCID: PMC11252803 DOI: 10.1073/pnas.2322066121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/31/2024] [Indexed: 07/07/2024] Open
Abstract
The Wnt/Wingless signaling pathway plays critical roles in metazoan development and energy metabolism, but its role in regulating lipid homeostasis remains not fully understood. Here, we report that the activation of canonical Wnt/Wg signaling promotes lipolysis while concurrently inhibiting lipogenesis and fatty acid β-oxidation in both larval and adult adipocytes, as well as cultured S2R+ cells, in Drosophila. Using RNA-sequencing and CUT&RUN (Cleavage Under Targets & Release Using Nuclease) assays, we identified a set of Wnt target genes responsible for intracellular lipid homeostasis. Notably, active Wnt signaling directly represses the transcription of these genes, resulting in decreased de novo lipogenesis and fatty acid β-oxidation, but increased lipolysis. These changes lead to elevated free fatty acids and reduced triglyceride (TG) accumulation in adipocytes with active Wnt signaling. Conversely, downregulation of Wnt signaling in the fat body promotes TG accumulation in both larval and adult adipocytes. The attenuation of Wnt signaling also increases the expression of specific lipid metabolism-related genes in larval adipocytes, wing discs, and adult intestines. Taken together, these findings suggest that Wnt signaling-induced transcriptional repression plays an important role in regulating lipid homeostasis by enhancing lipolysis while simultaneously suppressing lipogenesis and fatty acid β-oxidation.
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Affiliation(s)
- Mengmeng Liu
- Department of Biochemistry and Molecular Biology, Louisiana Cancer Research Center, Tulane University School of Medicine, New Orleans, LA70112
| | | | - Xiao Li
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ08540
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Department of Molecular Systems Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Tzu-Hao Liu
- Department of Biochemistry and Molecular Biology, Louisiana Cancer Research Center, Tulane University School of Medicine, New Orleans, LA70112
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX78229
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Department of Molecular Systems Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Jun-Yuan Ji
- Department of Biochemistry and Molecular Biology, Louisiana Cancer Research Center, Tulane University School of Medicine, New Orleans, LA70112
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25
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Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Muñoz Gomez M, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RA. Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. Cell Stem Cell 2024; 31:1038-1057.e11. [PMID: 38733993 DOI: 10.1016/j.stem.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. Abundant EEC precursors expressed stage-specific genes and TFs. Before expressing pre-terminal NEUROD1, post-mitotic precursors oscillated between transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor accelerated EEC differentiation substantially and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and non-EC cell features. These TFs mainly bind cis-elements that are accessible in undifferentiated stem cells, and they tailor subsequent expression of TF combinations that underlie discrete EEC identities. Thus, early TF oscillations retard EEC maturation to enable accurate diversity within a medically important cell lineage.
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Affiliation(s)
- Pratik N P Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wei Gu
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shariq Madha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Allen W Lynch
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Swarnabh Bhattacharya
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Miguel Muñoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Qiao Zhou
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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26
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Atac D, Maggi K, Feil S, Maggi J, Cuevas E, Sowden JC, Koller S, Berger W. Identification and Characterization of ATOH7-Regulated Target Genes and Pathways in Human Neuroretinal Development. Cells 2024; 13:1142. [PMID: 38994994 PMCID: PMC11240604 DOI: 10.3390/cells13131142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/27/2024] [Accepted: 06/29/2024] [Indexed: 07/13/2024] Open
Abstract
The proneural transcription factor atonal basic helix-loop-helix transcription factor 7 (ATOH7) is expressed in early progenitors in the developing neuroretina. In vertebrates, this is crucial for the development of retinal ganglion cells (RGCs), as mutant animals show an almost complete absence of RGCs, underdeveloped optic nerves, and aberrations in retinal vessel development. Human mutations are rare and result in autosomal recessive optic nerve hypoplasia (ONH) or severe vascular changes, diagnosed as autosomal recessive persistent hyperplasia of the primary vitreous (PHPVAR). To better understand the role of ATOH7 in neuroretinal development, we created ATOH7 knockout and eGFP-expressing ATOH7 reporter human induced pluripotent stem cells (hiPSCs), which were differentiated into early-stage retinal organoids. Target loci regulated by ATOH7 were identified by Cleavage Under Targets and Release Using Nuclease with sequencing (CUT&RUN-seq) and differential expression by RNA sequencing (RNA-seq) of wildtype and mutant organoid-derived reporter cells. Additionally, single-cell RNA sequencing (scRNA-seq) was performed on whole organoids to identify cell type-specific genes. Mutant organoids displayed substantial deficiency in axon sprouting, reduction in RGCs, and an increase in other cell types. We identified 469 differentially expressed target genes, with an overrepresentation of genes belonging to axon development/guidance and Notch signaling. Taken together, we consolidate the function of human ATOH7 in guiding progenitor competence by inducing RGC-specific genes while inhibiting other cell fates. Furthermore, we highlight candidate genes responsible for ATOH7-associated optic nerve and retinovascular anomalies, which sheds light to potential future therapy targets for related disorders.
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Affiliation(s)
- David Atac
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Kevin Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Elisa Cuevas
- UCL Great Ormond Street Institute of Child Health, University College London and NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | - Jane C Sowden
- UCL Great Ormond Street Institute of Child Health, University College London and NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich, University and ETH Zurich, 8057 Zurich, Switzerland
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27
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Zhu M, Xu R, Yuan J, Wang J, Ren X, Cong T, You Y, Ju A, Xu L, Wang H, Zheng P, Tao H, Lin C, Yu H, Du J, Lin X, Xie W, Li Y, Lan X. Tracking-seq reveals the heterogeneity of off-target effects in CRISPR-Cas9-mediated genome editing. Nat Biotechnol 2024:10.1038/s41587-024-02307-y. [PMID: 38956324 DOI: 10.1038/s41587-024-02307-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 06/06/2024] [Indexed: 07/04/2024]
Abstract
The continued development of novel genome editors calls for a universal method to analyze their off-target effects. Here we describe a versatile method, called Tracking-seq, for in situ identification of off-target effects that is broadly applicable to common genome-editing tools, including Cas9, base editors and prime editors. Through tracking replication protein A (RPA)-bound single-stranded DNA followed by strand-specific library construction, Tracking-seq requires a low cell input and is suitable for in vitro, ex vivo and in vivo genome editing, providing a sensitive and practical genome-wide approach for off-target detection in various scenarios. We show, using the same guide RNA, that Tracking-seq detects heterogeneity in off-target effects between different editor modalities and between different cell types, underscoring the necessity of direct measurement in the original system.
