1
|
Shastry S, Samal D, Pethe P. Histone H2A deubiquitinase BAP1 is essential for endothelial cell differentiation from human pluripotent stem cells. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00935-x. [PMID: 38976206 DOI: 10.1007/s11626-024-00935-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/25/2024] [Indexed: 07/09/2024]
Abstract
Polycomb group proteins (PcGs) add repressive post translational histone modifications such as H2AK119ub1, and histone H2A deubiquitinases remove it. Mice lacking histone H2A deubiquitinases such as Usp16 and Bap1 die in embryonic stage, while mice lacking Usp3, Mysm1, Usp12, and Usp21 have been shown to be deficient in hematopoietic lineage differentiation, cell cycle regulation, and DNA repair. Thus, it is likely that histone deubiquitinases may also be required for human endothelial cell differentiation; however, there are no reports about the role of histone H2A deubiquitinase BAP1 in human endothelial cell development. We differentiated human pluripotent stem cells into the endothelial lineage which expressed stable inducible shRNA against BAP1. Our results show that BAP1 is required for human endothelial cell differentiation.
Collapse
Affiliation(s)
- Shruti Shastry
- Symbiosis Centre for Stem Cell Research (SCSCR), Symbiosis International (Deemed University), Pune, India
- Worcester Polytechnic Institute (WPI), Boston, USA
| | - Dharitree Samal
- Symbiosis Centre for Stem Cell Research (SCSCR), Symbiosis International (Deemed University), Pune, India
| | - Prasad Pethe
- Symbiosis Centre for Stem Cell Research (SCSCR), Symbiosis International (Deemed University), Pune, India.
| |
Collapse
|
2
|
Dagnino L. Ubiquitylated histone H2A: a molecular Jekyll and Hyde in the epidermis. Tissue Barriers 2024; 12:2236007. [PMID: 37459858 DOI: 10.1080/21688370.2023.2236007] [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: 07/03/2023] [Accepted: 07/08/2023] [Indexed: 07/23/2024] Open
Abstract
The epidermis of the skin provides a barrier between the organism and the external environment. It is constantly subjected to physical and chemical insults, and thus susceptible to wounding and to neoplastic transformation. Long-lasting epigenetic modifications in epidermal stem cells are now shown to link responses to skin injuries with cell priming for carcinoma development, through regulation of histone H2A ubiquitylation.
Collapse
Affiliation(s)
- Lina Dagnino
- Department of Physiology and Pharmacology, Department of Oncology, London Health Research Institute, Children's Health Research Institute, The University of Western Ontario, London, Ontario, Canada
| |
Collapse
|
3
|
Chen K, Dong Y, He G, He X, Pan M, Huang X, Yu X, Xia J. UBTF mediates activation of L3MBTL2 to suppress NISCH expression through histone H2AK119 monoubiquitination modification in breast cancer. Clin Exp Metastasis 2024:10.1007/s10585-024-10299-x. [PMID: 38935187 DOI: 10.1007/s10585-024-10299-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2) has been related to transcriptional inhibition and chromatin compaction. Nevertheless, the biological functions and mechanisms of L3MBTL2 are undefined in breast cancer (BRCA). Here, we revealed that L3MBTL2 is responsible for the decline of Nischarin (NISCH), a well-known tumor suppressor, in BRCA, and explored the detailed mechanism. Knockdown of L3MBTL2 reduced monoubiquitination of histone H2A at lysine-119 (H2AK119ub), leading to reduced binding to the NISCH promoter and increased expression of NISCH. Meanwhile, the knockdown of L3MBTL2 decreased proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) of BRCA cells, and increased apoptosis, which were abated by NISCH knockdown. Nucleolar transcription factor 1 (UBTF) induced the transcription of L3MBTL2 in BRCA, and the suppressing effects of UBTF silencing on EMT in BRCA cells were also reversed by NISCH knockdown. Knockdown of UBTF slowed tumor progression and attenuated lung tumor infiltration, whereas simultaneous knockdown of NISCH accelerated EMT and increased tumor lung metastasis. Taken together, our results show that L3MBTL2, transcriptionally activated by UBTF, exerts oncogenic functions in BRCA, by catalyzing H2AK119Ub and reducing expression of NISCH.
Collapse
Affiliation(s)
- Kun Chen
- Department of Technology and Social Services, Dazhou Vocational College of Chinese Medicine, Tongchuan District, Vocational Education Park, Dazhou, Sichuan, 635000, P.R. China
| | - Yun Dong
- Department of Traditional Chinese Medicine, Dazhou Vocational College of Chinese Medicine, Dazhou, Sichuan, 635000, P.R. China
| | - Gaojian He
- Dean's office, Dazhou Vocational College of Chinese Medicine, Dazhou, Sichuan, 635000, P.R. China
| | - Xuefeng He
- Department of Technology and Social Services, Dazhou Vocational College of Chinese Medicine, Tongchuan District, Vocational Education Park, Dazhou, Sichuan, 635000, P.R. China
| | - Meitong Pan
- Department of Technology and Social Services, Dazhou Vocational College of Chinese Medicine, Tongchuan District, Vocational Education Park, Dazhou, Sichuan, 635000, P.R. China
| | - Xuemei Huang
- Department of Oncology and Hematology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, 646099, P.R. China
| | - Xiaolan Yu
- Department of Obstetrics and Gynecology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, 646099, P.R. China.
| | - Jiyi Xia
- Department of Technology and Social Services, Dazhou Vocational College of Chinese Medicine, Tongchuan District, Vocational Education Park, Dazhou, Sichuan, 635000, P.R. China.
