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Mousa M, Liang Y, Tung LT, Wang H, Krawczyk C, Langlais D, Nijnik A. Chromatin-binding deubiquitinase MYSM1 acts in haematopoietic progenitors to control dendritic cell development and to program dendritic cell responses to microbial stimulation. Immunology 2024; 172:109-126. [PMID: 38316548 DOI: 10.1111/imm.13758] [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: 07/23/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Dendritic cells (DCs) are the most significant antigen presenting cells of the immune system, critical for the activation of naïve T cells. The pathways controlling DC development, maturation, and effector function therefore require precise regulation to allow for an effective induction of adaptive immune response. MYSM1 is a chromatin binding deubiquitinase (DUB) and an activator of gene expression via its catalytic activity for monoubiquitinated histone H2A (H2A-K119ub), which is a highly abundant repressive epigenetic mark. MYSM1 is an important regulator of haematopoiesis in mouse and human, and a systemic constitutive loss of Mysm1 in mice results in a depletion of many haematopoietic progenitors, including DC precursors, with the downstream loss of most DC lineage cells. However, the roles of MYSM1 at the later checkpoints in DC development, maturation, activation, and effector function at present remain unknown. In the current work, using a range of novel mouse models (Mysm1flCreERT2, Mysm1flCD11c-cre, Mysm1DN), we further the understanding of MYSM1 functions in the DC lineage: assessing the requirement for MYSM1 in DC development independently of other complex developmental phenotypes, exploring its role at the later checkpoints in DC maintenance and activation in response to microbial stimulation, and testing the requirement for the DUB catalytic activity of MYSM1 in these processes. Surprisingly, we demonstrate that MYSM1 expression and catalytic activity in DCs are dispensable for the maintenance of DC numbers in vivo or for DC activation in response to microbial stimulation. In contrast, MYSM1 acts via its DUB catalytic activity specifically in haematopoietic progenitors to allow normal DC lineage development, and its loss results not only in a severe DC depletion but also in the production of functionally altered DCs, with a dysregulation of many housekeeping transcriptional programs and significantly altered responses to microbial stimulation.
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Affiliation(s)
- Marwah Mousa
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
| | - Yue Liang
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
| | - Lin Tze Tung
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
| | - Connie Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, Michigan, United States
| | - David Langlais
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University Genome Centre, McGill University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
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2
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Gan L, Yang C, Zhao L, Wang S, Ye Y, Gao Z. L3MBTL3 Is a Potential Prognostic Biomarker and Correlates with Immune Infiltrations in Gastric Cancer. Cancers (Basel) 2023; 16:128. [PMID: 38201555 PMCID: PMC10778146 DOI: 10.3390/cancers16010128] [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: 10/10/2023] [Revised: 11/23/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Recent research has linked lethal (3) malignant brain tumor-like 3 (L3MBTL3) to cancer aggressiveness and a dismal prognosis, but its function in gastric cancer (GC) is unclear. This research investigated the association between L3MBTL3 expression and clinicopathological characteristics of GC cases, as well as its prognostic value and biological function based on large-scale databases and clinical samples. The results showed that L3MBTL3 expression was upregulated in malignant GC tissues, which was associated with a shortened survival time and poor clinicopathological characteristics, including TNM staging. A functional enrichment analysis including GO/KEGG and GSEA illustrated the enrichment of different L3MBTL3-associated pathways involved in carcinogenesis and immune response. In addition, the correlations between L3MBTL3 and tumor-infiltrating immune cells were determined based on the TIMER database; the results showed that L3MBTL3 was associated with the immune infiltration of macrophages and their polarization from M1 to M2. Furthermore, our findings suggested a possible function for L3MBTL3 in the regulation of the tumor immune microenvironment of GC. In summary, L3MBTL3 has diagnostic potential, and it also offers new insights into the development of aggressiveness and prognosis in GC.
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Affiliation(s)
- Lin Gan
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China;
| | - Changjiang Yang
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China; (C.Y.); (L.Z.); (S.W.)
- Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China; (C.Y.); (L.Z.); (S.W.)
- Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Shan Wang
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China; (C.Y.); (L.Z.); (S.W.)
- Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China; (C.Y.); (L.Z.); (S.W.)
- Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Zhidong Gao
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China; (C.Y.); (L.Z.); (S.W.)
- Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
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3
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Neupane A, Chariker JH, Rouchka EC. Analysis of Nucleotide Variations in Human G-Quadruplex Forming Regions Associated with Disease States. Genes (Basel) 2023; 14:2125. [PMID: 38136947 PMCID: PMC10742762 DOI: 10.3390/genes14122125] [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: 10/31/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
While the role of G quadruplex (G4) structures has been identified in cancers and metabolic disorders, single nucleotide variations (SNVs) and their effect on G4s in disease contexts have not been extensively studied. The COSMIC and CLINVAR databases were used to detect SNVs present in G4s to identify sequence level changes and their effect on the alteration of the G4 secondary structure. A total of 37,515 G4 SNVs in the COSMIC database and 2378 in CLINVAR were identified. Of those, 7236 COSMIC (19.3%) and 457 (19%) of the CLINVAR variants result in G4 loss, while 2728 (COSMIC) and 129 (CLINVAR) SNVs gain a G4 structure. The remaining variants potentially affect the folding energy without affecting the presence of a G4. Analysis of mutational patterns in the G4 structure shows a higher selective pressure (3-fold) in the coding region on the template strand compared to the reverse strand. At the same time, an equal proportion of SNVs were observed among intronic, promoter, and enhancer regions across strands.
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Affiliation(s)
- Aryan Neupane
- School of Graduate and Interdisciplinary Studies, University of Louisville, Louisville, KY 40292, USA;
| | - Julia H. Chariker
- Department of Neuroscience Training, University of Louisville, Louisville, KY 40292, USA;
- Kentucky IDeA Network of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
| | - Eric C. Rouchka
- Kentucky IDeA Network of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA
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4
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Zhao LY, Li P, Yao CC, Tian RH, Tang YX, Chen YZ, Zhou Z, Li Z. Low XIST expression in Sertoli cells of Klinefelter syndrome patients causes high susceptibility of these cells to an extra X chromosome. Asian J Androl 2023; 25:662-673. [PMID: 37202929 DOI: 10.4103/aja202315] [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: 12/04/2022] [Accepted: 03/23/2023] [Indexed: 05/20/2023] Open
Abstract
Klinefelter syndrome (KS) is the most common genetic cause of human male infertility. However, the effect of the extra X chromosome on different testicular cell types remains poorly understood. Here, we profiled testicular single-cell transcriptomes from three KS patients and normal karyotype control individuals. Among the different somatic cells, Sertoli cells showed the greatest transcriptome changes in KS patients. Further analysis showed that X-inactive-specific transcript ( XIST ), a key factor that inactivates one X chromosome in female mammals, was widely expressed in each testicular somatic cell type but not in Sertoli cells. The loss of XIST in Sertoli cells leads to an increased level of X chromosome genes, and further disrupts their transcription pattern and cellular function. This phenomenon was not detected in other somatic cells such as Leydig cells and vascular endothelial cells. These results proposed a new mechanism to explain why testicular atrophy in KS patients is heterogeneous with loss of seminiferous tubules but interstitial hyperplasia. Our study provides a theoretical basis for subsequent research and related treatment of KS by identifying Sertoli cell-specific X chromosome inactivation failure.
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Affiliation(s)
- Liang-Yu Zhao
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Department of Urology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
- Department of Interventional Medicine, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Peng Li
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Chen-Cheng Yao
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Ru-Hui Tian
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Yu-Xin Tang
- Department of Urology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
- Department of Interventional Medicine, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Yu-Zhuo Chen
- Department of Interventional Medicine, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Zhi Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200120, China
| | - Zheng Li
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
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5
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Ray S, Hewitt K. Sticky, Adaptable, and Many-sided: SAM protein versatility in normal and pathological hematopoietic states. Bioessays 2023; 45:e2300022. [PMID: 37318311 PMCID: PMC10527593 DOI: 10.1002/bies.202300022] [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: 02/01/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
With decades of research seeking to generalize sterile alpha motif (SAM) biology, many outstanding questions remain regarding this multi-tool protein module. Recent data from structural and molecular/cell biology has begun to reveal new SAM modes of action in cell signaling cascades and biomolecular condensation. SAM-dependent mechanisms underlie blood-related (hematologic) diseases, including myelodysplastic syndromes and leukemias, prompting our focus on hematopoiesis for this review. With the increasing coverage of SAM-dependent interactomes, a hypothesis emerges that SAM interaction partners and binding affinities work to fine tune cell signaling cascades in developmental and disease contexts, including hematopoiesis and hematologic disease. This review discusses what is known and remains unknown about the standard mechanisms and neoplastic properties of SAM domains and what the future might hold for developing SAM-targeted therapies.
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Affiliation(s)
- Suhita Ray
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, United States
| | - Kyle Hewitt
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, United States
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6
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Wang H, Langlais D, Nijnik A. Histone H2A deubiquitinases in the transcriptional programs of development and hematopoiesis: a consolidated analysis. Int J Biochem Cell Biol 2023; 157:106384. [PMID: 36738766 DOI: 10.1016/j.biocel.2023.106384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Monoubiquitinated lysine 119 of histone H2A (H2AK119ub) is a highly abundant epigenetic mark, associated with gene repression and deposited on chromatin by the polycomb repressor complex 1 (PRC1), which is an essential regulator of diverse transcriptional programs in mammalian development and tissue homeostasis. While multiple deubiquitinases (DUBs) with catalytic activity for H2AK119ub (H2A-DUBs) have been identified, we lack systematic analyses of their roles and cross-talk in transcriptional regulation. Here, we address H2A-DUB functions in epigenetic regulation of mammalian development and tissue maintenance by conducting a meta-analysis of 248 genomics datasets from 32 independent studies, focusing on the mouse model and covering embryonic stem cells (ESCs), hematopoietic, and immune cell lineages. This covers all the publicly available datasets that map genomic H2A-DUB binding and H2AK119ub distributions (ChIP-Seq), and all datasets assessing dysregulation in gene expression in the relevant H2A-DUB knockout models (RNA-Seq). Many accessory datasets for PRC1-2 and DUB-interacting proteins are also analyzed and interpreted, as well as further data assessing chromatin accessibility (ATAC-Seq) and transcriptional activity (RNA-seq). We report co-localization in the binding of H2A-DUBs BAP1, USP16, and to a lesser extent others that is conserved across different cell-types, and also the enrichment of antagonistic PRC1-2 protein complexes at the same genomic locations. Such conserved sites enriched for the H2A-DUBs and PRC1-2 are proximal to transcriptionally active genes that engage in housekeeping cellular functions. Nevertheless, they exhibit H2AK119ub levels significantly above the genomic average that can undergo further increase with H2A-DUB knockout. This indicates a cooperation between H2A-DUBs and PRC1-2 in the modulation of housekeeping transcriptional programs, conserved across many cell types, likely operating through their antagonistic effects on H2AK119ub and the regulation of local H2AK119ub turnover. Our study further highlights existing knowledge gaps and discusses important directions for future work.
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Affiliation(s)
- HanChen Wang
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, McGill University, QC, Canada
| | - David Langlais
- McGill University Research Centre on Complex Traits, McGill University, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada; McGill Genome Centre, Montreal, QC, Canada.
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, McGill University, QC, Canada.