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Affiliation(s)
- Ming Zhu
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China.
| | - Runda Xu
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China
| | - Junsong Yuan
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jiacheng Wang
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoyu Ren
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Tingting Cong
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yaxian You
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China
| | - Anji Ju
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China
| | - Longchen Xu
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Huimin Wang
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Peiyuan Zheng
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Huiying Tao
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- Department of Urology, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Chunhua Lin
- Department of Urology, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Honghao Yu
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- Key Laboratory of Medical Biotechnology and Translational Medicine, Guilin Medical University, Guilin, China
| | - Juanjuan Du
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Xin Lin
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Wei Xie
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yinqing Li
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China.
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
| | - Xun Lan
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China.
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28
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Hu S, Liu Y, Zhang Q, Bai J, Xu C. A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Mol Syst Biol 2024; 20:799-824. [PMID: 38745107 PMCID: PMC11220090 DOI: 10.1038/s44320-024-00038-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription factor (TF) residence on chromatin translates into quantitative transcriptional or structural outcomes on genome. Commonly used formaldehyde crosslinking fixes TF-DNA interactions cumulatively and compromises the measured occupancy level. Here we mapped the occupancy level of global or individual zinc finger TFs like CTCF and MAZ, in the form of highly resolved footprints, on native chromatin. By incorporating reinforcing perturbation conditions, we established S-score, a quantitative metric to proxy the continuum of CTCF or MAZ retention across different motifs on native chromatin. The native chromatin-retained CTCF sites harbor sequence features within CTCF motifs better explained by S-score than the metrics obtained from other crosslinking or native assays. CTCF retention on native chromatin correlates with local SUMOylation level, and anti-correlates with transcriptional activity. The S-score successfully delineates the otherwise-masked differential stability of chromatin structures mediated by CTCF, or by MAZ independent of CTCF. Overall, our study established a paradigm continuum of TF retention across binding sites on native chromatin, explaining the dynamic genome organization.
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Affiliation(s)
- Siling Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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29
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Gustavsson EK, Sethi S, Gao Y, Brenton JW, García-Ruiz S, Zhang D, Garza R, Reynolds RH, Evans JR, Chen Z, Grant-Peters M, Macpherson H, Montgomery K, Dore R, Wernick AI, Arber C, Wray S, Gandhi S, Esselborn J, Blauwendraat C, Douse CH, Adami A, Atacho DAM, Kouli A, Quaegebeur A, Barker RA, Englund E, Platt F, Jakobsson J, Wood NW, Houlden H, Saini H, Bento CF, Hardy J, Ryten M. The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1. SCIENCE ADVANCES 2024; 10:eadk1296. [PMID: 38924406 PMCID: PMC11204300 DOI: 10.1126/sciadv.adk1296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 05/17/2024] [Indexed: 06/28/2024]
Abstract
Mutations in GBA1 cause Gaucher disease and are the most important genetic risk factor for Parkinson's disease. However, analysis of transcription at this locus is complicated by its highly homologous pseudogene, GBAP1. We show that >50% of short RNA-sequencing reads mapping to GBA1 also map to GBAP1. Thus, we used long-read RNA sequencing in the human brain, which allowed us to accurately quantify expression from both GBA1 and GBAP1. We discovered significant differences in expression compared to short-read data and identify currently unannotated transcripts of both GBA1 and GBAP1. These included protein-coding transcripts from both genes that were translated in human brain, but without the known lysosomal function-yet accounting for almost a third of transcription. Analyzing brain-specific cell types using long-read and single-nucleus RNA sequencing revealed region-specific variations in transcript expression. Overall, these findings suggest nonlysosomal roles for GBA1 and GBAP1 with implications for our understanding of the role of GBA1 in health and disease.
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Affiliation(s)
- Emil K. Gustavsson
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Siddharth Sethi
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, UK
| | - Yujing Gao
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, UK
| | - Jonathan W. Brenton
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sonia García-Ruiz
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - David Zhang
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund, Sweden
| | - Regina H. Reynolds
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - James R. Evans
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Zhongbo Chen
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Melissa Grant-Peters
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Hannah Macpherson
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Kylie Montgomery
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Rhys Dore
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Anna I. Wernick
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Charles Arber
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Selina Wray
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Sonia Gandhi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Julian Esselborn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, UK
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher H. Douse
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Anita Adami
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund, Sweden
| | - Diahann A. M. Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund, Sweden
| | - Antonina Kouli
- Wellcome-MRC Cambridge Stem Cell Institute and John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Annelies Quaegebeur
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Clinical Neurosciences, University of Cambridge, Clifford Albutt Building, Cambridge, UK
| | - Roger A. Barker
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Wellcome-MRC Cambridge Stem Cell Institute and John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - Frances Platt
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Johan Jakobsson
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund, Sweden
| | - Nicholas W. Wood
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Harpreet Saini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, UK
| | - Carla F. Bento
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, UK
| | - John Hardy
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, UCL, London, UK
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, UCL, London, UK
- NIHR University College London Hospitals Biomedical Research Centre, London, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
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30
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Quan S, Huang H. Epigenetic contribution to cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 387:1-25. [PMID: 39179345 DOI: 10.1016/bs.ircmb.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
Epigenetics has transformed our understanding of cancer by revealing how changes in gene activity, which do not alter the DNA itself, can initiate and progress the disease. These changes include adjustments in DNA methylation, histone configuration, and non-coding RNA activity. For instance, DNA methylation can inactivate genes that typically protect against cancer, leading to broader genomic instability. Histone modifications can alter how tightly DNA is wound, influencing which genes are active or silenced; while non-coding RNAs can interfere with the messages that direct protein production, impacting cancer-related processes. Unlike genetic mutations, which are permanent and irreversible, epigenetic changes provide a malleable target for therapeutic intervention, allowing potentially reversible adjustments to gene expression patterns. This flexibility is essential in the complex landscape of cancer where static genetic solutions may be insufficient. Additionally, epigenetics bridges the gap between genetic predispositions and environmental influences on cancer, offering a comprehensive framework for understanding how lifestyle factors and external exposures impact cancer risk and progression. The integration of epigenetics into cancer research not only enhances our understanding of the disease but also opens innovative avenues for intervention that were previously unexplored in traditional genetic-focused studies. Technologies like advanced sequencing and precise epigenetic modification are paving the way for early cancer detection and more personalized treatment approaches, highlighting the critical role of epigenetics in modern cancer care.
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Affiliation(s)
- Songhua Quan
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Hao Huang
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.