- Dazhou Chinese medicine research and development center, Dazhou, Sichuan, 635000, P.R. China.
| |
Collapse
|
4
|
West EC, Chiappetta M, Mattingly AA, Congedo MT, Evangelista J, Campanella A, Sassorossi C, Flamini S, Rossi T, Pistoni M, Abenavoli L, Margaritora S, Lococo F, Boccuto L. BRCA1-associated protein 1: Tumor predisposition syndrome and Kury-Isidor syndrome, from genotype-phenotype correlation to clinical management. Clin Genet 2024; 105:589-595. [PMID: 38506155 DOI: 10.1111/cge.14507] [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: 01/27/2024] [Accepted: 02/07/2024] [Indexed: 03/21/2024]
Abstract
The BAP1 tumor suppressor gene encodes a deubiquitinase enzyme involved in several cellular activities, including DNA repair and apoptosis. Germline pathogenic variants in BAP1 have been associated with heritable conditions including BAP1 tumor predisposition syndrome 1 (BAP1-TPDS1) and a neurodevelopmental disorder known as Kury-Isidor syndrome (KURIS). Both these conditions are caused by monoallelic, dominant alterations of BAP1 but have never been reported in the same subject or family, suggesting a mutually exclusive genotype-phenotype correlation. This distinction is extremely important considering the early onset and aggressive nature of the types of cancer reported in individuals with TPDS1. Genetic counseling in subjects with germline BAP1 variants is fundamental to predicting the effect of the variant and the expected phenotype, assessing the potential risk of developing cancer for the tested subject and the family members who may carry the same variant and providing the multidisciplinary clinical team with the proper information to establish precise surveillance and management protocols.
Collapse
Affiliation(s)
- Elizabeth Casey West
- Healthcare Genetics and Genomics, School of Nursing, Clemson University, Clemson, South Carolina, USA
| | - Marco Chiappetta
- Thoracic Surgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Aubrey Anne Mattingly
- Healthcare Genetics and Genomics, School of Nursing, Clemson University, Clemson, South Carolina, USA
| | - Maria Teresa Congedo
- Thoracic Surgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Jessica Evangelista
- Thoracic Surgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Annalisa Campanella
- Thoracic Surgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Carolina Sassorossi
- Thoracic Surgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Sara Flamini
- Thoracic Surgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Teresa Rossi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Mariaelena Pistoni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Ludovico Abenavoli
- Department of Health Sciences, University "Magna Græcia", Catanzaro, Italy
| | - Stefano Margaritora
- Thoracic Surgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Catholic University of the Sacred Heart, Rome, Italy
| | - Filippo Lococo
- Thoracic Surgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Catholic University of the Sacred Heart, Rome, Italy
| | - Luigi Boccuto
- Healthcare Genetics and Genomics, School of Nursing, Clemson University, Clemson, South Carolina, USA
| |
Collapse
|
5
|
Ni S, Takada Y, Ando T, Yu S, Yamashita Y, Takahashi Y, Sawada M, Oba M, Itoh Y, Suzuki T. Identification of a novel histone H2A mono-ubiquitination-inhibiting cell-active small molecule. Bioorg Med Chem Lett 2024; 105:129759. [PMID: 38636717 DOI: 10.1016/j.bmcl.2024.129759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Histone H2A mono-ubiquitination plays important roles in epigenetic gene expression and is also involved in tumorigenesis. Small molecules controlling H2A ubiquitination are of interest as potential chemical tools and anticancer drugs. To identify novel small molecule inhibitors of H2A ubiquitination, we synthesized and evaluated several compounds designed based on PRT4165 (1), which is a reported histone ubiquitin ligase RING1A inhibitor. We found that compound 11b strongly inhibited the viability and reduced histone H2A mono-ubiquitination in human osteosarcoma U2OS cells. Therefore, compound 11b is a promising lead compound for the development of H2A histone ubiquitination-inhibiting small molecules.
Collapse
Affiliation(s)
- Siyao Ni
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuri Takada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takaaki Ando
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Shengwang Yu
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | | | - Yukari Takahashi
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Miho Sawada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Makoto Oba
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukihiro Itoh
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Takayoshi Suzuki
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| |
Collapse
|
6
|
Guo J, Zou Z, Dou X, Zhao X, Wang Y, Wei L, Pi Y, Wang Y, He C, Guo S. Zebrafish Mbd5 binds to RNA m5C and regulates histone deubiquitylation and gene expression in development metabolism and behavior. Nucleic Acids Res 2024; 52:4257-4275. [PMID: 38366571 PMCID: PMC11077058 DOI: 10.1093/nar/gkae093] [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: 08/19/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
Complex biological processes are regulated by both genetic and epigenetic programs. One class of epigenetic modifications is methylation. Evolutionarily conserved methyl-CpG-binding domain (MBD)-containing proteins are known as readers of DNA methylation. MBD5 is linked to multiple human diseases but its mechanism of action remains unclear. Here we report that the zebrafish Mbd5 does not bind to methylated DNA; but rather, it directly binds to 5-methylcytosine (m5C)-modified mRNAs and regulates embryonic development, erythrocyte differentiation, iron metabolism, and behavior. We further show that Mbd5 facilitates removal of the monoubiquitin mark at histone H2A-K119 through an interaction with the Polycomb repressive deubiquitinase (PR-DUB) complex in vivo. The direct target genes of Mbd5 are enriched with both RNA m5C and H2A-K119 ubiquitylation signals. Together, we propose that zebrafish MBD5 is an RNA m5C reader that potentially links RNA methylation to histone modification and in turn transcription regulation in vivo.