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7
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Akcan TS, Vilov S, Heinig M. Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures. Nucleic Acids Res 2023; 51:1608-1624. [PMID: 36727445 PMCID: PMC9976927 DOI: 10.1093/nar/gkac1272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/09/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023] Open
Abstract
Promoter-proximal Polymerase II (Pol II) pausing is a key rate-limiting step for gene expression. DNA and RNA-binding trans-acting factors regulating the extent of pausing have been identified. However, we lack a quantitative model of how interactions of these factors determine pausing, therefore the relative importance of implicated factors is unknown. Moreover, previously unknown regulators might exist. Here we address this gap with a machine learning model that accurately predicts the extent of promoter-proximal Pol II pausing from large-scale genome and transcriptome binding maps and gene annotation and sequence composition features. We demonstrate high accuracy and generalizability of the model by validation on an independent cell line which reveals the model's cell line agnostic character. Model interpretation in light of prior knowledge about molecular functions of regulatory factors confirms the interconnection of pausing with other RNA processing steps. Harnessing underlying feature contributions, we assess the relative importance of each factor, quantify their predictive effects and systematically identify previously unknown regulators of pausing. We additionally identify 16 previously unknown 7SK ncRNA interacting RNA-binding proteins predictive of pausing. Our work provides a framework to further our understanding of the regulation of the critical early steps in transcriptional elongation.
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Affiliation(s)
- Toray S Akcan
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, Munich, Germany
| | - Sergey Vilov
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich, 10785 Berlin, Germany
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8
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Neupane A, Chariker JH, Rouchka EC. Analysis of nucleotide variations in human g-quadruplex forming regions associated with disease states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526341. [PMID: 36778288 PMCID: PMC9915501 DOI: 10.1101/2023.01.30.526341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
While the role of G4 G quadruplex structures has been identified in cancers and metabolic disorders, single nucleotide variations (SNVs) and their effect on G4s in disease contexts have not been extensively studied. The COSMIC and CLINVAR databases were used to detect SNVs present in G4s to identify sequence level changes and their effect on alteration of G4 secondary structure. 37,515 G4 SNVs in the COSMIC database and 2,115 in CLINVAR were identified. Of those, 7,236 COSMIC (19.3%) and 416 (18%) of the CLINVAR variants result in G4 loss, while 2,728 (COSMIC) and 112 (CLINVAR) SNVs gain a G4 structure. The gene ontology term "GnRH (Gonadotropin-releasing hormone) secretion" is enriched in 21 genes in this pathway that have a G4 destabilizing SNV. Analysis of mutational patterns in the G4 structure show a higher selective pressure (3-fold) in the coding region on the template strand compared to the non-template strand. At the same time, an equal proportion of SNVs were observed among intronic, promoter and enhancer regions across strands. Using GO and pathway enrichment, genes with SNVs for G4 forming propensity in the coding region are enriched for Regulation of Ras protein signal transduction and Src homology 3 (SH3) domain binding.
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Affiliation(s)
- Aryan Neupane
- School of Graduate and Interdisciplinary Studies, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Julia H. Chariker
- Department of Neuroscience Training, University of Louisville, Louisville, Kentucky, 40292, United States of America
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, Kentucky, 40292, United States of America
| | - Eric C. Rouchka
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, Kentucky, 40292, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky 40292, United States of America
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9
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Hall D, Giaimo BD, Park SS, Hemmer W, Friedrich T, Ferrante F, Bartkuhn M, Yuan Z, Oswald F, Borggrefe T, Rual JF, Kovall R. The structure, binding and function of a Notch transcription complex involving RBPJ and the epigenetic reader protein L3MBTL3. Nucleic Acids Res 2022; 50:13083-13099. [PMID: 36477367 PMCID: PMC9825171 DOI: 10.1093/nar/gkac1137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 10/01/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
The Notch pathway transmits signals between neighboring cells to elicit downstream transcriptional programs. Notch is a major regulator of cell fate specification, proliferation, and apoptosis, such that aberrant signaling leads to a pleiotropy of human diseases, including developmental disorders and cancers. The pathway signals through the transcription factor CSL (RBPJ in mammals), which forms an activation complex with the intracellular domain of the Notch receptor and the coactivator Mastermind. CSL can also function as a transcriptional repressor by forming complexes with one of several different corepressor proteins, such as FHL1 or SHARP in mammals and Hairless in Drosophila. Recently, we identified L3MBTL3 as a bona fide RBPJ-binding corepressor that recruits the repressive lysine demethylase LSD1/KDM1A to Notch target genes. Here, we define the RBPJ-interacting domain of L3MBTL3 and report the 2.06 Å crystal structure of the RBPJ-L3MBTL3-DNA complex. The structure reveals that L3MBTL3 interacts with RBPJ via an unusual binding motif compared to other RBPJ binding partners, which we comprehensively analyze with a series of structure-based mutants. We also show that these disruptive mutations affect RBPJ and L3MBTL3 function in cells, providing further insights into Notch mediated transcriptional regulation.
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Affiliation(s)
- Daniel Hall
- University of Cincinnati College of Medicine, Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, USA
| | | | - Sung-Soo Park
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Wiebke Hemmer
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine 1, Albert-Einstein-Allee 23, 89081Ulm, Germany
| | - Tobias Friedrich
- Institute of Biochemistry, University of Giessen, 35392 Giessen, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, 35392 Giessen, Germany
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, University of Giessen, 35392 Giessen, Germany
| | - Zhenyu Yuan
- University of Cincinnati College of Medicine, Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, USA
| | - Franz Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine 1, Albert-Einstein-Allee 23, 89081Ulm, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, 35392 Giessen, Germany
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rhett A Kovall
- To whom correspondence should be addressed. Tel: +1 513 558 4631;
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10
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Takano J, Ito S, Dong Y, Sharif J, Nakajima-Takagi Y, Umeyama T, Han YW, Isono K, Kondo T, Iizuka Y, Miyai T, Koseki Y, Ikegaya M, Sakihara M, Nakayama M, Ohara O, Hasegawa Y, Hashimoto K, Arner E, Klose RJ, Iwama A, Koseki H, Ikawa T. PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment. Nat Commun 2022; 13:7159. [PMID: 36443290 PMCID: PMC9705430 DOI: 10.1038/s41467-022-34856-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Polycomb group proteins (PcG), polycomb repressive complexes 1 and 2 (PRC1 and 2), repress lineage inappropriate genes during development to maintain proper cellular identities. It has been recognized that PRC1 localizes at the replication fork, however, the precise functions of PRC1 during DNA replication are elusive. Here, we reveal that a variant PRC1 containing PCGF1 (PCGF1-PRC1) prevents overloading of activators and chromatin remodeling factors on nascent DNA and thereby mediates proper deposition of nucleosomes and correct downstream chromatin configurations in hematopoietic stem and progenitor cells (HSPCs). This function of PCGF1-PRC1 in turn facilitates PRC2-mediated repression of target genes such as Hmga2 and restricts premature myeloid differentiation. PCGF1-PRC1, therefore, maintains the differentiation potential of HSPCs by linking proper nucleosome configuration at the replication fork with PcG-mediated gene silencing to ensure life-long hematopoiesis.
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Affiliation(s)
- Junichiro Takano
- grid.509459.40000 0004 0472 0267Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa Japan ,grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan ,grid.136304.30000 0004 0370 1101Department of Cellular and Molecular Medicine, Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Shinsuke Ito
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Yixing Dong
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Jafar Sharif
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Yaeko Nakajima-Takagi
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Taichi Umeyama
- grid.7597.c0000000094465255Laboratory for Microbiome Sciences, RIKEN-IMS, Yokohama, Kanagawa Japan
| | - Yong-Woon Han
- grid.7597.c0000000094465255Laboratory for Integrative Genomics, RIKEN-IMS, Yokohama, Kanagawa Japan
| | - Kyoichi Isono
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan ,grid.412857.d0000 0004 1763 1087Laboratory Animal Center, Wakayama Medical University, Wakayama, Japan
| | - Takashi Kondo
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Yusuke Iizuka
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Tomohiro Miyai
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Yoko Koseki
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Mika Ikegaya
- grid.509459.40000 0004 0472 0267Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa Japan ,grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Mizuki Sakihara
- grid.143643.70000 0001 0660 6861Division of Immunology and Allergy, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Manabu Nakayama
- grid.410858.00000 0000 9824 2470Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Osamu Ohara
- grid.410858.00000 0000 9824 2470Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Yoshinori Hasegawa
- grid.410858.00000 0000 9824 2470Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Kosuke Hashimoto
- grid.136593.b0000 0004 0373 3971Laboratory of Computational Biology, Institute for Protein Research, Osaka University Osaka, Japan ,grid.7597.c0000000094465255Laboratory for Transcriptome Technology, RIKEN-IMS, Yokohama, Kanagawa Japan
| | - Erik Arner
- grid.7597.c0000000094465255Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN-IMS, Yokohama, Kanagawa Japan
| | - Robert J. Klose
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, UK
| | - Atsushi Iwama
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Haruhiko Koseki
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan ,grid.136304.30000 0004 0370 1101Department of Cellular and Molecular Medicine, Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Tomokatsu Ikawa
- grid.509459.40000 0004 0472 0267Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa Japan ,grid.143643.70000 0001 0660 6861Division of Immunology and Allergy, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
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11
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Lan X, Ding S, Zhang T, Yi Y, Li C, Jin W, Chen J, Liang K, Wang H, Jiang W. PCGF6 controls neuroectoderm specification of human pluripotent stem cells by activating SOX2 expression. Nat Commun 2022; 13:4601. [PMID: 35933409 PMCID: PMC9357003 DOI: 10.1038/s41467-022-32295-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 07/25/2022] [Indexed: 11/28/2022] Open
Abstract
Polycomb group (PcG) proteins are known to repress developmental genes during embryonic development and tissue homeostasis. Here, we report that PCGF6 controls neuroectoderm specification of human pluripotent stem cells (PSCs) by activating SOX2 gene. Human PSCs with PCGF6 depletion display impaired neuroectoderm differentiation coupled with increased mesendoderm outcomes. Transcriptome analysis reveals that de-repression of the WNT/β-catenin signaling pathway is responsible for the differentiation of PSC toward the mesendodermal lineage. Interestingly, PCGF6 and MYC directly interact and co-occupy a distal regulatory element of SOX2 to activate SOX2 expression, which likely accounts for the regulation in neuroectoderm differentiation. Supporting this notion, genomic deletion of the SOX2-regulatory element phenocopies the impaired neuroectoderm differentiation, while overexpressing SOX2 rescues the neuroectoderm phenotype caused by PCGF6-depletion. Together, our study reveals that PCGF6 can function as lineage switcher between mesendoderm and neuroectoderm in human PSCs by both suppression and activation mechanisms. Variant Polycomb complexes can have tissue-specific roles during development. Here they show that PCGF6 controls lineage-specification in human PSCs by promoting neuroectoderm differentiation and repressing mesendoderm differentiation via distinct downstream targets.
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Affiliation(s)
- Xianchun Lan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Song Ding
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Ying Yi
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Conghui Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenwen Jin
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Jian Chen
- Chinese Institute for Brain Research (Beijing), Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, 102206, Beijing, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Hengbin Wang
- Department of Internal Medicine, Division of Hematology, Oncology, and Palliative Care, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China. .,Human Genetics Resource Preservation Center of Wuhan University, Wuhan, China. .,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China.
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12
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Oss-Ronen L, Sarusi T, Cohen I. Histone Mono-Ubiquitination in Transcriptional Regulation and Its Mark on Life: Emerging Roles in Tissue Development and Disease. Cells 2022; 11:cells11152404. [PMID: 35954248 PMCID: PMC9368181 DOI: 10.3390/cells11152404] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation plays an essential role in driving precise transcriptional programs during development and homeostasis. Among epigenetic mechanisms, histone mono-ubiquitination has emerged as an important post-transcriptional modification. Two major histone mono-ubiquitination events are the mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub), placed by Polycomb repressive complex 1 (PRC1), and histone H2B lysine 120 mono-ubiquitination (H2BK120ub), placed by the heteromeric RNF20/RNF40 complex. Both of these events play fundamental roles in shaping the chromatin epigenetic landscape and cellular identity. In this review we summarize the current understandings of molecular concepts behind histone mono-ubiquitination, focusing on their recently identified roles in tissue development and pathologies.