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31
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Willnow P, Teleman AA. Nuclear position and local acetyl-CoA production regulate chromatin state. Nature 2024; 630:466-474. [PMID: 38839952 PMCID: PMC11168921 DOI: 10.1038/s41586-024-07471-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
Histone acetylation regulates gene expression, cell function and cell fate1. Here we study the pattern of histone acetylation in the epithelial tissue of the Drosophila wing disc. H3K18ac, H4K8ac and total lysine acetylation are increased in the outer rim of the disc. This acetylation pattern is controlled by nuclear position, whereby nuclei continuously move from apical to basal locations within the epithelium and exhibit high levels of H3K18ac when they are in proximity to the tissue surface. These surface nuclei have increased levels of acetyl-CoA synthase, which generates the acetyl-CoA for histone acetylation. The carbon source for histone acetylation in the rim is fatty acid β-oxidation, which is also increased in the rim. Inhibition of fatty acid β-oxidation causes H3K18ac levels to decrease in the genomic proximity of genes involved in disc development. In summary, there is a physical mark of the outer rim of the wing and other imaginal epithelia in Drosophila that affects gene expression.
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Affiliation(s)
- Philipp Willnow
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Heidelberg University, Heidelberg, Germany.
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32
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Li L, Lai F, Liu L, Lu X, Hu X, Liu B, Lin Z, Fan Q, Kong F, Xu Q, Xie W. Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos. Nat Struct Mol Biol 2024; 31:950-963. [PMID: 38243114 DOI: 10.1038/s41594-023-01199-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/05/2023] [Indexed: 01/21/2024]
Abstract
During the first lineage segregation, a mammalian totipotent embryo differentiates into the inner cell mass (ICM) and trophectoderm (TE). However, how transcription factors (TFs) regulate this earliest cell-fate decision in vivo remains elusive, with their regulomes primarily inferred from cultured cells. Here, we investigated the TF regulomes during the first lineage specification in early mouse embryos, spanning the pre-initiation, initiation, commitment, and maintenance phases. Unexpectedly, we found that TFAP2C, a trophoblast regulator, bound and activated both early TE and inner cell mass (ICM) genes at the totipotent (two- to eight-cell) stages ('bipotency activation'). Tfap2c deficiency caused downregulation of early ICM genes, including Nanog, Nr5a2, and Tdgf1, and early TE genes, including Tfeb and Itgb5, in eight-cell embryos. Transcription defects in both ICM and TE lineages were also found in blastocysts, accompanied by increased apoptosis and reduced cell numbers in ICMs. Upon trophoblast commitment, TFAP2C left early ICM genes but acquired binding to late TE genes in blastocysts, where it co-bound with CDX2, and later to extra-embryonic ectoderm (ExE) genes, where it cooperatively co-occupied with the former ICM regulator SOX2. Finally, 'bipotency activation' in totipotent embryos also applied to a pluripotency regulator NR5A2, which similarly bound and activated both ICM and TE lineage genes at the eight-cell stage. These data reveal a unique transcription circuity of totipotency underpinned by highly adaptable lineage regulators.
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Affiliation(s)
- Lijia Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xukun Lu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xiaoyu Hu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zili Lin
- College of Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qianhua Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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33
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Huber K, Giralt A, Dreos R, Michenthaler H, Geller S, Barquissau V, Ziegler DV, Tavernari D, Gallart-Ayala H, Krajina K, Jonas K, Ciriello G, Ivanisevic J, Prokesch A, Pichler M, Fajas L. E2F transcription factor-1 modulates expression of glutamine metabolic genes in mouse embryonic fibroblasts and uterine sarcoma cells. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119721. [PMID: 38580088 DOI: 10.1016/j.bbamcr.2024.119721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
Abstract
Metabolic reprogramming is considered as a hallmark of cancer and is clinically exploited as a novel target for therapy. The E2F transcription factor-1 (E2F1) regulates various cellular processes, including proliferative and metabolic pathways, and acts, depending on the cellular and molecular context, as an oncogene or tumor suppressor. The latter is evident by the observation that E2f1-knockout mice develop spontaneous tumors, including uterine sarcomas. This dual role warrants a detailed investigation of how E2F1 loss impacts metabolic pathways related to cancer progression. Our data indicate that E2F1 binds to the promoter of several glutamine metabolism-related genes. Interestingly, the expression of genes in the glutamine metabolic pathway were increased in mouse embryonic fibroblasts (MEFs) lacking E2F1. In addition, we confirm that E2f1-/- MEFs are more efficient in metabolizing glutamine and producing glutamine-derived precursors for proliferation. Mechanistically, we observe a co-occupancy of E2F1 and MYC on glutamine metabolic promoters, increased MYC binding after E2F1 depletion and that silencing of MYC decreased the expression of glutamine-related genes in E2f1-/- MEFs. Analyses of transcriptomic profiles in 29 different human cancers identified uterine sarcoma that showed a negative correlation between E2F1 and glutamine metabolic genes. CRISPR/Cas9 knockout of E2F1 in the uterine sarcoma cell line SK-UT-1 confirmed elevated glutamine metabolic gene expression, increased proliferation and increased MYC binding to glutamine-related promoters upon E2F1 loss. Together, our data suggest a crucial role of E2F1 in energy metabolism and metabolic adaptation in uterine sarcoma cells.
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Affiliation(s)
- Katharina Huber
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Albert Giralt
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Helene Michenthaler
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Sarah Geller
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Valentin Barquissau
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Dorian V Ziegler
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Daniele Tavernari
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Léman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hector Gallart-Ayala
- Metabolomics Unit, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Katarina Krajina
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Katharina Jonas
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Léman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Unit, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Andreas Prokesch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria; Translational Oncology, II. Med. Clinics, University Hospital of Augsburg, Augsburg, Germany
| | - Lluis Fajas
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
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Wang L, Yi S, Cui X, Guo Z, Wang M, Kou X, Zhao Y, Wang H, Jiang C, Gao S, Yang G, Chen J, Gao R. Chromatin landscape instructs precise transcription factor regulome during embryonic lineage specification. Cell Rep 2024; 43:114136. [PMID: 38643480 DOI: 10.1016/j.celrep.2024.114136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/10/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024] Open
Abstract
Embryos, originating from fertilized eggs, undergo continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Chromatin regulators, including transcription factors (TFs), play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was identified as crucial in initiating early cell fate decisions. However, Tfap2c transcripts persist in both the inner cell mass and trophectoderm of blastocysts, prompting inquiry into Tfap2c's function in post-lineage establishment. In this study, we delineate the dynamics of TFAP2C during the mouse peri-implantation stage and elucidate its collaboration with the key lineage regulators CDX2 and NANOG. Importantly, we propose that de novo formation of H3K9me3 in the extraembryonic ectoderm during implantation antagonizes TFAP2C binding to crucial developmental genes, thereby maintaining its lineage identity. Together, these results highlight the plasticity of the chromatin environment in designating the genomic binding of highly adaptable lineage-specific TFs and regulating embryonic cell fates.