Collapse
Affiliation(s)
- Jianhua Guo
- State Key Laboratory of Genetic Engineering, National Demonstration Center for Experimental Biology Education, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhongyu Zou
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaoyang Dou
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Xiang Zhao
- Department of Bioengineering and Therapeutic Sciences, Programs in Human Genetics and Biological Sciences, University of California, San Francisco, CA 94143, USA
| | - Yimin Wang
- Department of Neurology, Children's Hospital of Fudan University, National Children's Medical Center, No. 399, Wanyuan Road, Minhang District, Shanghai, China
| | - Liqiang Wei
- State Key Laboratory of Genetic Engineering, National Demonstration Center for Experimental Biology Education, School of Life Sciences, Fudan University, Shanghai, China
- Department of Bioengineering and Therapeutic Sciences, Programs in Human Genetics and Biological Sciences, University of California, San Francisco, CA 94143, USA
| | - Yan Pi
- State Key Laboratory of Genetic Engineering, National Demonstration Center for Experimental Biology Education, School of Life Sciences, Fudan University, Shanghai, China
- Department of Bioengineering and Therapeutic Sciences, Programs in Human Genetics and Biological Sciences, University of California, San Francisco, CA 94143, USA
| | - Yi Wang
- Department of Neurology, Children's Hospital of Fudan University, National Children's Medical Center, No. 399, Wanyuan Road, Minhang District, Shanghai, China
| | - Chuan He
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Su Guo
- Department of Bioengineering and Therapeutic Sciences, Programs in Human Genetics and Biological Sciences, University of California, San Francisco, CA 94143, USA
| |
Collapse
|
7
|
Shi TH, Sugishita H, Gotoh Y. Crosstalk within and beyond the Polycomb repressive system. J Cell Biol 2024; 223:e202311021. [PMID: 38506728 PMCID: PMC10955045 DOI: 10.1083/jcb.202311021] [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: 11/06/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
The development of multicellular organisms depends on spatiotemporally controlled differentiation of numerous cell types and their maintenance. To generate such diversity based on the invariant genetic information stored in DNA, epigenetic mechanisms, which are heritable changes in gene function that do not involve alterations to the underlying DNA sequence, are required to establish and maintain unique gene expression programs. Polycomb repressive complexes represent a paradigm of epigenetic regulation of developmentally regulated genes, and the roles of these complexes as well as the epigenetic marks they deposit, namely H3K27me3 and H2AK119ub, have been extensively studied. However, an emerging theme from recent studies is that not only the autonomous functions of the Polycomb repressive system, but also crosstalks of Polycomb with other epigenetic modifications, are important for gene regulation. In this review, we summarize how these crosstalk mechanisms have improved our understanding of Polycomb biology and how such knowledge could help with the design of cancer treatments that target the dysregulated epigenome.
Collapse
Affiliation(s)
- Tianyi Hideyuki Shi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroki Sugishita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
8
|
Nie H, Kong X, Song X, Guo X, Li Z, Fan C, Zhai B, Yang X, Wang Y. Roles of histone post-translational modifications in meiosis†. Biol Reprod 2024; 110:648-659. [PMID: 38224305 DOI: 10.1093/biolre/ioae011] [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: 09/11/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024] Open
Abstract
Histone post-translational modifications, such as phosphorylation, methylation, acetylation, and ubiquitination, play vital roles in various chromatin-based cellular processes. Meiosis is crucial for organisms that depend on sexual reproduction to produce haploid gametes, during which chromatin undergoes intricate conformational changes. An increasing body of evidence is clarifying the essential roles of histone post-translational modifications during meiotic divisions. In this review, we concentrate on the post-translational modifications of H2A, H2B, H3, and H4, as well as the linker histone H1, that are required for meiosis, and summarize recent progress in understanding how these modifications influence diverse meiotic events. Finally, challenges and exciting open questions for future research in this field are discussed. Summary Sentence Diverse histone post-translational modifications exert important effects on the meiotic cell cycle and these "histone codes" in meiosis might lead to the development of novel therapeutic strategies against reproductive diseases.
Collapse
Affiliation(s)
- Hui Nie
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xueyu Kong
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiaoyu Song
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiaoyu Guo
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Zhanyu Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Cunxian Fan
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Binyuan Zhai
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiao Yang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Ying Wang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| |
Collapse
|
9
|
Del Vecchio A, Mulé P, Fernández-Pérez D, Amato S, Lattanzi G, Zanotti M, Rustichelli S, Pivetti S, Oldani P, Mariani A, Iommazzo F, Koseki H, Facciotti F, Tamburri S, Ferrari KJ, Pasini D. PCGF6 controls murine Tuft cell differentiation via H3K9me2 modification independently of Polycomb repression. Dev Cell 2024; 59:368-383.e7. [PMID: 38228142 DOI: 10.1016/j.devcel.2023.12.015] [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: 03/27/2023] [Revised: 10/01/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024]
Abstract
Cell fate is determined by specific transcription programs that are essential for tissue homeostasis and regeneration. The E3-ligases RING1A and B represent the core activity of the Polycomb repressive complex 1 (PRC1) that deposits repressive histone H2AK119 mono-ubiquitination (H2AK119ub1), which is essential for mouse intestinal homeostasis by preserving stem cell functions. However, the specific role of different PRC1 forms, which are defined by the six distinct PCGF1-6 paralogs, remains largely unexplored in vivo. We report that PCGF6 regulates mouse intestinal Tuft cell differentiation independently of H2AK119ub1 deposition. We show that PCGF6 chromatin occupancy expands outside Polycomb repressive domains, associating with unique promoter and distal regulatory elements. This occurs in the absence of RING1A/B and involves MGA-mediated E-BOX recognition and specific H3K9me2 promoter deposition. PCGF6 inactivation induces an epithelial autonomous accumulation of Tuft cells that was not phenocopied by RING1A/B loss. This involves direct PCGF6 association with a Tuft cell differentiation program that identified Polycomb-independent properties of PCGF6 in adult tissues homeostasis.