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Affiliation(s)
| | | | - Idan Cohen
- Correspondence: ; Tel.: +972-8-6477593; Fax: +972-8-6477626
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13
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Hussain M, Lu Y, Tariq M, Jiang H, Shu Y, Luo S, Zhu Q, Zhang J, Liu J. A small-molecule Skp1 inhibitor elicits cell death by p53-dependent mechanism. iScience 2022; 25:104591. [PMID: 35789855 PMCID: PMC9249674 DOI: 10.1016/j.isci.2022.104591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 04/21/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022] Open
Abstract
Skp1 overexpression promotes tumor growth, whereas reduced Skp1 activity is also linked with genomic instability and neoplastic transformation. This highlights the need to gain better understanding of Skp1 biology in cancer settings. To this context, potent and cellularly active small-molecule Skp1 inhibitors may be of great value. Using a hypothesis-driven, structure-guided approach, we herein identify Z0933M as a potent Skp1 inhibitor with KD ∼0.054 μM. Z0933M occupies a hydrophobic hotspot (P1) – encompassing an aromatic cage of two phenylalanines (F101 and F139) – alongside C-terminal extension of Skp1 and, thus, hampers its ability to interact with F-box proteins, a prerequisite step to constitute intact and active SCF E3 ligase(s) complexes. In cellulo, Z0933M disrupted SCF E3 ligase(s) functioning, recapitulated previously reported effects of Skp1-reduced activity, and elicited cell death by a p53-dependent mechanism. We propose Z0933M as valuable tool for future efforts toward probing Skp1 cancer biology, with implications for cancer therapy. Z0933M manifests strong binding with Skp1 and inhibits Skp1-F-box PPIs Z0933M interacts with a P1 hotspot alongside C-terminal extension of Skp1 Z0933M alters SCF E3 ligase functioning, leading to substrate accumulation/modulation Z0933M causes cell-cycle arrest, and elicits cell death by p53-dependent mechanism
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Affiliation(s)
- Muzammal Hussain
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yongzhi Lu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Muqddas Tariq
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Hao Jiang
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
| | - Yahai Shu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
| | - Shuang Luo
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Qiang Zhu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Jiancun Zhang
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Corresponding author
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14
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Ne E, Crespo R, Izquierdo-Lara R, Rao S, Koçer S, Górska A, van Staveren T, Kan TW, van de Vijver D, Dekkers D, Rokx C, Moulos P, Hatzis P, Palstra RJ, Demmers J, Mahmoudi T. Catchet-MS identifies IKZF1-targeting thalidomide analogues as novel HIV-1 latency reversal agents. Nucleic Acids Res 2022; 50:5577-5598. [PMID: 35640596 PMCID: PMC9177988 DOI: 10.1093/nar/gkac407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/11/2022] [Accepted: 05/24/2022] [Indexed: 12/27/2022] Open
Abstract
A major pharmacological strategy toward HIV cure aims to reverse latency in infected cells as a first step leading to their elimination. While the unbiased identification of molecular targets physically associated with the latent HIV-1 provirus would be highly valuable to unravel the molecular determinants of HIV-1 transcriptional repression and latency reversal, due to technical limitations, this has been challenging. Here we use a dCas9 targeted chromatin and histone enrichment strategy coupled to mass spectrometry (Catchet-MS) to probe the differential protein composition of the latent and activated HIV-1 5′LTR. Catchet-MS identified known and novel latent 5′LTR-associated host factors. Among these, IKZF1 is a novel HIV-1 transcriptional repressor, required for Polycomb Repressive Complex 2 recruitment to the LTR. We find the clinically advanced thalidomide analogue iberdomide, and the FDA approved analogues lenalidomide and pomalidomide, to be novel LRAs. We demonstrate that, by targeting IKZF1 for degradation, these compounds reverse HIV-1 latency in CD4+ T-cells isolated from virally suppressed people living with HIV-1 and that they are able to synergize with other known LRAs.
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Affiliation(s)
- Enrico Ne
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Ray Izquierdo-Lara
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Selin Koçer
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Alicja Górska
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Thomas van Staveren
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
| | - David van de Vijver
- Department of Viroscience, Erasmus University Medical Center, The Netherlands
| | - Dick Dekkers
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Casper Rokx
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rg-530, PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
| | - Jeroen Demmers
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
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15
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Lu S, Louphrasitthiphol P, Goradia N, Lambert JP, Schmidt J, Chauhan J, Rughani MG, Larue L, Wilmanns M, Goding CR. TBX2 controls a proproliferative gene expression program in melanoma. Genes Dev 2021; 35:1657-1677. [PMID: 34819350 PMCID: PMC8653791 DOI: 10.1101/gad.348746.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022]
Abstract
Senescence shapes embryonic development, plays a key role in aging, and is a critical barrier to cancer initiation, yet how senescence is regulated remains incompletely understood. TBX2 is an antisenescence T-box family transcription repressor implicated in embryonic development and cancer. However, the repertoire of TBX2 target genes, its cooperating partners, and how TBX2 promotes proliferation and senescence bypass are poorly understood. Here, using melanoma as a model, we show that TBX2 lies downstream from PI3K signaling and that TBX2 binds and is required for expression of E2F1, a key antisenescence cell cycle regulator. Remarkably, TBX2 binding in vivo is associated with CACGTG E-boxes, present in genes down-regulated by TBX2 depletion, more frequently than the consensus T-element DNA binding motif that is restricted to Tbx2 repressed genes. TBX2 is revealed to interact with a wide range of transcription factors and cofactors, including key components of the BCOR/PRC1.1 complex that are recruited by TBX2 to the E2F1 locus. Our results provide key insights into how PI3K signaling modulates TBX2 function in cancer to drive proliferation.
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Affiliation(s)
- Sizhu Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom.,Department of Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Nishit Goradia
- European Molecular Biology Laboratory, Hamburg Unit, 22607 Hamburg, Germany
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Medicine and Cancer Research Centre, Université Laval, Québec City, Québec G1R 3S3, Canada; CHU de Québec Research Center, Centre Hospitalier de l'Université Laval, Québec City, Québec G1V 4G2, Canada
| | - Johannes Schmidt
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jagat Chauhan
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Milap G Rughani
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Lionel Larue
- Institut Curie, PSL Research University, U1021, Institut National de la Santé et de la Recherche Médicale, Normal and Pathological Development of Melanocytes, 91405 Orsay Cedex, France.,Université Paris-Sud, Université Paris-Saclay, UMR 3347 Centre National de la Recherche Scientifique, 91405 Orsay Cedex, France.,Equipe Labellisée Ligue Contre le Cancer, 91405 Orsay Cedex, France
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, 22607 Hamburg, Germany.,University Hamburg Clinical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
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16
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Trotman JB, Braceros KCA, Cherney RE, Murvin MM, Calabrese JM. The control of polycomb repressive complexes by long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1657. [PMID: 33861025 PMCID: PMC8500928 DOI: 10.1002/wrna.1657] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/12/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
The polycomb repressive complexes 1 and 2 (PRCs; PRC1 and PRC2) are conserved histone-modifying enzymes that often function cooperatively to repress gene expression. The PRCs are regulated by long noncoding RNAs (lncRNAs) in complex ways. On the one hand, specific lncRNAs cause the PRCs to engage with chromatin and repress gene expression over genomic regions that can span megabases. On the other hand, the PRCs bind RNA with seemingly little sequence specificity, and at least in the case of PRC2, direct RNA-binding has the effect of inhibiting the enzyme. Thus, some RNAs appear to promote PRC activity, while others may inhibit it. The reasons behind this apparent dichotomy are unclear. The most potent PRC-activating lncRNAs associate with chromatin and are predominantly unspliced or harbor unusually long exons. Emerging data imply that these lncRNAs promote PRC activity through internal RNA sequence elements that arise and disappear rapidly in evolutionary time. These sequence elements may function by interacting with common subsets of RNA-binding proteins that recruit or stabilize PRCs on chromatin. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Jackson B. Trotman
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Keean C. A. Braceros
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rachel E. Cherney
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - McKenzie M. Murvin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - J. Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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17
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Flora P, Dalal G, Cohen I, Ezhkova E. Polycomb Repressive Complex(es) and Their Role in Adult Stem Cells. Genes (Basel) 2021; 12:1485. [PMID: 34680880 PMCID: PMC8535826 DOI: 10.3390/genes12101485] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 12/31/2022] Open
Abstract
Populations of resident stem cells (SCs) are responsible for maintaining, repairing, and regenerating adult tissues. In addition to having the capacity to generate all the differentiated cell types of the tissue, adult SCs undergo long periods of quiescence within the niche to maintain themselves. The process of SC renewal and differentiation is tightly regulated for proper tissue regeneration throughout an organisms' lifetime. Epigenetic regulators, such as the polycomb group (PcG) of proteins have been implicated in modulating gene expression in adult SCs to maintain homeostatic and regenerative balances in adult tissues. In this review, we summarize the recent findings that elucidate the composition and function of the polycomb repressive complex machinery and highlight their role in diverse adult stem cell compartments.
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Affiliation(s)
- Pooja Flora
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA;
| | - Gil Dalal
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Elena Ezhkova
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA;
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18
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Oss-Ronen L, Cohen I. Epigenetic regulation and signalling pathways in Merkel cell development. Exp Dermatol 2021; 30:1051-1064. [PMID: 34152646 DOI: 10.1111/exd.14415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/20/2022]
Abstract
Merkel cells are specialized epithelial cells connected to afferent nerve endings responsible for light-touch sensations, formed at specific locations in touch-sensitive regions of the mammalian skin. Although Merkel cells are descendants of the epidermal lineage, little is known about the mechanisms responsible for the development of these unique mechanosensory cells. Recent studies have highlighted that the Polycomb group (PcG) of proteins play a significant role in spatiotemporal regulation of Merkel cell formation. In addition, several of the major signalling pathways involved in skin development have been shown to regulate Merkel cell development as well. Here, we summarize the current understandings of the role of developmental regulators in Merkel cell formation, including the interplay between the epigenetic machinery and key signalling pathways, and the lineage-specific transcription factors involved in the regulation of Merkel cell development.
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Affiliation(s)
- Liat Oss-Ronen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer Sheva, Israel
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19
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Chagraoui J, Girard S, Spinella JF, Simon L, Bonneil E, Mayotte N, MacRae T, Coulombe-Huntington J, Bertomeu T, Moison C, Tomellini E, Thibault P, Tyers M, Marinier A, Sauvageau G. UM171 Preserves Epigenetic Marks that Are Reduced in Ex Vivo Culture of Human HSCs via Potentiation of the CLR3-KBTBD4 Complex. Cell Stem Cell 2021; 28:48-62.e6. [PMID: 33417871 DOI: 10.1016/j.stem.2020.12.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/22/2020] [Accepted: 12/03/2020] [Indexed: 01/11/2023]
Abstract
Human hematopoietic stem cells (HSCs) exhibit attrition of their self-renewal capacity when cultured ex vivo, a process that is partially reversed upon treatment with epigenetic modifiers, most notably inhibitors of histone deacetylases (HDACs) or lysine-specific demethylase LSD1. A recent study showed that the human HSC self-renewal agonist UM171 modulates the CoREST complex, leading to LSD1 degradation, whose inhibition mimics the activity of UM171. The mechanism underlying the UM171-mediated loss of CoREST function remains undetermined. We now report that UM171 potentiates the activity of a CULLIN3-E3 ubiquitin ligase (CRL3) complex whose target specificity is dictated by the poorly characterized Kelch/BTB domain protein KBTBD4. CRL3KBTBD4 targets components of the LSD1/RCOR1 corepressor complex for proteasomal degradation, hence re-establishing H3K4me2 and H3K27ac epigenetic marks, which are rapidly decreased upon ex vivo culture of human HSCs.