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Affiliation(s)
- Liping Wang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanru Yi
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xinyu Cui
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Zhenxiang Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai 200120, China.
| | - Guang Yang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Rui Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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35
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Seasock MJ, Shafiquzzaman M, Ruiz-Echartea ME, Kanchi RS, Tran BT, Simon LM, Meyer MD, Erice PA, Lotlikar SL, Wenlock SC, Ochsner SA, Enright A, Carisey AF, Romero F, Rosas IO, King KY, McKenna NJ, Coarfa C, Rodriguez A. Let-7 restrains an oncogenic epigenetic circuit in AT2 cells to prevent ectopic formation of fibrogenic transitional cell intermediates and pulmonary fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595205. [PMID: 38826218 PMCID: PMC11142151 DOI: 10.1101/2024.05.22.595205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Analysis of lung alveolar type 2 (AT2) progenitor stem cells has highlighted fundamental mechanisms that direct their differentiation into alveolar type 1 cells (AT1s) in lung repair and disease. However, microRNA (miRNA) mediated post-transcriptional mechanisms which govern this nexus remain understudied. We show here that the let-7 miRNA family serves a homeostatic role in governance of AT2 quiescence, specifically by preventing the uncontrolled accumulation of AT2 transitional cells and by promoting AT1 differentiation to safeguard the lung from spontaneous alveolar destruction and fibrosis. Using mice and organoid models with genetic ablation of let-7a1/let-7f1/let-7d cluster (let-7afd) in AT2 cells, we demonstrate prevents AT1 differentiation and results in aberrant accumulation of AT2 transitional cells in progressive pulmonary fibrosis. Integration of enhanced AGO2 UV-crosslinking and immunoprecipitation sequencing (AGO2-eCLIP) with RNA-sequencing from AT2 cells uncovered the induction of direct targets of let-7 in an oncogene feed-forward regulatory network including BACH1/EZH2 which drives an aberrant fibrotic cascade. Additional analyses by CUT&RUN-sequencing revealed loss of let-7afd hampers AT1 differentiation by eliciting aberrant histone EZH2 methylation which prevents the exit of AT2 transitional cells into terminal AT1s. This study identifies let-7 as a key gatekeeper of post-transcriptional and epigenetic chromatin signals to prevent AT2-driven pulmonary fibrosis.
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Affiliation(s)
- Matthew J. Seasock
- Immunology & Microbiology Graduate Program, Baylor College of Medicine, Houston, TX, 77030
- Department of Medicine, Immunology & Allergy Rheumatology, Baylor College of Medicine Houston TX, 77030
| | - Md Shafiquzzaman
- Department of Medicine, Immunology & Allergy Rheumatology, Baylor College of Medicine Houston TX, 77030
| | - Maria E. Ruiz-Echartea
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
| | - Rupa S. Kanchi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine Houston, TX, 77030
| | - Brandon T. Tran
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030
- Department of Pediatrics, Division of Infectious Diseases, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, 77030
| | - Lukas M. Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, 77030
| | | | - Phillip A. Erice
- Immunology & Microbiology Graduate Program, Baylor College of Medicine, Houston, TX, 77030
- Department of Medicine, Immunology & Allergy Rheumatology, Baylor College of Medicine Houston TX, 77030
| | - Shivani L. Lotlikar
- Department of Medicine, Immunology & Allergy Rheumatology, Baylor College of Medicine Houston TX, 77030
| | | | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
| | - Anton Enright
- Department of Pathology, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Alex F. Carisey
- William T. Shearer Center for Immunobiology, Texas Children’s Hospital, Houston, TX, 77030
- Current Address: Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Freddy Romero
- Department of Medicine, Section of Pulmonary and Critical Care, Baylor College of Medicine. Houston, TX, 77030
- Current Address: Vertex Pharmaceuticals, 3215 Merryfield Row, San Diego, CA, 92121
| | - Ivan O. Rosas
- Department of Medicine, Section of Pulmonary and Critical Care, Baylor College of Medicine. Houston, TX, 77030
| | - Katherine Y. King
- Department of Pediatrics, Division of Infectious Diseases, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, 77030
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine Houston, TX, 77030
| | - Antony Rodriguez
- Department of Medicine, Immunology & Allergy Rheumatology, Baylor College of Medicine Houston TX, 77030
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine Houston, TX, 77030
- Center for Translational Research on Inflammatory Diseases, Michael E. Debakey, Baylor College of Medicine, Houston, TX, 77030
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36
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Fang Y, Barrows D, Dabas Y, Carroll T, Singer S, Tap W, Nacev B. ATRX guards against aberrant differentiation in mesenchymal progenitor cells. Nucleic Acids Res 2024; 52:4950-4968. [PMID: 38477352 PMCID: PMC11109985 DOI: 10.1093/nar/gkae160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/19/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024] Open
Abstract
Alterations in the tumor suppressor ATRX are recurrently observed in mesenchymal neoplasms. ATRX has multiple epigenetic functions including heterochromatin formation and maintenance and regulation of transcription through modulation of chromatin accessibility. Here, we show in murine mesenchymal progenitor cells (MPCs) that Atrx deficiency aberrantly activated mesenchymal differentiation programs. This includes adipogenic pathways where ATRX loss induced expression of adipogenic transcription factors and enhanced adipogenic differentiation in response to differentiation stimuli. These changes are linked to loss of heterochromatin near mesenchymal lineage genes together with increased chromatin accessibility and gains of active chromatin marks. We additionally observed depletion of H3K9me3 at transposable elements, which are derepressed including near mesenchymal genes where they could serve as regulatory elements. Finally, we demonstrated that loss of ATRX in a mesenchymal malignancy, undifferentiated pleomorphic sarcoma, results in similar epigenetic disruption and de-repression of transposable elements. Together, our results reveal a role for ATRX in maintaining epigenetic states and transcriptional repression in mesenchymal progenitors and tumor cells and in preventing aberrant differentiation in the progenitor context.