Collapse
Affiliation(s)
- Annachiara Del Vecchio
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Patrizia Mulé
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Daniel Fernández-Pérez
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simona Amato
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Georgia Lattanzi
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Marika Zanotti
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Samantha Rustichelli
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Silvia Pivetti
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Paola Oldani
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Andrea Mariani
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Fabiola Iommazzo
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Haruhiko Koseki
- RIKEN Centre for Integrative Medical Sciences, Laboratory for Developmental Genetics, 1-7-22 Suehiuro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Federica Facciotti
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza, 2, 20126 Milan, Italy
| | - Simone Tamburri
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì 8, 20142 Milan, Italy
| | - Karin J Ferrari
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Diego Pasini
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì 8, 20142 Milan, Italy.
| |
Collapse
|
10
|
Luan R, He M, Li H, Bai Y, Wang A, Sun G, Zhou B, Wang M, Wang C, Wang S, Zeng K, Feng J, Lin L, Wei Y, Kato S, Zhang Q, Zhao Y. MYSM1 acts as a novel co-activator of ERα to confer antiestrogen resistance in breast cancer. EMBO Mol Med 2024; 16:10-39. [PMID: 38177530 PMCID: PMC10883278 DOI: 10.1038/s44321-023-00003-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] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 01/06/2024] Open
Abstract
Endocrine resistance is a crucial challenge in estrogen receptor alpha (ERα)-positive breast cancer (BCa). Aberrant alteration in modulation of E2/ERα signaling pathway has emerged as the putative contributor for endocrine resistance in BCa. Herein, we demonstrate that MYSM1 as a deubiquitinase participates in modulating ERα action via histone and non-histone deubiquitination. MYSM1 is involved in maintenance of ERα stability via ERα deubiquitination. MYSM1 regulates relevant histone modifications on cis regulatory elements of ERα-regulated genes, facilitating chromatin decondensation. MYSM1 is highly expressed in clinical BCa samples. MYSM1 depletion attenuates BCa-derived cell growth in xenograft models and increases the sensitivity of antiestrogen agents in BCa cells. A virtual screen shows that the small molecule Imatinib could potentially interact with catalytic MPN domain of MYSM1 to inhibit BCa cell growth via MYSM1-ERα axis. These findings clarify the molecular mechanism of MYSM1 as an epigenetic modifier in regulation of ERα action and provide a potential therapeutic target for endocrine resistance in BCa.
Collapse
Affiliation(s)
- Ruina Luan
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Mingcong He
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Hao Li
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Yu Bai
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Anqi Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
- First Clinical Medical College, China Medical University, 110001, Shenyang City, Liaoning Province, China
| | - Ge Sun
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Baosheng Zhou
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Manlin Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Chunyu Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Shengli Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Kai Zeng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Jianwei Feng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Lin Lin
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Yuntao Wei
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, 110042, Shenyang City, Liaoning Province, China
| | - Shigeaki Kato
- Graduate School of Life Science and Engineering, Iryo Sosei University, Iino, Chuo-dai, Iwaki, Fukushima, 9708551, Japan
- Research Institute of Innovative Medicine, Tokiwa Foundation, Iwaki, Fukushima, Japan
| | - Qiang Zhang
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, 110042, Shenyang City, Liaoning Province, China.
| | - Yue Zhao
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China.
| |
Collapse
|
11
|
de Potter B, Raas MWD, Seidl MF, Verrijzer CP, Snel B. Uncoupled evolution of the Polycomb system and deep origin of non-canonical PRC1. Commun Biol 2023; 6:1144. [PMID: 37949928 PMCID: PMC10638273 DOI: 10.1038/s42003-023-05501-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: 07/10/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Polycomb group proteins, as part of the Polycomb repressive complexes, are essential in gene repression through chromatin compaction by canonical PRC1, mono-ubiquitylation of histone H2A by non-canonical PRC1 and tri-methylation of histone H3K27 by PRC2. Despite prevalent models emphasizing tight functional coupling between PRC1 and PRC2, it remains unclear whether this paradigm indeed reflects the evolution and functioning of these complexes. Here, we conduct a comprehensive analysis of the presence or absence of cPRC1, nPRC1 and PRC2 across the entire eukaryotic tree of life, and find that both complexes were present in the Last Eukaryotic Common Ancestor (LECA). Strikingly, ~42% of organisms contain only PRC1 or PRC2, showing that their evolution since LECA is largely uncoupled. The identification of ncPRC1-defining subunits in unicellular relatives of animals and fungi suggests ncPRC1 originated before cPRC1, and we propose a scenario for the evolution of cPRC1 from ncPRC1. Together, our results suggest that crosstalk between these complexes is a secondary development in evolution.