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Affiliation(s)
- Jalila Chagraoui
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Simon Girard
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Jean-Francois Spinella
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Laura Simon
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Eric Bonneil
- Departments of Biochemistry and Chemistry, Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Nadine Mayotte
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Tara MacRae
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Jasmin Coulombe-Huntington
- Department of Medicine, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Thierry Bertomeu
- Department of Medicine, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Celine Moison
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Elisa Tomellini
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Pierre Thibault
- Departments of Biochemistry and Chemistry, Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Mike Tyers
- Department of Medicine, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Anne Marinier
- Faculty of Arts and Science, Université de Montréal, Montreal, QC, Canada
| | - Guy Sauvageau
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada.
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20
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BMI1 regulates multiple myeloma-associated macrophage's pro-myeloma functions. Cell Death Dis 2021; 12:495. [PMID: 33993198 PMCID: PMC8124065 DOI: 10.1038/s41419-021-03748-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023]
Abstract
Multiple myeloma (MM) is an aggressive malignancy characterized by terminally differentiated plasma cells accumulation in the bone marrow (BM). MM BM exhibits elevated MΦs (macrophages) numbers relative to healthy BM. Current evidence indicates that MM-MΦs (MM-associated macrophages) have pro-myeloma functions, and BM MM-MΦs numbers negatively correlate with patient survival. Here, we found that BMI1, a polycomb-group protein, modulates the pro-myeloma functions of MM-MΦs, which expressed higher BMI1 levels relative to normal MΦs. In the MM tumor microenvironment, hedgehog signaling in MΦs was activated by MM-derived sonic hedgehog, and BMI1 transcription subsequently activated by c-Myc. Relative to wild-type MM-MΦs, BMI1-KO (BMI1 knockout) MM-MΦs from BM cells of BMI1-KO mice exhibited reduced proliferation and suppressed expression of angiogenic factors. Additionally, BMI1-KO MM-MΦs lost their ability to protect MM cells from chemotherapy-induced cell death. In vivo analysis showed that relative to wild-type MM-MΦs, BMI1-KO MM-MΦs lost their pro-myeloma effects. Together, our data show that BMI1 mediates the pro-myeloma functions of MM-MΦs.
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21
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BCOR gene alterations in hematological diseases. Blood 2021; 138:2455-2468. [PMID: 33945606 DOI: 10.1182/blood.2021010958] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022] Open
Abstract
The BCL6 co-repressor (BCOR) is a transcription factor involved in the control of embryogenesis, mesenchymal stem cells function, hematopoiesis and lymphoid development. Recurrent somatic clonal mutations of the BCOR gene and its homologue BCORL1 have been detected in several hematological malignancies and aplastic anemia. They are scattered across the whole gene length and mostly represent frameshifts (deletions, insertions), nonsense and missence mutations. These disruptive events lead to the loss of full-length BCOR protein and to the lack or low expression of a truncated form of the protein, both consistent with the tumor suppressor role of BCOR. BCOR and BCORL1 mutations are similar to those causing two rare X-linked diseases: the oculo-facio-cardio-dental (OFCD) and the Shukla-Vernon syndromes, respectively. Here, we focus on the structure and function of normal BCOR and BCORL1 in normal hematopoietic and lymphoid tissues and review the frequency and clinical significance of the mutations of these genes in malignant and non-malignant hematological diseases. Moreover, we discuss the importance of mouse models to better understand the role of Bcor loss, alone and combined with alterations of other genes (e.g. Dnmt3a and Tet2), in promoting hematological malignancies and in providing a useful platform for the development of new targeted therapies.
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22
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Heterochromatin and Polycomb as regulators of haematopoiesis. Biochem Soc Trans 2021; 49:805-814. [PMID: 33929498 PMCID: PMC8106494 DOI: 10.1042/bst20200737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/23/2022]
Abstract
Haematopoiesis is the process by which multipotent haematopoietic stem cells are transformed into each and every type of terminally differentiated blood cell. Epigenetic silencing is critical for this process by regulating the transcription of cell-cycle genes critical for self-renewal and differentiation, as well as restricting alternative fate genes to allow lineage commitment and appropriate differentiation. There are two distinct forms of transcriptionally repressed chromatin: H3K9me3-marked heterochromatin and H3K27me3/H2AK119ub1-marked Polycomb (often referred to as facultative heterochromatin). This review will discuss the role of these distinct epigenetic silencing mechanisms in regulating normal haematopoiesis, how these contribute to age-related haematopoietic dysfunction, and the rationale for therapeutic targeting of these pathways in the treatment of haematological malignancies.
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23
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Lin YH, Liang Y, Wang H, Tung LT, Förster M, Subramani PG, Di Noia JM, Clare S, Langlais D, Nijnik A. Regulation of B Lymphocyte Development by Histone H2A Deubiquitinase BAP1. Front Immunol 2021; 12:626418. [PMID: 33912157 PMCID: PMC8072452 DOI: 10.3389/fimmu.2021.626418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/12/2021] [Indexed: 01/08/2023] Open
Abstract
BAP1 is a deubiquitinase (DUB) of the Ubiquitin C-terminal Hydrolase (UCH) family that regulates gene expression and other cellular processes, via deubiquitination of histone H2AK119ub and other substrates. BAP1 is an important tumor suppressor in human, expressed and functional across many cell-types and tissues, including those of the immune system. B lymphocytes are the mediators of humoral immune response, however the role of BAP1 in B cell development and physiology remains poorly understood. Here we characterize a mouse line with a selective deletion of BAP1 within the B cell lineage (Bap1fl/fl mb1-Cre) and establish a cell intrinsic role of BAP1 in the regulation of B cell development. We demonstrate a depletion of large pre-B cells, transitional B cells, and mature B cells in Bap1fl/fl mb1-Cre mice. We characterize broad transcriptional changes in BAP1-deficient pre-B cells, map BAP1 binding across the genome, and analyze the effects of BAP1-loss on histone H2AK119ub levels and distribution. Overall, our work establishes a cell intrinsic role of BAP1 in B lymphocyte development, and suggests its contribution to the regulation of the transcriptional programs of cell cycle progression, via the deubiquitination of histone H2AK119ub.
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Affiliation(s)
- Yun Hsiao Lin
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
| | - Yue Liang
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - Lin Tze Tung
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
| | - Michael Förster
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
| | - Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Javier M. Di Noia
- Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Biochemistry & Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Simon Clare
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - David Langlais
- McGill Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
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24
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AKT-mediated regulation of chromatin ubiquitylation and tumorigenesis through Mel18 phosphorylation. Oncogene 2021; 40:2422-2436. [PMID: 33664452 DOI: 10.1038/s41388-020-01602-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 11/25/2020] [Accepted: 12/03/2020] [Indexed: 01/31/2023]
Abstract
Polycomb repressor complex 1 (PRC1) is linked to the regulation of gene expression and histone ubiquitylation conformation, which contributes to carcinogenesis. However, the upstream regulators of PRC1 biogenesis machinery remain obscure. Here, we report that the polycomb group-related mammalian gene Mel18 is a target of the protein kinase AKT. AKT phosphorylates Mel18 at T334 to disrupt the interaction between Mel18 and other PRC1 members, leading to attenuated PRC1-dependent ubiquitylation of histone H2A at Lys119. As such, PRC1 target genes, many of which are known oncogenes, are derepressed upon T334-Mel18 phosphorylation, which promotes malignant behaviours, including cell proliferation, tumour formation, migration and invasion, bone and brain metastatic lesion formation. Notably, a positive correlation between AKT activity and pT334-Mel18 is observed, and prognostic models based on p-AKT and pT334-Mel18 that predicted overall survival and distant metastasis-free survival in breast cancer patients are established. These findings have implications for understanding the role of AKT and its associated proteins in chromatin ubiquitylation, and also indicate the AKT-Mel18-H2AK119ub axis as a novel prognostic biomarker and therapeutic target for cancer patients.
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25
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Cohen I, Bar C, Liu H, Valdes VJ, Zhao D, Galbo PM, Silva JM, Koseki H, Zheng D, Ezhkova E. Polycomb complexes redundantly maintain epidermal stem cell identity during development. Genes Dev 2021; 35:354-366. [PMID: 33602871 PMCID: PMC7919412 DOI: 10.1101/gad.345363.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
In this study, Cohen et al. sought to understand the functional contribution of PRC1 and PRC2, which largely overlap in their genomic binding and cooperate to establish repressive chromatin domains demarcated by H2AK119ub and H3K27me3, to gene repression. By using the developing murine epidermis as a paradigm, they uncovered a previously unappreciated functional redundancy between Polycomb complexes, and their findings show how PRC1 and PRC2 function as two independent counterparts, providing a repressive safety net that protects and preserves lineage identity. Polycomb repressive complex 1 (PRC1) and PRC2 are critical epigenetic developmental regulators. PRC1 and PRC2 largely overlap in their genomic binding and cooperate to establish repressive chromatin domains demarcated by H2AK119ub and H3K27me3. However, the functional contribution of each complex to gene repression has been a subject of debate, and understanding of its physiological significance requires further studies. Here, using the developing murine epidermis as a paradigm, we uncovered a previously unappreciated functional redundancy between Polycomb complexes. Coablation of PRC1 and PRC2 in embryonic epidermal progenitors resulted in severe defects in epidermal stratification, a phenotype not observed in the single PRC1-null or PRC2-null epidermis. Molecular dissection indicated a loss of epidermal identity that was coupled to a strong derepression of nonlineage transcription factors, otherwise repressed by either PRC1 or PRC2 in the absence of its counterpart. Ectopic expression of subsets of PRC1/2-repressed nonepidermal transcription factors in wild-type epidermal stem cells was sufficient to suppress epidermal identity genes, highlighting the importance of functional redundancy between PRC1 and PRC2. Altogether, our studies show how PRC1 and PRC2 function as two independent counterparts, thereby providing a repressive safety net that protects and preserves lineage identity.
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Affiliation(s)
- Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Carmit Bar
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Hequn Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Victor J Valdes
- Department of Cell Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Dejian Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Yale Center for Genome Analysis, Yale University, New Haven, Connecticut 06510, USA.,Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Phillip M Galbo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Jose M Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Tsurumi-ku, Yokohama 230-0045, Japan.,AMED-CREST, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Neurology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Elena Ezhkova
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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26
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Cordonnier G, Mandoli A, Cagnard N, Hypolite G, Lhermitte L, Verhoeyen E, Asnafi V, Dillon N, Macintyre E, Martens JHA, Bond J. CBFβ-SMMHC Affects Genome-wide Polycomb Repressive Complex 1 Activity in Acute Myeloid Leukemia. Cell Rep 2021; 30:299-307.e3. [PMID: 31940477 DOI: 10.1016/j.celrep.2019.12.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/16/2019] [Accepted: 12/06/2019] [Indexed: 10/25/2022] Open
Abstract
Mutations and deletions of polycomb repressive complex (PRC) components are increasingly recognized to affect tumor biology in a range of cancers. However, little is known about how genetic alterations of PRC-interacting molecules such as the core binding factor (CBF) complex influence polycomb activity. We report that the acute myeloid leukemia (AML)-associated CBFβ-SMMHC fusion oncoprotein physically interacts with the PRC1 complex and that these factors co-localize across the AML genome in an apparently PRC2-independent manner. Depletion of CBFβ-SMMHC caused substantial increases in genome-wide PRC1 binding and marked changes in the association between PRC1 and the CBF DNA-binding subunit RUNX1. PRC1 was more likely to be associated with actively transcribed genes in CBFβ-SMMHC-expressing cells. CBFβ-SMMHC depletion had heterogeneous effects on gene expression, including significant reductions in transcription of ribosomal loci occupied by PRC1. Our results provide evidence that CBFβ-SMMHC markedly and diversely affects polycomb recruitment and transcriptional regulation across the AML genome.