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Affiliation(s)
- Yan Fang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065, USA
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY10065, USA
| | - Yakshi Dabas
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY10065, USA
| | - Sam Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY10065, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065, USA
| | - Benjamin A Nacev
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
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37
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Innis SM, Cabot RA. Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development. Epigenetics Chromatin 2024; 17:16. [PMID: 38773546 PMCID: PMC11106951 DOI: 10.1186/s13072-024-00542-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/16/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Given their physiological similarities to humans, pigs are increasingly used as model organisms in human-oriented biomedical studies. Additionally, their value to animal agriculture across the globe has led to the development of numerous studies to investigate how to improve livestock welfare and production efficiency. As such, pigs are uniquely poised as compelling models that can yield findings with potential implications in both human and animal contexts. Despite this, many gaps remain in our knowledge about the foundational mechanisms that govern gene expression in swine across different developmental stages, particularly in early development. To address some of these gaps, we profiled the histone marks H3K4me3, H3K27ac, and H3K27me3 and the SWI/SNF central ATPase BRG1 in two porcine cell lines representing discrete early developmental time points and used the resulting information to construct predicted chromatin state maps for these cells. We combined this approach with analysis of publicly available RNA-seq data to examine the relationship between epigenetic status and gene expression in these cell types. RESULTS In porcine fetal fibroblast (PFF) and trophectoderm cells (PTr2), we saw expected patterns of enrichment for each of the profiled epigenetic features relative to specific genomic regions. H3K4me3 was primarily enriched at and around global gene promoters, H3K27ac was enriched in promoter and intergenic regions, H3K27me3 had broad stretches of enrichment across the genome and narrower enrichment patterns in and around the promoter regions of some genes, and BRG1 primarily had detectable enrichment at and around promoter regions and in intergenic stretches, with many instances of H3K27ac co-enrichment. We used this information to perform genome-wide chromatin state predictions for 10 different states using ChromHMM. Using the predicted chromatin state maps, we identified a subset of genomic regions marked by broad H3K4me3 enrichment, and annotation of these regions revealed that they were highly associated with essential developmental processes and consisted largely of expressed genes. We then compared the identities of the genes marked by these regions to genes identified as cell-type-specific using transcriptome data and saw that a subset of broad H3K4me3-marked genes was also specifically expressed in either PFF or PTr2 cells. CONCLUSIONS These findings enhance our understanding of the epigenetic landscape present in early swine development and provide insight into how variabilities in chromatin state are linked to cell identity. Furthermore, this data captures foundational epigenetic details in two valuable porcine cell lines and contributes to the growing body of knowledge surrounding the epigenetic landscape in this species.
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Affiliation(s)
- Sarah M Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Ryan A Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA.
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Saha D, Animireddy S, Lee J, Thommen A, Murvin MM, Lu Y, Calabrese JM, Bartholomew B. Enhancer switching in cell lineage priming is linked to eRNA, Brg1's AT-hook, and SWI/SNF recruitment. Mol Cell 2024; 84:1855-1869.e5. [PMID: 38593804 PMCID: PMC11104297 DOI: 10.1016/j.molcel.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 11/24/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
RNA transcribed from enhancers, i.e., eRNA, has been suggested to directly activate transcription by recruiting transcription factors and co-activators. Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find that the AT-hook of SWI/SNF preferentially binds RNA and, as part of the esBAF complex, associates with eRNA transcribed from intronic and intergenic regions. Our data suggest that SWI/SNF is globally recruited in cis by eRNA to cell-type-specific enhancers, representative of two distinct stages that mimic early mammalian development, and not at enhancers that are shared between the two stages. In this manner, SWI/SNF facilitates recruitment and/or activation of MLL3/4, p300/CBP, and Mediator to stage-specific enhancers and super-enhancers that regulate the transcription of metabolic and cell lineage priming-related genes. These findings highlight a connection between ATP-dependent chromatin remodeling and eRNA in cell identity and typical- and super-enhancer activation.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Junwoo Lee
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Anna Thommen
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - McKenzie M Murvin
- Department of Pharmacology, RNA Discovery Center, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA; Curriculum in Mechanistic, Interdisciplinary Studies in Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA
| | - J Mauro Calabrese
- Department of Pharmacology, RNA Discovery Center, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA; Curriculum in Mechanistic, Interdisciplinary Studies in Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA.
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Duque-Wilckens N, Maradiaga N, Szu-Ying Y, Joseph D, Srinavasan V, Thelen K, Sotomayor F, Durga K, Nestler E, Moeser AJ, Robison AJ. Activity-dependent FosB gene expression negatively regulates mast cell functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592755. [PMID: 38766119 PMCID: PMC11100602 DOI: 10.1101/2024.05.06.592755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Mast cells are innate immune cells that play a crucial role in numerous physiological processes across tissues by releasing pre-stored and newly synthesized mediators in response to stimuli, an activity largely driven by changes in gene expression. Given their widespread influence, dysfunction in mast cells can contribute to a variety of pathologies including allergies, long COVID, and autoimmune and neuroinflammatory disorders. Despite this, the specific transcriptional mechanisms that control mast cell mediator release remain poorly understood, significantly hindering the development of effective therapeutic strategies. We found that the two proteins encoded by the transcription factor FosB, FOSB and the highly stable variant ΔFOSB, are robustly expressed upon stimulation in both murine and human mast cell progenitors. Motivated by these findings, we generated a novel mouse model with targeted ablation of FosB gene expression specifically in mast cells (MC FosB- ) by crossing a mast cell-specific Cre reporter line (Mcpt5-Cre) with a Cre-dependent floxed FosB mouse lines. We found that mast cell progenitors derived from MC FosB- mice, compared to wild types (WT), exhibit baseline increased histamine content and vesicle numbers. Additionally, they show enhanced calcium mobilization, degranulation, and histamine release following allergy-related IgE-mediated stimulation, along with heightened IL-6 release in response to infection-like LPS stimulation. In vivo experiments with IgE- mediated and LPS challenges revealed that MC FosB- mice experience greater drops in body temperature, heightened activation of tissue-resident mast cells, and increased release of pro-inflammatory mediators compared to their WT counterparts. These findings suggest that FosB products play a crucial regulatory role in moderating stimulus-induced mast cell activation in response to both IgE and LPS stimuli. Lastly, by integrating CUT&RUN and RNAseq data, we identified several genes targeted by ΔFOSB that could mediate these observed effects, including Mir155hg, CLCF1, DUSP4, and Trib1. Together, this study provides the first evidence that FOSB/ΔFOSB modulate mast cell functions and provides a new possible target for therapeutic interventions aimed at ameliorating mast cell-related diseases.