Collapse
Affiliation(s)
- Bastiaan de Potter
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, Utrecht, Netherlands
- Hubrecht institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, Netherlands
| | - Maximilian W D Raas
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, Utrecht, Netherlands
- Hubrecht institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, Netherlands
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, Utrecht, Netherlands
| | - C Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, Utrecht, Netherlands.
| |
Collapse
|
12
|
Liu Y, Hu G, Yang S, Yao M, Liu Z, Yan C, Wen Y, Ping W, Wang J, Song Y, Dong X, Pan G, Yao H. Functional dissection of PRC1 subunits RYBP and YAF2 during neural differentiation of embryonic stem cells. Nat Commun 2023; 14:7164. [PMID: 37935677 PMCID: PMC10630410 DOI: 10.1038/s41467-023-42507-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/12/2023] [Indexed: 11/09/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) comprises two different complexes: CBX-containing canonical PRC1 (cPRC1) and RYBP/YAF2-containing variant PRC1 (vPRC1). RYBP-vPRC1 or YAF2-vPRC1 catalyzes H2AK119ub through a positive-feedback model; however, whether RYBP and YAF2 have different regulatory functions is still unclear. Here, we show that the expression of RYBP and YAF2 decreases and increases, respectively, during neural differentiation of embryonic stem cells (ESCs). Rybp knockout impairs neural differentiation by activating Wnt signaling and derepressing nonneuroectoderm-associated genes. However, Yaf2 knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 cotargeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. Taken together, this study reveals that RYBP and YAF2 function differentially in regulating mESC neural differentiation.
Collapse
Affiliation(s)
- Yanjiang Liu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gongcheng Hu
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Shengxiong Yang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Mingze Yao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Zicong Liu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Chenghong Yan
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yulin Wen
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wangfang Ping
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Juehan Wang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yawei Song
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiaotao Dong
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Guangjin Pan
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongjie Yao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
13
|
Feng M, Wang J, Li K, Nakamura F. UBE2A/B is the trans-acting factor mediating mechanotransduction and contact inhibition. Biochem J 2023; 480:1659-1674. [PMID: 37818922 DOI: 10.1042/bcj20230208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
Mechanotransduction and contact inhibition (CI) control gene expression to regulate proliferation, differentiation, and even tumorigenesis of cells. However, their downstream trans-acting factors (TAFs) are not well known due to a lack of a high-throughput method to quantitatively detect them. Here, we developed a method to identify TAFs on the cis-acting sequences that reside in open chromatin or DNaseI-hypersensitive sites (DHSs) and to detect nucleocytoplasmic shuttling TAFs using computational and experimental screening. The DHS-proteomics revealed over 1000 potential mechanosensing TAFs and UBE2A/B (Ubiquitin-conjugating enzyme E2 A) was experimentally identified as a force- and CI-dependent nucleocytoplasmic shuttling TAF. We found that translocation of YAP/TAZ and UBE2A/B are distinctively regulated by inhibition of myosin contraction, actin-polymerization, and CI depending on cell types. Next-generation sequence analysis revealed many downstream genes including YAP are transcriptionally regulated by ubiquitination of histone by UBE2A/B. Our results suggested a YAP-independent mechanotransduction and CI pathway mediated by UBE2A/B.
Collapse
Affiliation(s)
- Mingwei Feng
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jiale Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Kangjing Li
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Fumihiko Nakamura
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| |
Collapse
|
14
|
Duong P, Ramesh R, Schneider A, Won S, Cooper AJ, Svaren J. Modulation of Schwann cell homeostasis by the BAP1 deubiquitinase. Glia 2023; 71:1466-1480. [PMID: 36790040 PMCID: PMC10073320 DOI: 10.1002/glia.24351] [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: 09/01/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/16/2023]
Abstract
Schwann cell programming during myelination involves transcriptional networks that activate gene expression but also repress genes that are active in neural crest/embryonic differentiation of Schwann cells. We previously found that a Schwann cell-specific deletion of the EED subunit of the Polycomb Repressive Complex (PRC2) led to inappropriate activation of many such genes. Moreover, some of these genes become re-activated in the pro-regenerative response of Schwann cells to nerve injury, and we found premature activation of the nerve injury program in a Schwann cell-specific knockout of Eed. Polycomb-associated histone modifications include H3K27 trimethylation formed by PRC2 and H2AK119 monoubiquitination (H2AK119ub1), deposited by Polycomb repressive complex 1 (PRC1). We recently found dynamic regulation of H2AK119ub1 in Schwann cell genes after injury. Therefore, we hypothesized that H2AK119 deubiquitination modulates the dynamic polycomb repression of genes involved in Schwann cell maturation. To determine the role of H2AK119 deubiquitination, we generated a Schwann cell-specific knockout of the H2AK119 deubiquitinase Bap1 (BRCA1-associated protein). We found that loss of Bap1 causes tomacula formation, decreased axon diameters and eventual loss of myelinated axons. The gene expression changes are accompanied by redistribution of H2AK119ub1 and H3K27me3 modifications to extragenic sites throughout the genome. BAP1 interacts with OGT in the PR-DUB complex, and our data suggest that the PR-DUB complex plays a multifunctional role in repression of the injury program. Overall, our results indicate Bap1 is required to restrict the spread of polycomb-associated histone modifications in Schwann cells and to promote myelin homeostasis in peripheral nerve.
Collapse
Affiliation(s)
- Phu Duong
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Raghu Ramesh
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Comparative Biomedical Sciences Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrew Schneider
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Seongsik Won
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aaron J Cooper
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John Svaren
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department Of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
15
|
Pathania AS. Crosstalk between Noncoding RNAs and the Epigenetics Machinery in Pediatric Tumors and Their Microenvironment. Cancers (Basel) 2023; 15:2833. [PMID: 37345170 DOI: 10.3390/cancers15102833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
According to the World Health Organization, every year, an estimated 400,000+ new cancer cases affect children under the age of 20 worldwide. Unlike adult cancers, pediatric cancers develop very early in life due to alterations in signaling pathways that regulate embryonic development, and environmental factors do not contribute much to cancer development. The highly organized complex microenvironment controlled by synchronized gene expression patterns plays an essential role in the embryonic stages of development. Dysregulated development can lead to tumor initiation and growth. The low mutational burden in pediatric tumors suggests the predominant role of epigenetic changes in driving the cancer phenotype. However, one more upstream layer of regulation driven by ncRNAs regulates gene expression and signaling pathways involved in the development. Deregulation of ncRNAs can alter the epigenetic machinery of a cell, affecting the transcription and translation profiles of gene regulatory networks required for cellular proliferation and differentiation during embryonic development. Therefore, it is essential to understand the role of ncRNAs in pediatric tumor development to accelerate translational research to discover new treatments for childhood cancers. This review focuses on the role of ncRNA in regulating the epigenetics of pediatric tumors and their tumor microenvironment, the impact of their deregulation on driving pediatric tumor progress, and their potential as effective therapeutic targets.