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Affiliation(s)
- Gaëlle Cordonnier
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France; Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker-Enfants Malades, Paris, France
| | - Amit Mandoli
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Nicolas Cagnard
- Sorbonne Universités, Université Paris Descartes, Bioinformatics Platform, Paris, France
| | - Guillaume Hypolite
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France; Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker-Enfants Malades, Paris, France
| | - Ludovic Lhermitte
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France; Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker-Enfants Malades, Paris, France
| | - Els Verhoeyen
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, INSERM U1111, Lyon, France; Université Côte d'Azur, INSERM, C3M, 06204 Nice, France
| | - Vahid Asnafi
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France; Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker-Enfants Malades, Paris, France
| | - Niall Dillon
- Gene Regulation and Chromatin Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Elizabeth Macintyre
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France; Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker-Enfants Malades, Paris, France
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Jonathan Bond
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France; Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker-Enfants Malades, Paris, France; Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland; National Children's Research Centre, Children's Health Ireland at Crumlin, Dublin, Ireland.
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27
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Boulay G, Cironi L, Garcia SP, Rengarajan S, Xing YH, Lee L, Awad ME, Naigles B, Iyer S, Broye LC, Keskin T, Cauderay A, Fusco C, Letovanec I, Chebib I, Nielsen PG, Tercier S, Cherix S, Nguyen-Ngoc T, Cote G, Choy E, Provero P, Suvà ML, Rivera MN, Stamenkovic I, Riggi N. The chromatin landscape of primary synovial sarcoma organoids is linked to specific epigenetic mechanisms and dependencies. Life Sci Alliance 2020; 4:4/2/e202000808. [PMID: 33361335 PMCID: PMC7768195 DOI: 10.26508/lsa.202000808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/01/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022] Open
Abstract
We have addressed the mechanisms by which the fusion protein SS18-SSX modifies the epigenome toward the development of synovial sarcoma and the establishment of its potentially targetable vulnerabilities. Synovial sarcoma (SyS) is an aggressive mesenchymal malignancy invariably associated with the chromosomal translocation t(X:18; p11:q11), which results in the in-frame fusion of the BAF complex gene SS18 to one of three SSX genes. Fusion of SS18 to SSX generates an aberrant transcriptional regulator, which, in permissive cells, drives tumor development by initiating major chromatin remodeling events that disrupt the balance between BAF-mediated gene activation and polycomb-dependent repression. Here, we developed SyS organoids and performed genome-wide epigenomic profiling of these models and mesenchymal precursors to define SyS-specific chromatin remodeling mechanisms and dependencies. We show that SS18-SSX induces broad BAF domains at its binding sites, which oppose polycomb repressor complex (PRC) 2 activity, while facilitating recruitment of a non-canonical (nc)PRC1 variant. Along with the uncoupling of polycomb complexes, we observed H3K27me3 eviction, H2AK119ub deposition and the establishment of de novo active regulatory elements that drive SyS identity. These alterations are completely reversible upon SS18-SSX depletion and are associated with vulnerability to USP7 loss, a core member of ncPRC1.1. Using the power of primary tumor organoids, our work helps define the mechanisms of epigenetic dysregulation on which SyS cells are dependent.
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Affiliation(s)
- Gaylor Boulay
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Luisa Cironi
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sara P Garcia
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shruthi Rengarajan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yu-Hang Xing
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lukuo Lee
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mary E Awad
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Beverly Naigles
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sowmya Iyer
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Liliane C Broye
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tugba Keskin
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alexandra Cauderay
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Carlo Fusco
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Igor Letovanec
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Ivan Chebib
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Petur Gunnalugur Nielsen
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stéphane Tercier
- Department of Woman-Mother Child, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Stéphane Cherix
- Department of Orthopedics, Faculty of Biology and Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Tu Nguyen-Ngoc
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Gregory Cote
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Edwin Choy
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Paolo Provero
- Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Miguel N Rivera
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ivan Stamenkovic
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland .,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Nicolò Riggi
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland .,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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28
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Targeting Chromatin Complexes in Myeloid Malignancies and Beyond: From Basic Mechanisms to Clinical Innovation. Cells 2020; 9:cells9122721. [PMID: 33371192 PMCID: PMC7767226 DOI: 10.3390/cells9122721] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/13/2020] [Accepted: 12/20/2020] [Indexed: 12/12/2022] Open
Abstract
The aberrant function of chromatin regulatory networks (epigenetics) is a hallmark of cancer promoting oncogenic gene expression. A growing body of evidence suggests that the disruption of specific chromatin-associated protein complexes has therapeutic potential in malignant conditions, particularly those that are driven by aberrant chromatin modifiers. Of note, a number of enzymatic inhibitors that block the catalytic function of histone modifying enzymes have been established and entered clinical trials. Unfortunately, many of these molecules do not have potent single-agent activity. One potential explanation for this phenomenon is the fact that those drugs do not profoundly disrupt the integrity of the aberrant network of multiprotein complexes on chromatin. Recent advances in drug development have led to the establishment of novel inhibitors of protein–protein interactions as well as targeted protein degraders that may provide inroads to longstanding effort to physically disrupt oncogenic multiprotein complexes on chromatin. In this review, we summarize some of the current concepts on the role epigenetic modifiers in malignant chromatin states with a specific focus on myeloid malignancies and recent advances in early-phase clinical trials.
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29
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Hamline MY, Corcoran CM, Wamstad JA, Miletich I, Feng J, Lohr JL, Hemberger M, Sharpe PT, Gearhart MD, Bardwell VJ. OFCD syndrome and extraembryonic defects are revealed by conditional mutation of the Polycomb-group repressive complex 1.1 (PRC1.1) gene BCOR. Dev Biol 2020; 468:110-132. [PMID: 32692983 PMCID: PMC9583620 DOI: 10.1016/j.ydbio.2020.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/16/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022]
Abstract
BCOR is a critical regulator of human development. Heterozygous mutations of BCOR in females cause the X-linked developmental disorder Oculofaciocardiodental syndrome (OFCD), and hemizygous mutations of BCOR in males cause gestational lethality. BCOR associates with Polycomb group proteins to form one subfamily of the diverse Polycomb repressive complex 1 (PRC1) complexes, designated PRC1.1. Currently there is limited understanding of differing developmental roles of the various PRC1 complexes. We therefore generated a conditional exon 9-10 knockout Bcor allele and a transgenic conditional Bcor expression allele and used these to define multiple roles of Bcor, and by implication PRC1.1, in mouse development. Females heterozygous for Bcor exhibiting mosaic expression due to the X-linkage of the gene showed reduced postnatal viability and had OFCD-like defects. By contrast, Bcor hemizygosity in the entire male embryo resulted in embryonic lethality by E9.5. We further dissected the roles of Bcor, focusing on some of the tissues affected in OFCD through use of cell type specific Cre alleles. Mutation of Bcor in neural crest cells caused cleft palate, shortening of the mandible and tympanic bone, ectopic salivary glands and abnormal tongue musculature. We found that defects in the mandibular region, rather than in the palate itself, led to palatal clefting. Mutation of Bcor in hindlimb progenitor cells of the lateral mesoderm resulted in 2/3 syndactyly. Mutation of Bcor in Isl1-expressing lineages that contribute to the heart caused defects including persistent truncus arteriosus, ventricular septal defect and fetal lethality. Mutation of Bcor in extraembryonic lineages resulted in placental defects and midgestation lethality. Ubiquitous over expression of transgenic Bcor isoform A during development resulted in embryonic defects and midgestation lethality. The defects we have found in Bcor mutants provide insights into the etiology of the OFCD syndrome and how BCOR-containing PRC1 complexes function in development.
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Affiliation(s)
- Michelle Y Hamline
- The Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, 55455, USA; University of Minnesota Medical Scientist Training Program, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Connie M Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joseph A Wamstad
- The Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Isabelle Miletich
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Jifan Feng
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Jamie L Lohr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Myriam Hemberger
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Paul T Sharpe
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK; Medical Research Council Centre for Transplantation, King's College London, London, SE1 9RT, UK
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Vivian J Bardwell
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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30
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Qu W, Wang Z, Zhang H. Phase separation of the C. elegans Polycomb protein SOP-2 is modulated by RNA and sumoylation. Protein Cell 2020; 11:202-207. [PMID: 31894537 PMCID: PMC7026206 DOI: 10.1007/s13238-019-00680-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Wenyan Qu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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31
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Sportoletti P, Sorcini D, Guzman AG, Reyes JM, Stella A, Marra A, Sartori S, Brunetti L, Rossi R, Papa BD, Adamo FM, Pianigiani G, Betti C, Scialdone A, Guarente V, Spinozzi G, Tini V, Martelli MP, Goodell MA, Falini B. Bcor deficiency perturbs erythro-megakaryopoiesis and cooperates with Dnmt3a loss in acute erythroid leukemia onset in mice. Leukemia 2020; 35:1949-1963. [PMID: 33159179 PMCID: PMC8257496 DOI: 10.1038/s41375-020-01075-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/19/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022]
Abstract
Recurrent loss-of-function mutations of BCL6 co-repressor (BCOR) gene are found in about 4% of AML patients with normal karyotype and are associated with DNMT3a mutations and poor prognosis. Therefore, new anti-leukemia treatments and mouse models are needed for this combinatorial AML genotype. For this purpose, we first generated a Bcor-/- knockout mouse model characterized by impaired erythroid development (macrocytosis and anemia) and enhanced thrombopoiesis, which are both features of myelodysplasia/myeloproliferative neoplasms. We then created and characterized double Bcor-/-/Dnmt3a-/- knockout mice. Interestingly, these animals developed a fully penetrant acute erythroid leukemia (AEL) characterized by leukocytosis secondary to the expansion of blasts expressing c-Kit+ and the erythroid marker Ter119, macrocytic anemia and progressive reduction of the thrombocytosis associated with loss of Bcor alone. Transcriptomic analysis of double knockout bone marrow progenitors revealed that aberrant erythroid skewing was induced by epigenetic changes affecting specific transcriptional factors (GATA1-2) and cell-cycle regulators (Mdm2, Tp53). These findings prompted us to investigate the efficacy of demethylating agents in AEL, with significant impact on progressive leukemic burden and mice overall survival. Information gained from our model expands the knowledge on the biology of AEL and may help designing new rational treatments for patients suffering from this high-risk leukemia.
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Affiliation(s)
- Paolo Sportoletti
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy.
| | - Daniele Sorcini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Anna G Guzman
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jaime M Reyes
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arianna Stella
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Andrea Marra
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Sara Sartori
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Lorenzo Brunetti
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Roberta Rossi
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Beatrice Del Papa
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Francesco Maria Adamo
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Giulia Pianigiani
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Camilla Betti
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Annarita Scialdone
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Valerio Guarente
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Giulio Spinozzi
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Valentina Tini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Maria Paola Martelli
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Margaret A Goodell
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brunangelo Falini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy.
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32
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Varlet E, Ovejero S, Martinez AM, Cavalli G, Moreaux J. Role of Polycomb Complexes in Normal and Malignant Plasma Cells. Int J Mol Sci 2020; 21:ijms21218047. [PMID: 33126754 PMCID: PMC7662980 DOI: 10.3390/ijms21218047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 02/01/2023] Open
Abstract
Plasma cells (PC) are the main effectors of adaptive immunity, responsible for producing antibodies to defend the body against pathogens. They are the result of a complex highly regulated cell differentiation process, taking place in several anatomical locations and involving unique genetic events. Pathologically, PC can undergo tumorigenesis and cause a group of diseases known as plasma cell dyscrasias, including multiple myeloma (MM). MM is a severe disease with poor prognosis that is characterized by the accumulation of malignant PC within the bone marrow, as well as high clinical and molecular heterogeneity. MM patients frequently develop resistance to treatment, leading to relapse. Polycomb group (PcG) proteins are epigenetic regulators involved in cell fate and carcinogenesis. The emerging roles of PcG in PC differentiation and myelomagenesis position them as potential therapeutic targets in MM. Here, we focus on the roles of PcG proteins in normal and malignant plasma cells, as well as their therapeutic implications.