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40
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Duval KL, Artis AR, Goll MG. The emerging H3K9me3 chromatin landscape during zebrafish embryogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.582530. [PMID: 38496550 PMCID: PMC10942377 DOI: 10.1101/2024.03.05.582530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The structural organization of eukaryotic genomes is contingent upon the fractionation of DNA into transcriptionally permissive euchromatin and repressive heterochromatin. However, we have a limited understanding of how these distinct states are first established during animal embryogenesis. Histone 3 lysine 9 trimethylation (H3K9me3) is critical to heterochromatin formation and bulk establishment of this mark is thought to help drive large-scale remodeling of an initially naive chromatin state during animal embryogenesis. However, a detailed understanding of this process is lacking. Here, we leverage CUT&RUN to define the emerging H3K9me3 landscape of the zebrafish embryo with high sensitivity and temporal resolution. Despite the prevalence of DNA transposons in the zebrafish genome, we found that LTR transposons are preferentially targeted for embryonic H3K9me3 deposition, with different families exhibiting distinct establishment timelines. High signal-to-noise ratios afforded by CUT&RUN revealed new, emerging sites of low-amplitude H3K9me3 that initiated before the major wave of zygotic genome activation (ZGA). Early sites of establishment predominated at specific subsets of transposons and were particularly enriched for transposon sequences with maternal piRNAs and pericentromeric localization. Notably, the number of H3K9me3 enriched sites increased linearly across blastula development, while quantitative comparison revealed a >10-fold genome-wide increase in H3K9me3 signal at established sites over just 30 minutes at the onset of ZGA. Continued maturation of the H3K9me3 landscape was observed beyond the initial wave of bulk establishment.
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Affiliation(s)
| | - Ashley R. Artis
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Mary G. Goll
- Department of Genetics, University of Georgia, Athens, GA, USA
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Gao R, Yang G, Wang M, Xiao J, Yi S, Huang Y, Guo Z, Kang Y, Fu Q, Wang M, Xu B, Shen S, Zhu Q, Liu M, Wang L, Cui X, Yi S, Kou X, Zhao Y, Gu L, Wang H, Gao S, Jiang C, Chen J. Defining a TFAP2C-centered transcription factor network during murine peri-implantation. Dev Cell 2024; 59:1146-1158.e6. [PMID: 38574734 DOI: 10.1016/j.devcel.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/07/2023] [Accepted: 03/06/2024] [Indexed: 04/06/2024]
Abstract
Transcription factors (TFs) play important roles in early embryonic development, but factors regulating TF action, relationships in signaling cascade, genome-wide localizations, and impacts on cell fate transitions during this process have not been clearly elucidated. In this study, we used uliCUT&RUN-seq to delineate a TFAP2C-centered regulatory network, showing that it involves promoter-enhancer interactions and regulates TEAD4 and KLF5 function to mediate cell polarization. Notably, we found that maternal retinoic acid metabolism regulates TFAP2C expression and function by inducing the active demethylation of SINEs, indicating that the RARG-TFAP2C-TEAD4/KLF5 axis connects the maternal-to-zygotic transition to polarization. Moreover, we found that both genomic imprinting and SNP-transferred genetic information can influence TF positioning to regulate parental gene expressions in a sophisticated manner. In summary, we propose a ternary model of TF regulation in murine embryonic development with TFAP2C as the core element and metabolic, epigenetic, and genetic information as nodes connecting the pathways.
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Affiliation(s)
- Rui Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Guang Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Jing Xiao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanru Yi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanxin Huang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Zhenxiang Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yunzhe Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Qianzheng Fu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mingzhu Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Ben Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shijun Shen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Meng Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xinyu Cui
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanshan Yi
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai 200120, China.
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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42
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Nordin A, Pagella P, Zambanini G, Cantù C. Exhaustive identification of genome-wide binding events of transcriptional regulators. Nucleic Acids Res 2024; 52:e40. [PMID: 38499482 PMCID: PMC11040144 DOI: 10.1093/nar/gkae180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication-duplicates or triplicates-and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regions, the targets of the co-factor β-catenin, and those of the transcription factor TBX3, in human colorectal cancer cells. The ICEBERG datasets allow benchmarking of individual replicates, comparing the performance of peak calling and replication approaches, and expose the arbitrary nature of strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG establishes a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that underlie novel mechanisms of colorectal cancer progression.
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Affiliation(s)
- Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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43
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Romero P, Richart L, Aflaki S, Petitalot A, Burton M, Michaud A, Masliah-Planchon J, Kuhnowski F, Le Cam S, Baliñas-Gavira C, Méaudre C, Luscan A, Hamza A, Legoix P, Vincent-Salomon A, Wassef M, Holoch D, Margueron R. EZH2 mutations in follicular lymphoma distort H3K27me3 profiles and alter transcriptional responses to PRC2 inhibition. Nat Commun 2024; 15:3452. [PMID: 38658543 PMCID: PMC11043461 DOI: 10.1038/s41467-024-47701-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
Mutations in chromatin regulators are widespread in cancer. Among them, the histone H3 lysine 27 methyltransferase Polycomb Repressive Complex 2 (PRC2) shows distinct alterations according to tumor type. This specificity is poorly understood. Here, we model several PRC2 alterations in one isogenic system to reveal their comparative effects. Focusing then on lymphoma-associated EZH2 mutations, we show that Ezh2Y641F induces aberrant H3K27 methylation patterns even without wild-type Ezh2, which are alleviated by partial PRC2 inhibition. Remarkably, Ezh2Y641F rewires the response to PRC2 inhibition, leading to induction of antigen presentation genes. Using a unique longitudinal follicular lymphoma cohort, we further link EZH2 status to abnormal H3K27 methylation. We also uncover unexpected variability in the mutational landscape of successive biopsies, pointing to frequent co-existence of different clones and cautioning against stratifying patients based on single sampling. Our results clarify how oncogenic PRC2 mutations disrupt chromatin and transcription, and the therapeutic vulnerabilities this creates.
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Affiliation(s)
- Pierre Romero
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
- Institut Curie, Department of Pathology, Paris Sciences et Lettres Research University, Paris, France
| | - Laia Richart
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Setareh Aflaki
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Ambre Petitalot
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Megan Burton
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Audrey Michaud
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Julien Masliah-Planchon
- Institut Curie, Pharmacogenetics Unit, Department of Genetics, Paris Sciences et Lettres Research University, Paris, France
| | - Frédérique Kuhnowski
- Institut Curie, Department of Clinical Hematology, Paris Sciences et Lettres Research University, Paris, France
| | - Samuel Le Cam
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Carlos Baliñas-Gavira
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Céline Méaudre
- Institut Curie, Department of Pathology, Paris Sciences et Lettres Research University, Paris, France
| | - Armelle Luscan
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Abderaouf Hamza
- Institut Curie, Pharmacogenetics Unit, Department of Genetics, Paris Sciences et Lettres Research University, Paris, France
| | - Patricia Legoix
- Institut Curie, Genomics of Excellence (ICGex) Platform, Paris Sciences et Lettres Research University, Paris, France
| | - Anne Vincent-Salomon
- Institut Curie, Department of Pathology, Paris Sciences et Lettres Research University, Paris, France
| | - Michel Wassef
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Daniel Holoch
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France.
| | - Raphaël Margueron
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France.