Collapse
Affiliation(s)
- Anup S Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
16
|
Zhou H, Feng W, Yu J, Shafiq TA, Paulo JA, Zhang J, Luo Z, Gygi SP, Moazed D. SENP3 and USP7 regulate Polycomb-rixosome interactions and silencing functions. Cell Rep 2023; 42:112339. [PMID: 37014752 PMCID: PMC10777863 DOI: 10.1016/j.celrep.2023.112339] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/14/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
The rixosome and PRC1 silencing complexes are associated with deSUMOylating and deubiquitinating enzymes, SENP3 and USP7, respectively. How deSUMOylation and deubiquitylation contribute to rixosome- and Polycomb-mediated silencing is not fully understood. Here, we show that the enzymatic activities of SENP3 and USP7 are required for silencing of Polycomb target genes. SENP3 deSUMOylates several rixosome subunits, and this activity is required for association of the rixosome with PRC1. USP7 associates with canonical PRC1 (cPRC1) and deubiquitinates the chromodomain subunits CBX2 and CBX4, and inhibition of USP activity results in disassembly of cPRC1. Finally, both SENP3 and USP7 are required for Polycomb- and rixosome-dependent silencing at an ectopic reporter locus. These findings demonstrate that SUMOylation and ubiquitination regulate the assembly and activities of the rixosome and Polycomb complexes and raise the possibility that these modifications provide regulatory mechanisms that may be utilized during development or in response to environmental challenges.
Collapse
Affiliation(s)
- Haining Zhou
- Howard Hughes Medical Institute, Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Wenzhi Feng
- Howard Hughes Medical Institute, Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Juntao Yu
- Howard Hughes Medical Institute, Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Tiasha A Shafiq
- Howard Hughes Medical Institute, Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jiuchun Zhang
- Initiative for Genome Editing and Neurodegeneration, Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Zhenhua Luo
- Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Steven P Gygi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Danesh Moazed
- Howard Hughes Medical Institute, Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
17
|
Affiliation(s)
- Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
| |
Collapse
|
18
|
Yang Y, Zhang M, Wang Y. The roles of histone modifications in tumorigenesis and associated inhibitors in cancer therapy. JOURNAL OF THE NATIONAL CANCER CENTER 2022; 2:277-290. [PMID: 39036551 PMCID: PMC11256729 DOI: 10.1016/j.jncc.2022.09.002] [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: 08/07/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022] Open
Abstract
Histone modifications are key factors in chromatin packaging, and are responsible for gene regulation during cell fate determination and development. Abnormal alterations in histone modifications potentially affect the stability of the genome and disrupt gene expression patterns, leading to many diseases, including cancer. In recent years, mounting evidence has shown that various histone modifications altered by aberrantly expressed modifier enzymes contribute to tumor development and metastasis through the induction of epigenetic, transcriptional, and phenotypic changes. In this review, we will discuss the existing histone modifications, both well-studied and rare ones, and their roles in solid tumors and hematopoietic cancers, to identify the molecular pathways involved and investigate targeted therapeutic drugs to reorganize the chromatin and enhance cancer treatment efficiency. Finally, clinical inhibitors of histone modifications are summarized to better understand the developmental stage of cancer therapy in using these drugs to inhibit the histone modification enzymes.
Collapse
Affiliation(s)
| | | | - Yan Wang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
19
|
Sijm A, Atlasi Y, van der Knaap JA, Wolf van der Meer J, Chalkley GE, Bezstarosti K, Dekkers DHW, Doff WAS, Ozgur Z, van IJcken WFJ, Demmers JAA, Verrijzer CP. USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3. SCIENCE ADVANCES 2022; 8:eabq7598. [PMID: 36332031 PMCID: PMC9635827 DOI: 10.1126/sciadv.abq7598] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/16/2022] [Indexed: 05/29/2023]
Abstract
Ubiquitin-specific protease 7 (USP7) has been implicated in cancer progression and neurodevelopment. However, its molecular targets remain poorly characterized. We combined quantitative proteomics, transcriptomics, and epigenomics to define the core USP7 network. Our multi-omics analysis reveals USP7 as a control hub that links genome regulation, tumor suppression, and histone H2A ubiquitylation (H2AK119ub1) by noncanonical Polycomb-repressive complexes (ncPRC1s). USP7 strongly stabilizes ncPRC1.6 and, to a lesser extent, ncPRC1.1. Moreover, USP7 represses expression of AUTS2, which suppresses H2A ubiquitylation by ncPRC1.3/5. Collectively, these USP7 activities promote the genomic deposition of H2AK119ub1 by ncPRC1, especially at transcriptionally repressed loci. Notably, USP7-dependent changes in H2AK119ub1 levels are uncoupled from H3K27me3. Even complete loss of the PRC1 catalytic core and H2AK119ub1 has only a limited effect on H3K27me3. Besides defining the USP7 regulome, our results reveal that H2AK119ub1 dosage is largely disconnected from H3K27me3.