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Affiliation(s)
- Emmanuel Varlet
- Institute of Human Genetics, UMR 9002 Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, 34396 Montpellier, France; (E.V.); (S.O.); (A.-M.M.); (G.C.)
| | - Sara Ovejero
- Institute of Human Genetics, UMR 9002 Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, 34396 Montpellier, France; (E.V.); (S.O.); (A.-M.M.); (G.C.)
- Department of Biological Hematology, CHU Montpellier, 34295 Montpellier, France
| | - Anne-Marie Martinez
- Institute of Human Genetics, UMR 9002 Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, 34396 Montpellier, France; (E.V.); (S.O.); (A.-M.M.); (G.C.)
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002 Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, 34396 Montpellier, France; (E.V.); (S.O.); (A.-M.M.); (G.C.)
| | - Jerome Moreaux
- Institute of Human Genetics, UMR 9002 Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, 34396 Montpellier, France; (E.V.); (S.O.); (A.-M.M.); (G.C.)
- Department of Biological Hematology, CHU Montpellier, 34295 Montpellier, France
- UFR Medicine, University of Montpellier, 34003 Montpellier, France
- Institut Universitaire de France (IUF), 75005 Paris, France
- Correspondence: ; Tel.: +33-04-6733-7903
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33
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Balakrishnan I, Danis E, Pierce A, Madhavan K, Wang D, Dahl N, Sanford B, Birks DK, Davidson N, Metselaar DS, Meel MH, Lemma R, Donson A, Vijmasi T, Katagi H, Sola I, Fosmire S, Alimova I, Steiner J, Gilani A, Hulleman E, Serkova NJ, Hashizume R, Hawkins C, Carcaboso AM, Gupta N, Monje M, Jabado N, Jones K, Foreman N, Green A, Vibhakar R, Venkataraman S. Senescence Induced by BMI1 Inhibition Is a Therapeutic Vulnerability in H3K27M-Mutant DIPG. Cell Rep 2020; 33:108286. [PMID: 33086074 PMCID: PMC7574900 DOI: 10.1016/j.celrep.2020.108286] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/05/2020] [Accepted: 09/25/2020] [Indexed: 01/19/2023] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is an incurable brain tumor of childhood characterized by histone mutations at lysine 27, which results in epigenomic dysregulation. There has been a failure to develop effective treatment for this tumor. Using a combined RNAi and chemical screen targeting epigenomic regulators, we identify the polycomb repressive complex 1 (PRC1) component BMI1 as a critical factor for DIPG tumor maintenance in vivo. BMI1 chromatin occupancy is enriched at genes associated with differentiation and tumor suppressors in DIPG cells. Inhibition of BMI1 decreases cell self-renewal and attenuates tumor growth due to induction of senescence. Prolonged BMI1 inhibition induces a senescence-associated secretory phenotype, which promotes tumor recurrence. Clearance of senescent cells using BH3 protein mimetics co-operates with BMI1 inhibition to enhance tumor cell killing in vivo.
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Affiliation(s)
- Ilango Balakrishnan
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Etienne Danis
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Angela Pierce
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Krishna Madhavan
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Dong Wang
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Nathan Dahl
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Bridget Sanford
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Diane K Birks
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Nate Davidson
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Dennis S Metselaar
- Princess Máxima Center for Pediatric Oncology, Utrecht and Departments of Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Michaël Hananja Meel
- Princess Máxima Center for Pediatric Oncology, Utrecht and Departments of Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Rakeb Lemma
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew Donson
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Trinka Vijmasi
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Hiroaki Katagi
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ismail Sola
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Susan Fosmire
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Irina Alimova
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Jenna Steiner
- Departments of Radiology, Radiation Oncology, and Anesthesiology, Colorado Animal Imaging Shared Resource (AISR), University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ahmed Gilani
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology, Utrecht and Departments of Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Natalie J Serkova
- Departments of Radiology, Radiation Oncology, and Anesthesiology, Colorado Animal Imaging Shared Resource (AISR), University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rintaro Hashizume
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Cynthia Hawkins
- Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Angel M Carcaboso
- Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona 08950, Spain
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Michelle Monje
- Departments of Neurology, Neurosurgery, Pediatrics, and Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada
| | - Kenneth Jones
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Nicholas Foreman
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Adam Green
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Rajeev Vibhakar
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA.
| | - Sujatha Venkataraman
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA.
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Abstract
The interaction between polycomb-repressive complexes 1/2 (PRC1/2) and long non-coding RNA (lncRNA), such as the X inactive specific transcript Xist and the HOX transcript antisense RNA (HOTAIR), has been the subject of intense debate. While cross-linking, immuno-precipitation and super-resolution microscopy argue against direct interaction of Polycomb with some lncRNAs, there is increasing evidence supporting the ability of both PRC1 and PRC2 to functionally associate with RNA. Recent data indicate that these interactions are in most cases spurious, but nonetheless crucial for a number of cellular activities. In this review, we suggest that while PRC1/2 recruitment by HOTAIR might be direct, in the case of Xist, it might occur indirectly and, at least in part, through the process of liquid-liquid phase separation. We present recent models of lncRNA-mediated PRC1/2 recruitment to their targets and describe potential RNA-mediated roles in the three-dimensional organization of the nucleus.
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Affiliation(s)
- Andrea Cerase
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluis Companys, 08010 Barcelona, Spain.,Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy.,Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163, Genoa, Italy
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35
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Giner-Laguarda N, Vidal M. Functions of Polycomb Proteins on Active Targets. EPIGENOMES 2020; 4:17. [PMID: 34968290 PMCID: PMC8594714 DOI: 10.3390/epigenomes4030017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Chromatin regulators of the Polycomb group of genes are well-known by their activities as transcriptional repressors. Characteristically, their presence at genomic sites occurs with specific histone modifications and sometimes high-order chromatin structures correlated with silencing of genes involved in cell differentiation. However, evidence gathered in recent years, on flies and mammals, shows that in addition to these sites, Polycomb products bind to a large number of active regulatory regions. Occupied sites include promoters and also intergenic regions, containing enhancers and super-enhancers. Contrasting with occupancies at repressed targets, characteristic histone modifications are low or undetectable. Functions on active targets are dual, restraining gene expression at some targets while promoting activity at others. Our aim here is to summarize the evidence available and discuss the convenience of broadening the scope of research to include Polycomb functions on active targets.
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Affiliation(s)
| | - Miguel Vidal
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Ramiro de Maeztu 9, 28040 Madrid, Spain;
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36
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Belle JI, Wang H, Fiore A, Petrov JC, Lin YH, Feng CH, Nguyen TTM, Tung J, Campeau PM, Behrends U, Brunet T, Leszinski GS, Gros P, Langlais D, Nijnik A. MYSM1 maintains ribosomal protein gene expression in hematopoietic stem cells to prevent hematopoietic dysfunction. JCI Insight 2020; 5:125690. [PMID: 32641579 DOI: 10.1172/jci.insight.125690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/21/2020] [Indexed: 01/09/2023] Open
Abstract
Ribosomopathies are congenital disorders caused by mutations in the genes encoding ribosomal and other functionally related proteins. They are characterized by anemia, other hematopoietic and developmental abnormalities, and p53 activation. Ribosome assembly requires coordinated expression of many ribosomal protein (RP) genes; however, the regulation of RP gene expression, especially in hematopoietic stem cells (HSCs), remains poorly understood. MYSM1 is a transcriptional regulator essential for HSC function and hematopoiesis. We established that HSC dysfunction in Mysm1 deficiency is driven by p53; however, the mechanisms of p53 activation remained unclear. Here, we describe the transcriptome of Mysm1-deficient mouse HSCs and identify MYSM1 genome-wide DNA binding sites. We establish a direct role for MYSM1 in RP gene expression and show a reduction in protein synthesis in Mysm1-/- HSCs. Loss of p53 in mice fully rescues Mysm1-/- anemia phenotype but not RP gene expression, indicating that RP gene dysregulation is a direct outcome of Mysm1 deficiency and an upstream mediator of Mysm1-/- phenotypes through p53 activation. We characterize a patient with a homozygous nonsense MYSM1 gene variant, and we demonstrate reduced protein synthesis and increased p53 levels in patient hematopoietic cells. Our work provides insights into the specialized mechanisms regulating RP gene expression in HSCs and establishes a common etiology of MYSM1 deficiency and ribosomopathy syndromes.
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Affiliation(s)
- Jad I Belle
- Department of Physiology.,McGill University Research Centre on Complex Traits, and
| | - HanChen Wang
- Department of Physiology.,McGill University Research Centre on Complex Traits, and.,Department of Human Genetics, McGill University, Quebec, Canada
| | - Amanda Fiore
- Department of Physiology.,McGill University Research Centre on Complex Traits, and
| | - Jessica C Petrov
- Department of Physiology.,McGill University Research Centre on Complex Traits, and
| | - Yun Hsiao Lin
- Department of Physiology.,McGill University Research Centre on Complex Traits, and
| | - Chu-Han Feng
- Department of Physiology.,McGill University Research Centre on Complex Traits, and
| | - Thi Tuyet Mai Nguyen
- Centre Hospitalier Universitaire St. Justine Research Center, University of Montreal, Quebec, Canada
| | - Jacky Tung
- Department of Physiology.,McGill University Research Centre on Complex Traits, and
| | - Philippe M Campeau
- Centre Hospitalier Universitaire St. Justine Research Center, University of Montreal, Quebec, Canada
| | | | - Theresa Brunet
- Institute of Human Genetics, Technische Universität München (TUM), Munich, Germany
| | - Gloria Sarah Leszinski
- Institute of Human Genetics, Technische Universität München (TUM), Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Philippe Gros
- McGill University Research Centre on Complex Traits, and.,Department of Biochemistry and.,The Rosalind and Morris Goodman Cancer Research Centre, McGill University, Quebec, Canada
| | - David Langlais
- McGill University Research Centre on Complex Traits, and.,Department of Human Genetics, McGill University, Quebec, Canada.,McGill University Genome Centre, Montreal, Quebec, Canada
| | - Anastasia Nijnik
- Department of Physiology.,McGill University Research Centre on Complex Traits, and
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37
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Kang SJ, Chun T. Structural heterogeneity of the mammalian polycomb repressor complex in immune regulation. Exp Mol Med 2020; 52:1004-1015. [PMID: 32636442 PMCID: PMC8080698 DOI: 10.1038/s12276-020-0462-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/21/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
Epigenetic regulation is mainly mediated by enzymes that can modify the structure of chromatin by altering the structure of DNA or histones. Proteins involved in epigenetic processes have been identified to study the detailed molecular mechanisms involved in the regulation of specific mRNA expression. Evolutionarily well-conserved polycomb group (PcG) proteins can function as transcriptional repressors by the trimethylation of histone H3 at the lysine 27 residue (H3K27me3) and the monoubiquitination of histone H2A at the lysine 119 residue (H2AK119ub). PcG proteins form two functionally distinct protein complexes: polycomb repressor complex 1 (PRC1) and PRC2. In mammals, the structural heterogeneity of each PRC complex is dramatically increased by several paralogs of its subunit proteins. Genetic studies with transgenic mice along with RNA-seq and chromatin immunoprecipitation (ChIP)-seq analyses might be helpful for defining the cell-specific functions of paralogs of PcG proteins. Here, we summarize current knowledge about the immune regulatory role of PcG proteins related to the compositional diversity of each PRC complex and introduce therapeutic drugs that target PcG proteins in hematopoietic malignancy. Protein complexes that suppress gene activity by remodeling chromatin, the substance that contains most of a cell’s DNA, play a critical role in regulating the immune system and provide a therapeutic target for treating blood cancers. Seok-Jin Kang and Taehoon Chun from Korea University in Seoul, South Korea, review how polycomb group proteins, best known for their function in embryonic development, also contribute to the formation of immune cells from blood stem cell precursors. Studies with stem cells and cancer cells have begun to reveal many targets of these proteins, and drug companies are evaluating candidate agents directed against some polycomb group proteins in patients with lymphoma and other cancers. More comprehensive profiling of protein function across a broad range of immune cell types could reveal new targets for additional diseases associated with immune dysfunction.