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44
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Boddu PC, Gupta AK, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer JT, Chandhok NS, King D, Nannya Y, Ogawa S, Lin H, Simon MD, Dray E, Kupfer GM, Verma A, Neugebauer KM, Pillai MM. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Mol Cell 2024; 84:1475-1495.e18. [PMID: 38521065 PMCID: PMC11061666 DOI: 10.1016/j.molcel.2024.02.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/26/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.
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Affiliation(s)
- Prajwal C Boddu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Abhishek K Gupta
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Rahul Roy
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Bárbara De La Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Anne Olazabal-Herrero
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Namrata S Chandhok
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Darren King
- Section of Hematology and Medical Oncology, Department of Internal Medicine and Rogel Cancer Center, University of Michigan Health, Ann Arbor, MI, USA
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Haifan Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Gary M Kupfer
- Department of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Amit Verma
- Division of Hemato-Oncology, Department of Medicine and Department of Developmental and Molecular Biology, Albert Einstein-Montefiore Cancer Center, New York, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA
| | - Manoj M Pillai
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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45
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Freie B, Carroll PA, Varnum-Finney BJ, Ramsey EL, Ramani V, Bernstein I, Eisenman RN. A germline point mutation in the MYC-FBW7 phosphodegron initiates hematopoietic malignancies. Genes Dev 2024; 38:253-272. [PMID: 38565249 PMCID: PMC11065175 DOI: 10.1101/gad.351292.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
Oncogenic activation of MYC in cancers predominantly involves increased transcription rather than coding region mutations. However, MYC-dependent lymphomas frequently acquire point mutations in the MYC phosphodegron, including at threonine 58 (T58), where phosphorylation permits binding via the FBW7 ubiquitin ligase triggering MYC degradation. To understand how T58 phosphorylation functions in normal cell physiology, we introduced an alanine mutation at T58 (T58A) into the endogenous c-Myc locus in the mouse germline. While MYC-T58A mice develop normally, lymphomas and myeloid leukemias emerge in ∼60% of adult homozygous T58A mice. We found that primitive hematopoietic progenitor cells from MYC-T58A mice exhibit aberrant self-renewal normally associated with hematopoietic stem cells (HSCs) and up-regulate a subset of MYC target genes important in maintaining stem/progenitor cell balance. In lymphocytes, genomic occupancy by MYC-T58A was increased at all promoters compared with WT MYC, while genes differentially expressed in a T58A-dependent manner were significantly more proximal to MYC-bound enhancers. MYC-T58A lymphocyte progenitors exhibited metabolic alterations and decreased activation of inflammatory and apoptotic pathways. Our data demonstrate that a single point mutation stabilizing MYC is sufficient to skew target gene expression, producing a profound gain of function in multipotential hematopoietic progenitors associated with self-renewal and initiation of lymphomas and leukemias.
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Affiliation(s)
- Brian Freie
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA;
| | - Patrick A Carroll
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | | | - Erin L Ramsey
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Vijay Ramani
- Gladstone Institute for Data Science and Biotechnology, University of California, San Francisco, San Francisco, California 94158, USA
| | - Irwin Bernstein
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Robert N Eisenman
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA;
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Shi W, Wasson LK, Dorr KM, Robbe ZL, Wilczewski CM, Hepperla AJ, Davis IJ, Seidman CE, Seidman JG, Conlon FL. CHD4 and SMYD1 repress common transcriptional programs in the developing heart. Development 2024; 151:dev202505. [PMID: 38619323 PMCID: PMC11112163 DOI: 10.1242/dev.202505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
Regulation of chromatin states is essential for proper temporal and spatial gene expression. Chromatin states are modulated by remodeling complexes composed of components that have enzymatic activities. CHD4 is the catalytic core of the nucleosome remodeling and deacetylase (NuRD) complex, which represses gene transcription. However, it remains to be determined how CHD4, a ubiquitous enzyme that remodels chromatin structure, functions in cardiomyocytes to maintain heart development. In particular, whether other proteins besides the NuRD components interact with CHD4 in the heart is controversial. Using quantitative proteomics, we identified that CHD4 interacts with SMYD1, a striated muscle-restricted histone methyltransferase that is essential for cardiomyocyte differentiation and cardiac morphogenesis. Comprehensive transcriptomic and chromatin accessibility studies of Smyd1 and Chd4 null embryonic mouse hearts revealed that SMYD1 and CHD4 repress a group of common genes and pathways involved in glycolysis, response to hypoxia, and angiogenesis. Our study reveals a mechanism by which CHD4 functions during heart development, and a previously uncharacterized mechanism regarding how SMYD1 represses cardiac transcription in the developing heart.
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Affiliation(s)
- Wei Shi
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lauren K. Wasson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine and Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Kerry M. Dorr
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zachary L. Robbe
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Caralynn M. Wilczewski
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Austin J. Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian J. Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine and Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Frank L. Conlon
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Peeters JGC, Silveria S, Ozdemir M, Ramachandran S, DuPage M. Increased EZH2 function in regulatory T cells promotes their capacity to suppress autoimmunity by driving effector differentiation prior to activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588284. [PMID: 38645261 PMCID: PMC11030251 DOI: 10.1101/2024.04.05.588284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The immunosuppressive function of regulatory T (Treg) cells is essential for maintaining immune homeostasis. Enhancer of zeste homolog 2 (EZH2), a histone H3 lysine 27 (H3K27) methyltransferase, plays a key role in maintaining Treg cell function upon CD28 co-stimulation, and Ezh2 deletion in Treg cells causes autoimmunity. Here we assessed whether increased EZH2 activity in Treg cells would improve Treg cell function. Using an Ezh2 gain-of-function mutation, Ezh2 Y641F , we found that Treg cells expressing Ezh2 Y641F displayed an increased effector Treg phenotype and were poised for improved homing to organ tissues. Expression of Ezh2 Y641F in Treg cells led to more rapid remission from autoimmunity. H3K27me3 profiling and transcriptomic analysis revealed a redistribution of H3K27me3, which prompted a gene expression profile in naïve Ezh2 Y641F Treg cells that recapitulated aspects of CD28-activated Ezh2 WT Treg cells. Altogether, increased EZH2 activity promotes the differentiation of effector Treg cells that can better suppress autoimmunity. Highlights EZH2 function promotes effector differentiation of Treg cells.EZH2 function promotes Treg cell migration to organ tissues.EZH2 function in Treg cells improves remission from autoimmunity.EZH2 function poises naïve Treg cells to adopt a CD28-activated phenotype.