Collapse
Affiliation(s)
- Ayestha Sijm
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Yaser Atlasi
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Jan A. van der Knaap
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Gillian E. Chalkley
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Karel Bezstarosti
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Dick H. W. Dekkers
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Wouter A. S. Doff
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Zeliha Ozgur
- Center for Biomics, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Jeroen A. A. Demmers
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - C. Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| |
Collapse
|
20
|
Abstract
The Polycomb system modulates chromatin structure to maintain gene repression during cell differentiation. Polycomb repression involves methylation of histone H3K27 (H3K27me3) by Polycomb repressive complex 2 (PRC2), monoubiquitylation of H2A (H2Aub1) by noncanonical PRC1 (ncPRC1), and chromatin compaction by canonical PRC1 (cPRC1), which is independent of its enzymatic activity. Puzzlingly, Polycomb repression also requires deubiquitylation of H2Aub1 by Polycomb repressive deubiquitinase (PR-DUB). In this issue of Genes & Development, Bonnet and colleagues (pp. 1046-1061) resolve this paradox by showing that high levels of H2Aub1 in Drosophila lacking PR-DUB activity promotes open chromatin and gene expression in spite of normal H3K27me3 levels and PRC binding. Pertinently, gene repression is restored by concomitant loss of PRC1 E3 ubiquitin ligase activity but depends on its chromatin compaction activity. These findings suggest that PR-DUB ensures just-right levels of H2Aub1 to allow chromatin compaction by cPRC1.
Collapse
|
21
|
Quantitative Assessment of Histone H2B Monoubiquitination in Yeast Using Immunoblotting. Methods Protoc 2022; 5:mps5050074. [PMID: 36287046 PMCID: PMC9609377 DOI: 10.3390/mps5050074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 02/07/2023] Open
Abstract
Studies in Saccharomyces cerevisiae and Schizosaccharomyces pombe have enhanced our understanding of the regulation and functions of histone H2B monoubiquitination (H2Bub1), a key epigenetic marker with important roles in transcription and other processes. The detection of H2Bub1 in yeasts using immunoblotting has been greatly facilitated by the commercial availability of antibodies against yeast histone H2B and the cross-reactivity of an antibody raised against monoubiquitinated human H2BK120. These antibodies have obviated the need to express epitope-tagged histone H2B to detect H2Bub1 in yeasts. Here, we provide a step-by-step protocol and best practices for the quantification of H2Bub1 in yeast systems, from cell extract preparation to immunoblotting using the commercially available antibodies. We demonstrate that the commercial antibodies can effectively and accurately detect H2Bub1 in S. cerevisiae and S. pombe. Further, we show that the C-terminal epitope-tagging of histone H2B alters the steady-state levels of H2Bub1 in yeast systems. We report a sectioned blot probing approach combined with the serial dilution of protein lysates and the use of reversibly stained proteins as loading controls that together provide a cost-effective and sensitive method for the quantitative evaluation of H2Bub1 in yeast.
Collapse
|
22
|
Doyle EJ, Morey L, Conway E. Know when to fold 'em: Polycomb complexes in oncogenic 3D genome regulation. Front Cell Dev Biol 2022; 10:986319. [PMID: 36105358 PMCID: PMC9464936 DOI: 10.3389/fcell.2022.986319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin is spatially and temporally regulated through a series of orchestrated processes resulting in the formation of 3D chromatin structures such as topologically associating domains (TADs), loops and Polycomb Bodies. These structures are closely linked to transcriptional regulation, with loss of control of these processes a frequent feature of cancer and developmental syndromes. One such oncogenic disruption of the 3D genome is through recurrent dysregulation of Polycomb Group Complex (PcG) functions either through genetic mutations, amplification or deletion of genes that encode for PcG proteins. PcG complexes are evolutionarily conserved epigenetic complexes. They are key for early development and are essential transcriptional repressors. PcG complexes include PRC1, PRC2 and PR-DUB which are responsible for the control of the histone modifications H2AK119ub1 and H3K27me3. The spatial distribution of the complexes within the nuclear environment, and their associated modifications have profound effects on the regulation of gene transcription and the 3D genome. Nevertheless, how PcG complexes regulate 3D chromatin organization is still poorly understood. Here we glean insights into the role of PcG complexes in 3D genome regulation and compaction, how these processes go awry during tumorigenesis and the therapeutic implications that result from our insights into these mechanisms.
Collapse
Affiliation(s)
- Emma J. Doyle
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Lluis Morey
- Sylvester Comprehensive Cancer Centre, Miami, FL, United States
- Department of Human Genetics, Biomedical Research Building, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Eric Conway
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| |
Collapse
|
23
|
De Novo Polycomb Recruitment and Repressive Domain Formation. EPIGENOMES 2022; 6:epigenomes6030025. [PMID: 35997371 PMCID: PMC9397058 DOI: 10.3390/epigenomes6030025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
Abstract
Every cell of an organism shares the same genome; even so, each cellular lineage owns a different transcriptome and proteome. The Polycomb group proteins (PcG) are essential regulators of gene repression patterning during development and homeostasis. However, it is unknown how the repressive complexes, PRC1 and PRC2, identify their targets and elicit new Polycomb domains during cell differentiation. Classical recruitment models consider the pre-existence of repressive histone marks; still, de novo target binding overcomes the absence of both H3K27me3 and H2AK119ub. The CpG islands (CGIs), non-core proteins, and RNA molecules are involved in Polycomb recruitment. Nonetheless, it is unclear how de novo targets are identified depending on the physiological context and developmental stage and which are the leading players stabilizing Polycomb complexes at domain nucleation sites. Here, we examine the features of de novo sites and the accessory elements bridging its recruitment and discuss the first steps of Polycomb domain formation and transcriptional regulation, comprehended by the experimental reconstruction of the repressive domains through time-resolved genomic analyses in mammals.