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Affiliation(s)
- Seok-Jin Kang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Taehoon Chun
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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38
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Rafiee M, Sigismondo G, Kalxdorf M, Förster L, Brügger B, Béthune J, Krijgsveld J. Protease-resistant streptavidin for interaction proteomics. Mol Syst Biol 2020; 16:e9370. [PMID: 32400114 PMCID: PMC7218406 DOI: 10.15252/msb.20199370] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 11/12/2022] Open
Abstract
Streptavidin-mediated enrichment is a powerful strategy to identify biotinylated biomolecules and their interaction partners; however, intense streptavidin-derived peptides impede protein identification by mass spectrometry. Here, we present an approach to chemically modify streptavidin, thus rendering it resistant to proteolysis by trypsin and LysC. This modification results in over 100-fold reduction of streptavidin contamination and in better coverage of proteins interacting with various biotinylated bait molecules (DNA, protein, and lipid) in an overall simplified workflow.
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Affiliation(s)
- Mahmoud‐Reza Rafiee
- Division of Proteomics of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
- Present address:
The Francis Crick InstituteLondonUK
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
| | - Mathias Kalxdorf
- Division of Proteomics of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
| | - Laura Förster
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | - Julien Béthune
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
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39
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Fiore A, Liang Y, Lin YH, Tung J, Wang H, Langlais D, Nijnik A. Deubiquitinase MYSM1 in the Hematopoietic System and beyond: A Current Review. Int J Mol Sci 2020; 21:ijms21083007. [PMID: 32344625 PMCID: PMC7216186 DOI: 10.3390/ijms21083007] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 01/21/2023] Open
Abstract
MYSM1 has emerged as an important regulator of hematopoietic stem cell function, blood cell production, immune response, and other aspects of mammalian physiology. It is a metalloprotease family protein with deubiquitinase catalytic activity, as well as SANT and SWIRM domains. MYSM1 normally localizes to the nucleus, where it can interact with chromatin and regulate gene expression, through deubiquitination of histone H2A and non-catalytic contacts with other transcriptional regulators. A cytosolic form of MYSM1 protein was also recently described and demonstrated to regulate signal transduction pathways of innate immunity, by promoting the deubiquitination of TRAF3, TRAF6, and RIP2. In this work we review the current knowledge on the molecular mechanisms of action of MYSM1 protein in transcriptional regulation, signal transduction, and potentially other cellular processes. The functions of MYSM1 in different cell types and aspects of mammalian physiology are also reviewed, highlighting the key checkpoints in hematopoiesis, immunity, and beyond regulated by MYSM1. Importantly, mutations in MYSM1 in human were recently linked to a rare hereditary disorder characterized by leukopenia, anemia, and other hematopoietic and developmental abnormalities. Our growing knowledge of MYSM1 functions and mechanisms of actions sheds important insights into its role in mammalian physiology and the etiology of the MYSM1-deficiency disorder in human.
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Affiliation(s)
- Amanda Fiore
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - Yue Liang
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - Yun Hsiao Lin
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - Jacky Tung
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
- Department of Human Genetics, McGill University, Montreal, QC 3640, Canada
| | - David Langlais
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
- Department of Human Genetics, McGill University, Montreal, QC 3640, Canada
- McGill University Genome Centre, Montreal, QC 740, Canada
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
- Correspondence: ; Tel.: +1-514-398-5567
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40
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Zhang Y, Shi J, Liu X, Xiao Z, Lei G, Lee H, Koppula P, Cheng W, Mao C, Zhuang L, Ma L, Li W, Gan B. H2A Monoubiquitination Links Glucose Availability to Epigenetic Regulation of the Endoplasmic Reticulum Stress Response and Cancer Cell Death. Cancer Res 2020; 80:2243-2256. [PMID: 32273282 DOI: 10.1158/0008-5472.can-19-3580] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/11/2020] [Accepted: 04/06/2020] [Indexed: 02/06/2023]
Abstract
Epigenetic regulation of gene transcription has been shown to coordinate with nutrient availability, yet the mechanisms underlying this coordination remain incompletely understood. Here, we show that glucose starvation suppresses histone 2A K119 monoubiquitination (H2Aub), a histone modification that correlates with gene repression. Glucose starvation suppressed H2Aub levels independently of energy stress-mediated AMP-activated protein kinase activation and possibly through NADPH depletion and subsequent inhibition of BMI1, an integral component of polycomb-repressive complex 1 (PRC1) that catalyzes H2Aub on chromatin. Integrated transcriptomic and epigenomic analyses linked glucose starvation-mediated H2Aub repression to the activation of genes involved in the endoplasmic reticulum (ER) stress response. We further showed that this epigenetic mechanism has a role in glucose starvation-induced cell death and that pharmacologic inhibition of glucose transporter 1 and PRC1 synergistically promoted ER stress and suppressed tumor growth in vivo. Together, these results reveal a hitherto unrecognized epigenetic mechanism coupling glucose availability to the ER stress response. SIGNIFICANCE: These findings link glucose deprivation and H2A ubiquitination to regulation of the ER stress response in tumor growth and demonstrate pharmacologic susceptibility to inhibition of polycomb and glucose transporters.
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Affiliation(s)
- Yilei Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiejun Shi
- Department of Biological Chemistry, University of California, Irvine, Irvine, California.,Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Xiaoguang Liu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhenna Xiao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guang Lei
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hyemin Lee
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pranavi Koppula
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
| | - Weijie Cheng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chao Mao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Li Zhuang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
| | - Wei Li
- Department of Biological Chemistry, University of California, Irvine, Irvine, California. .,Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Boyi Gan
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
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41
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Gutierrez-Diaz BT, Gu W, Ntziachristos P. Deubiquitinases: Pro-oncogenic Activity and Therapeutic Targeting in Blood Malignancies. Trends Immunol 2020; 41:327-340. [PMID: 32139316 PMCID: PMC7258259 DOI: 10.1016/j.it.2020.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
Abstract
Deubiquitinases are enzymes that remove ubiquitin moieties from the vast majority of cellular proteins, controlling their stability, interactions, and localization. The expression and activity of deubiquitinases are critical for physiology and can go awry in various diseases, including cancer. Based on recent findings in human blood cancers, we discuss the functions of selected deubiquitinases in acute leukemia and efforts to target these enzymes with the aim of blocking leukemia growth and improving disease outcomes. We focus on the emergence of the newest generation of preclinical inhibitors by discussing their modes of inhibition and their effects on leukemia biology.
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Affiliation(s)
- Blanca T Gutierrez-Diaz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Wei Gu
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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42
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Raby L, Völkel P, Le Bourhis X, Angrand PO. The Polycomb Orthologues in Teleost Fishes and Their Expression in the Zebrafish Model. Genes (Basel) 2020; 11:genes11040362. [PMID: 32230868 PMCID: PMC7230241 DOI: 10.3390/genes11040362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/18/2020] [Accepted: 03/26/2020] [Indexed: 01/25/2023] Open
Abstract
The Polycomb Repressive Complex 1 (PRC1) is a chromatin-associated protein complex involved in transcriptional repression of hundreds of genes controlling development and differentiation processes, but also involved in cancer and stem cell biology. Within the canonical PRC1, members of Pc/CBX protein family are responsible for the targeting of the complex to specific gene loci. In mammals, the Pc/CBX protein family is composed of five members generating, through mutual exclusion, different PRC1 complexes with potentially distinct cellular functions. Here, we performed a global analysis of the cbx gene family in 68 teleost species and traced the distribution of the cbx genes through teleost evolution in six fish super-orders. We showed that after the teleost-specific whole genome duplication, cbx4, cbx7 and cbx8 are retained as pairs of ohnologues. In contrast, cbx2 and cbx6 are present as pairs of ohnologues in the genome of several teleost clades but as singletons in others. Furthermore, since zebrafish is a widely used vertebrate model for studying development, we report on the expression of the cbx family members during zebrafish development and in adult tissues. We showed that all cbx genes are ubiquitously expressed with some variations during early development.
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43
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Alexandrova E, Giurato G, Saggese P, Pecoraro G, Lamberti J, Ravo M, Rizzo F, Rocco D, Tarallo R, Nyman TA, Collina F, Cantile M, Di Bonito M, Botti G, Nassa G, Weisz A. Interaction Proteomics Identifies ERbeta Association with Chromatin Repressive Complexes to Inhibit Cholesterol Biosynthesis and Exert An Oncosuppressive Role in Triple-negative Breast Cancer. Mol Cell Proteomics 2020; 19:245-260. [PMID: 31792072 PMCID: PMC7000115 DOI: 10.1074/mcp.ra119.001817] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/27/2019] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is characterized by poor response to therapy and low overall patient survival. Recently, Estrogen Receptor beta (ERβ) has been found to be expressed in a fraction of TNBCs where, because of its oncosuppressive actions on the genome, it represents a potential therapeutic target, provided a better understanding of its actions in these tumors becomes available. To this end, the cell lines Hs 578T, MDA-MB-468 and HCC1806, representing the claudin-low, basal-like 1 and 2 TNBC molecular subtypes respectively, were engineered to express ERβ under the control of a Tetracycline-inducible promoter and used to investigate the effects of this transcription factor on gene activity. The antiproliferative effects of ERβ in these cells were confirmed by multiple functional approaches, including transcriptome profiling and global mapping of receptor binding sites in the genome, that revealed direct negative regulation by ERβ of genes, encoding for key components of cellular pathways associated to TNBC aggressiveness representing novel therapeutic targets such as angiogenesis, invasion, metastasis and cholesterol biosynthesis. Supporting these results, interaction proteomics by immunoprecipitation coupled to nano LC-MS/MS mass spectrometry revealed ERβ association with several potential nuclear protein partners, including key components of regulatory complexes known to control chromatin remodeling, transcriptional and post-transcriptional gene regulation and RNA splicing. Among these, ERβ association with the Polycomb Repressor Complexes 1 and 2 (PRC1/2), known for their central role in gene regulation in cancer cells, was confirmed in all three TNBC subtypes investigated, suggesting its occurrence independently from the cellular context. These results demonstrate a significant impact of ERβ in TNBC genome activity mediated by its cooperation with regulatory multiprotein chromatin remodeling complexes, providing novel ground to devise new strategies for the treatment of these diseases based on ligands affecting the activity of this nuclear receptor or some of its protein partners.
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Affiliation(s)
- Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy; Genomix4Life Srl, Spin-Off of the Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy; Genomix4Life Srl, Spin-Off of the Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Pasquale Saggese
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy; Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, 90095
| | - Giovanni Pecoraro
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Jessica Lamberti
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Maria Ravo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy; Genomix4Life Srl, Spin-Off of the Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Domenico Rocco
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, 0424 Oslo, Norway
| | - Francesca Collina
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples (NA), 80131 Italy
| | - Monica Cantile
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples (NA), 80131 Italy
| | - Maurizio Di Bonito
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples (NA), 80131 Italy
| | - Gerardo Botti
- Scientific Direction, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples (NA), 80131, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy.