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48
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Cathcart B, Cheedipudi SM, Rouhi L, Zhao Z, Gurha P, Marian AJ. DNA double-stranded breaks, a hallmark of aging, defined at the nucleotide resolution, are increased and associated with transcription in the cardiac myocytes in LMNA-cardiomyopathy. Cardiovasc Res 2024:cvae063. [PMID: 38577741 DOI: 10.1093/cvr/cvae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
AIMS An intrinsic feature of gene transcription is the formation of DNA superhelices near the transcription bubble, which are resolved upon induction of transient double-stranded breaks (DSBs) by topoisomerases. Unrepaired DSBs are pathogenic as they lead to cell cycle arrest, senescence, inflammation, and organ dysfunction. We posit that DSBs would be more prevalent at the genomic sites that are associated with gene expression. The objectives were to identify and characterize genome-wide DSBs at the nucleotide resolution and determine the association of DSBs with transcription in cardiac myocytes. METHODS AND RESULTS We identified the genome-wide DSBs in ∼1 million cardiac myocytes per heart in three wild-type and three myocyte-specific LMNA-deficient (Myh6-Cre:LmnaF/F) mice by END-Sequencing. The prevalence of DSBs was 0.8% and 2.2% in the wild-type and Myh6-Cre:LmnaF/F myocytes, respectively. The END-Seq signals were enriched for 8 and 6764 DSBs in the wild-type and Myh6-Cre:LmnaF/F myocytes, respectively (q < 0.05). The DSBs were preferentially localized to the gene regions, transcription initiation sites, cardiac transcription factor motifs, and the G quadruplex forming structures. Because LMNA regulates transcription through the lamin-associated domains (LADs), we defined the LADs in cardiac myocytes by a Cleavage Under Targets & Release Using Nuclease (CUT&RUN) assay (N = 5). On average there were 818 LADs per myocyte. Constitutive LADs (cLADs), defined as LADs that were shared by at least three genomes (N = 2572), comprised about a third of the mouse cardiac myocyte genomes. Transcript levels of the protein-coding genes located at the cLADs (N = 3975) were ∼16-fold lower than those at the non-LAD regions (N = ∼17 778). The prevalence of DSBs was higher in the non-LAD as compared to the cLAD regions. Likewise, DSBs were more common in the loss-of-LAD regions, defined as the genomic regions in the Myh6-Cre:LmnaF/F that were juxtaposed to the LAD regions in the wild-type myocytes. CONCLUSION To our knowledge, this is the first identification of the DSBs, at the nucleotide resolution in the cardiovascular system. The prevalence of DSBs was higher in the genomic regions associated with transcription. Because transcription is pervasive, DSBs are expected to be common and pathogenic in various states and aging.
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Affiliation(s)
- Benjamin Cathcart
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Sirisha M Cheedipudi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Leila Rouhi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics and School of Public Health, UTHealth, Houston, TX 77030, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Ali J Marian
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
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Yi C, Song H, Liang H, Ran Y, Tang J, Chen E, Li F, Fu L, Wang Y, Chen F, Wang Y, Ding Y, Xie Y. TBX3 reciprocally controls key trophoblast lineage decisions in villi during human placenta development in the first trimester. Int J Biol Macromol 2024; 263:130220. [PMID: 38368983 DOI: 10.1016/j.ijbiomac.2024.130220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/20/2024]
Abstract
Human trophoblastic lineage development is intertwined with placental development and pregnancy outcomes, but the regulatory mechanisms underpinning this process remain inadequately understood. In this study, based on single-nuclei RNA sequencing (snRNA-seq) analysis of the human early maternal-fetal interface, we compared the gene expression pattern of trophoblast at different developmental stages. Our findings reveal a predominant upregulation of TBX3 during the transition from villous cytotrophoblast (VCT) to syncytiotrophoblast (SCT), but downregulation of TBX3 as VCT progresses into extravillous trophoblast cells (EVT). Immunofluorescence analysis verified the primary expression of TBX3 in SCT, partial expression in MKi67-positive VCT, and absence in HLA-G-positive EVT, consistent with our snRNA-seq results. Using immortalized trophoblastic cell lines (BeWo and HTR8/SVneo) and human primary trophoblast stem cells (hTSCs), we observed that TBX3 knockdown impedes SCT formation through RAS-MAPK signaling, while TBX3 overexpression disrupts the cytoskeleton structure of EVT and hinders EVT differentiation by suppressing FAK signaling. In conclusion, our study suggests that the spatiotemporal expression of TBX3 plays a critical role in regulating trophoblastic lineage development via distinct signaling pathways. This underscores TBX3 as a key determinant during hemochorial placental development.
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Affiliation(s)
- Cen Yi
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Honglan Song
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Hongxiu Liang
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Yujie Ran
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jing Tang
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Enxiang Chen
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Fangfang Li
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Lijuan Fu
- Department of Gynecology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China 400021; Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, School of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 400016, China; Department of Basic Medical Sciences, Changsha Medical University, Hunan 410219, China
| | - Yaqi Wang
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Fengming Chen
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, 410129, China
| | - Yingxiong Wang
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Yubin Ding
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Youlong Xie
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China.
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50
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Swiatlowska P, Iskratsch T. Cardiovascular Mechano-Epigenetics: Force-Dependent Regulation of Histone Modifications and Gene Regulation. Cardiovasc Drugs Ther 2024; 38:215-222. [PMID: 36653625 PMCID: PMC10959834 DOI: 10.1007/s10557-022-07422-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/28/2022] [Indexed: 01/19/2023]
Abstract
The local mechanical microenvironment impacts on the cell behavior. In the cardiovascular system, cells in both the heart and the vessels are exposed to continuous blood flow, blood pressure, stretching forces, and changing extracellular matrix stiffness. The force-induced signals travel all the way to the nucleus regulating epigenetic changes such as chromatin dynamics and gene expression. Mechanical cues are needed at the very early stage for a faultless embryological development, while later in life, aberrant mechanical signaling can lead to a range of pathologies, including diverse cardiovascular diseases. Hence, an investigation of force-generated epigenetic alteration at different time scales is needed to understand fully the phenotypic changes in disease onset and progression. That being so, cardiovascular mechano-epigenetics emerges as an attractive field of study. Given the rapid advances in this emergent field of research, this short review aims to provide an analysis of the state of knowledge of force-induced epigenetic changes in the cardiovascular field.
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Affiliation(s)
- Pamela Swiatlowska
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Thomas Iskratsch
- School of Engineering and Materials Science, Queen Mary University of London, London, UK.
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