Collapse
|
24
|
Bölicke N, Albert M. Polycomb-mediated gene regulation in human brain development and neurodevelopmental disorders. Dev Neurobiol 2022; 82:345-363. [PMID: 35384339 DOI: 10.1002/dneu.22876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/09/2022] [Accepted: 03/28/2022] [Indexed: 12/17/2022]
Abstract
The neocortex is considered the seat of higher cognitive function in humans. It develops from a sheet of neural progenitor cells, most of which eventually give rise to neurons. This process of cell fate determination is controlled by precise temporal and spatial gene expression patterns that in turn are affected by epigenetic mechanisms including Polycomb group (PcG) regulation. PcG proteins assemble in multiprotein complexes and catalyze repressive posttranslational histone modifications. Their association with neurodevelopmental disease and various types of cancer of the central nervous system, as well as observations in mouse models, has implicated these epigenetic modifiers in controlling various stages of cortex development. The precise mechanisms conveying PcG-associated transcriptional repression remain incompletely understood and are an active field of research. PcG activity appears to be highly context-specific, raising the question of species-specific differences in the regulation of neural stem and progenitor regulation. In this review, we will discuss our growing understanding of how PcG regulation affects human cortex development, based on studies in murine model systems, but focusing mostly on findings obtained from examining impaired PcG activity in the context of human neurodevelopmental disorders and cancer. Furthermore, we will highlight relevant experimental approaches for functional investigations of PcG regulation in human cortex development.
Collapse
Affiliation(s)
- Nora Bölicke
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Mareike Albert
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
25
|
Pauli S, Berger H, Ufartes R, Borchers A. Comparing a Novel Malformation Syndrome Caused by Pathogenic Variants in FBRSL1 to AUTS2 Syndrome. Front Cell Dev Biol 2021; 9:779009. [PMID: 34805182 PMCID: PMC8602103 DOI: 10.3389/fcell.2021.779009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Truncating variants in specific exons of Fibrosin-like protein 1 (FBRSL1) were recently reported to cause a novel malformation and intellectual disability syndrome. The clinical spectrum includes microcephaly, facial dysmorphism, cleft palate, skin creases, skeletal anomalies and contractures, postnatal growth retardation, global developmental delay as well as respiratory problems, hearing impairment and heart defects. The function of FBRSL1 is largely unknown, but pathogenic variants in the FBRSL1 paralog Autism Susceptibility Candidate 2 (AUTS2) are causative for an intellectual disability syndrome with microcephaly (AUTS2 syndrome). Some patients with AUTS2 syndrome also show additional symptoms like heart defects and contractures overlapping with the phenotype presented by patients with FBRSL1 mutations. For AUTS2, a dual function, depending on different isoforms, was described and suggested for FBRSL1. Both, nuclear FBRSL1 and AUTS2 are components of the Polycomb subcomplexes PRC1.3 and PRC1.5. These complexes have essential roles in developmental processes, cellular differentiation and proliferation by regulating gene expression via histone modification. In addition, cytoplasmic AUTS2 controls neural development, neuronal migration and neurite extension by regulating the cytoskeleton. Here, we review recent data on FBRSL1 in respect to previously published data on AUTS2 to gain further insights into its molecular function, its role in development as well as its impact on human genetics.
Collapse
Affiliation(s)
- Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Hanna Berger
- Faculty of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
| | - Roser Ufartes
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Annette Borchers
- Faculty of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
| |
Collapse
|
26
|
Zhang K, Xu J, Ding Y, Shen C, Lin M, Dai X, Zhou H, Huang X, Xue B, Zheng B. BMI1 promotes spermatogonia proliferation through epigenetic repression of Ptprm. Biochem Biophys Res Commun 2021; 583:169-177. [PMID: 34739857 DOI: 10.1016/j.bbrc.2021.10.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/29/2021] [Indexed: 12/31/2022]
Abstract
Spermatogonia are accountable for spermatogenesis and male fertility, but the underlying mechanisms involved in spermatogonia maintenance are not clear. B lymphoma Mo-MLV insertion region 1 (BMI1) is a key component of epigenetic silencers. BMI1 is essential for stem-cell maintenance. Here, we attempted to uncover the role of BMI1 in spermatogonia maintenance using a mouse spermatogonia cell line (GC-1) and Bmi1-knockout (KO) mouse model. We showed that BMI1 promoted the proliferation and inhibited apoptosis of GC-1 cells. Mechanistically, we present in vitro and in vivo evidence to show that BMI1 binds to the promoter region of the Protein tyrosine phosphatase receptor type M (PTPRM) gene, thereby driving chromatin remodeling and gene silencing. Knockdown of Ptprm expression significantly improved spermatogonia proliferation in BMI1-deficient GC-1 cells. Collectively, our data show, for the first time, an epigenetic mechanism involving in BMI1-mediated gene silencing in spermatogonia maintenance, and provide potential targets for the treatment of male infertility.
Collapse
Affiliation(s)
- Ke Zhang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jinfu Xu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yue Ding
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
| | - Meng Lin
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xiuliang Dai
- Center of Clinical Reproductive Medicine, The Affiliated Changzhou Matemity and Child Health Care Hospital of Nanjing Medical University, Changzhou, China
| | - Hui Zhou
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Xiaoyan Huang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Boxin Xue
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China.
| | - Bo Zheng
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China.
| |
Collapse
|