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy.
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44
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Abstract
T cell development involves stepwise progression through defined stages that give rise to multiple T cell subtypes, and this is accompanied by the establishment of stage-specific gene expression. Changes in chromatin accessibility and chromatin modifications accompany changes in gene expression during T cell development. Chromatin-modifying enzymes that add or reverse covalent modifications to DNA and histones have a critical role in the dynamic regulation of gene expression throughout T cell development. As each chromatin-modifying enzyme has multiple family members that are typically all coexpressed during T cell development, their function is sometimes revealed only when two related enzymes are concurrently deleted. This work has also revealed that the biological effects of these enzymes often involve regulation of a limited set of targets. The growing diversity in the types and sites of modification, as well as the potential for a single enzyme to catalyze multiple modifications, is also highlighted.
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Affiliation(s)
- Michael J Shapiro
- Department of Immunology, Mayo Clinic, Rochester, Minnesota 55905, USA; ,
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45
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Ibáñez-Cabellos JS, Seco-Cervera M, Osca-Verdegal R, Pallardó FV, García-Giménez JL. Epigenetic Regulation in the Pathogenesis of Sjögren Syndrome and Rheumatoid Arthritis. Front Genet 2019; 10:1104. [PMID: 31798626 PMCID: PMC6863924 DOI: 10.3389/fgene.2019.01104] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/11/2019] [Indexed: 01/01/2023] Open
Abstract
Autoimmune rheumatic diseases, such as Sjögren syndrome (SS) and rheumatoid arthritis (RA), are characterized by chronic inflammation and autoimmunity, which cause joint tissue damage and destruction by triggering reduced mobility and debilitation in patients with these diseases. Initiation and maintenance of chronic inflammatory stages account for several mechanisms that involve immune cells as key players and the interaction of the immune cells with other tissues. Indeed, the overlapping of certain clinical and serologic manifestations between SS and RA may indicate that numerous immunologic-related mechanisms are involved in the physiopathology of both these diseases. It is widely accepted that epigenetic pathways play an essential role in the development and function of the immune system. Although many published studies have attempted to elucidate the relation between epigenetic modifications (e.g. DNA methylation, histone post-translational modifications, miRNAs) and autoimmune disorders, the contribution of epigenetic regulation to the pathogenesis of SS and RA is at present poorly understood. This review attempts to shed light from a critical point of view on the identification of the most relevant epigenetic mechanisms related to RA and SS by explaining intricate regulatory processes and phenotypic features of both autoimmune diseases. Moreover, we point out some epigenetic markers which can be used to monitor the inflammation status and the dysregulated immunity in SS and RA. Finally, we discuss the inconvenience of using epigenetic data obtained from bulk immune cell populations instead specific immune cell subpopulations.
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Affiliation(s)
- José Santiago Ibáñez-Cabellos
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Marta Seco-Cervera
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Rebeca Osca-Verdegal
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
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46
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Paschos K, Bazot Q, Lees J, Farrell PJ, Allday MJ. Requirement for PRC1 subunit BMI1 in host gene activation by Epstein-Barr virus protein EBNA3C. Nucleic Acids Res 2019; 47:2807-2821. [PMID: 30649516 PMCID: PMC6451101 DOI: 10.1093/nar/gky1323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/01/2018] [Accepted: 01/03/2019] [Indexed: 12/24/2022] Open
Abstract
Epstein-Barr virus proteins EBNA3A, EBNA3B and EBNA3C control hundreds of host genes after infection. Changes in epigenetic marks around EBNA3-regulated genes suggest that they exert transcriptional control in collaboration with epigenetic factors. The roles of polycomb repressive complex (PRC)2 subunit SUZ12 and of PRC1 subunit BMI1 were assessed for their importance in EBNA3-mediated repression and activation. ChIP-seq experiments for SUZ12 and BMI1 were performed to determine their global localization on chromatin and analysis offered further insight into polycomb protein distribution in differentiated cells. Their localization was compared to that of each EBNA3 to resolve longstanding questions about the EBNA3-polycomb relationship. SUZ12 did not co-localize with any EBNA3, whereas EBNA3C co-localized significantly and co-immunoprecipitated with BMI1. In cells expressing a conditional EBNA3C, BMI1 was sequestered to EBNA3C-binding sites after EBNA3C activation. When SUZ12 or BMI1 was knocked down in the same cells, SUZ12 did not contribute to EBNA3C-mediated regulation. Surprisingly, after BMI1 knockdown, EBNA3C repressed equally efficiently but host gene activation by EBNA3C was impaired. This overturns previous assumptions about BMI1/PRC1 functions during EBNA3C-mediated regulation, for the first time identifies directly a host factor involved in EBNA3-mediated activation and provides a new insight into how PRC1 can be involved in gene activation.
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Affiliation(s)
- Kostas Paschos
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Quentin Bazot
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Jonathan Lees
- Oxford Brookes University, Faculty of Health and Life Sciences, Oxford OX3 0BP, Oxfordshire, UK
| | - Paul J Farrell
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Martin J Allday
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, UK
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47
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Bangham CRM, Miura M, Kulkarni A, Matsuoka M. Regulation of Latency in the Human T Cell Leukemia Virus, HTLV-1. Annu Rev Virol 2019; 6:365-385. [PMID: 31283437 DOI: 10.1146/annurev-virology-092818-015501] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human T cell leukemia virus persists in vivo in 103 to 106 clones of T lymphocytes that appear to survive for the lifetime of the host. The plus strand of the provirus is typically transcriptionally silent in freshly isolated lymphocytes, but the strong, persistently activated cytotoxic T lymphocyte (CTL) response to the viral antigens indicates that the virus is not constantly latent in vivo. There is now evidence that the plus strand is transcribed in intense intermittent bursts that are triggered by cellular stress, modulated by hypoxia and glycolysis, and inhibited by polycomb repressive complex 1 (PRC1). The minus-strand gene hbz is transcribed at a lower, more constant level but is silent in a proportion of infected cells at a given time. Viral genes in the sense and antisense strands of the provirus play different respective roles in latency and de novo infection: Expression of the plus-strand gene tax is essential for de novo infection, whereas hbz appears to facilitate survival of the infected T cell clone in vivo.
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Affiliation(s)
- Charles R M Bangham
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, United Kingdom;
| | - Michi Miura
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, United Kingdom;
| | - Anurag Kulkarni
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, United Kingdom;
| | - Masao Matsuoka
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.,Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan;
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48
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Phc2 controls hematopoietic stem and progenitor cell mobilization from bone marrow by repressing Vcam1 expression. Nat Commun 2019; 10:3496. [PMID: 31375680 PMCID: PMC6677815 DOI: 10.1038/s41467-019-11386-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/12/2019] [Indexed: 01/04/2023] Open
Abstract
The timely mobilization of hematopoietic stem and progenitor cells (HSPCs) is essential for maintaining hematopoietic and tissue leukocyte homeostasis. Understanding how HSPCs migrate between bone marrow (BM) and peripheral tissues is of great significance in the clinical setting, where therapeutic strategies for modulating their migration capacity determine the clinical outcome. Here, we identify an epigenetic regulator, Phc2, as a critical modulator of HSPC trafficking. The genetic ablation of Phc2 in mice causes a severe defect in HSPC mobilization through the derepression of Vcam1 in bone marrow stromal cells (BMSCs), ultimately leading to a systemic immunodeficiency. Moreover, the pharmacological inhibition of VCAM-1 in Phc2-deficient mice reverses the symptoms. We further determine that Phc2-dependent Vcam1 repression in BMSCs is mediated by the epigenetic regulation of H3K27me3 and H2AK119ub. Together, our data demonstrate a cell-extrinsic role for Phc2 in controlling the mobilization of HSPCs by finely tuning their bone marrow niche. Mobilization of hematopoietic stem and progenitor cells (HSPCs) into the circulation is essential for maintaining homeostasis. Here, the authors show that Phc2 in bone marrow stromal cells represses the cell adhesion molecule Vcam1 and facilitates mobilization of HSPCs through regulation of epigenetic marks.
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49
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Pivetti S, Fernandez-Perez D, D’Ambrosio A, Barbieri CM, Manganaro D, Rossi A, Barnabei L, Zanotti M, Scelfo A, Chiacchiera F, Pasini D. Loss of PRC1 activity in different stem cell compartments activates a common transcriptional program with cell type-dependent outcomes. SCIENCE ADVANCES 2019; 5:eaav1594. [PMID: 31106267 PMCID: PMC6520019 DOI: 10.1126/sciadv.aav1594] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/02/2019] [Indexed: 05/11/2023]
Abstract
Polycomb repressive complexes are evolutionarily conserved complexes that maintain transcriptional repression during development and differentiation to establish and preserve cell identity. We recently described the fundamental role of PRC1 in preserving intestinal stem cell identity through the inhibition of non-lineage-specific transcription factors. To further elucidate the role of PRC1 in adult stem cell maintenance, we now investigated its role in LGR5+ hair follicle stem cells during regeneration. We show that PRC1 depletion severely affects hair regeneration and, different from intestinal stem cells, derepression of its targets induces the ectopic activation of an epidermal-specific program. Our data support a general role of PRC1 in preserving stem cell identity that is shared between different compartments. However, the final outcome of the ectopic activation of non-lineage-specific transcription factors observed upon loss of PRC1 is largely context-dependent and likely related to the transcription factors repertoire and specific epigenetic landscape of different cellular compartments.
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Affiliation(s)
- Silvia Pivetti
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | | | - Alessandro D’Ambrosio
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | | | - Daria Manganaro
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Alessandra Rossi
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Laura Barnabei
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Marika Zanotti
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Andrea Scelfo
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Fulvio Chiacchiera
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
- University of Trento, Department of Cellular, Computational and Integrative Biology–CIBIO, Trento, Italy
- Corresponding author. (F.C.); (D.P.)
| | - Diego Pasini
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
- University of Milan, Department of Health Sciences, Milan, Italy
- Corresponding author. (F.C.); (D.P.)
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50
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Kelly MJ, So J, Rogers AJ, Gregory G, Li J, Zethoven M, Gearhart MD, Bardwell VJ, Johnstone RW, Vervoort SJ, Kats LM. Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis. Nat Commun 2019; 10:1347. [PMID: 30902969 PMCID: PMC6430802 DOI: 10.1038/s41467-019-09250-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/28/2019] [Indexed: 12/26/2022] Open
Abstract
The BCL6 Corepressor (BCOR) is a component of a variant Polycomb repressive complex 1 (PRC1) that is essential for normal development. Recurrent mutations in the BCOR gene have been identified in acute myeloid leukaemia and myelodysplastic syndrome among other cancers; however, its function remains poorly understood. Here we examine the role of BCOR in haematopoiesis in vivo using a conditional mouse model that mimics the mutations observed in haematological malignancies. Inactivation of Bcor in haematopoietic stem cells (HSCs) results in expansion of myeloid progenitors and co-operates with oncogenic KrasG12D in the initiation of an aggressive and fully transplantable acute leukaemia. Gene expression analysis and chromatin immunoprecipitation sequencing reveals differential regulation of a subset of PRC1-target genes including HSC-associated transcription factors such as Hoxa7/9. This study provides mechanistic understanding of how BCOR regulates cell fate decisions and how loss of function contributes to the development of leukaemia.
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Affiliation(s)
- Madison J Kelly
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Joan So
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Amy J Rogers
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Gareth Gregory
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3052, Australia.,Monash Haematology, Monash Health and School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Jason Li
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Magnus Zethoven
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Vivian J Bardwell
- Department of Genetics, Cell Biology and Development and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ricky W Johnstone
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3052, Australia
| | | | - Lev M Kats
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia. .,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3052, Australia.
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