1
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Weissmiller AM, Fesik SW, Tansey WP. WD Repeat Domain 5 Inhibitors for Cancer Therapy: Not What You Think. J Clin Med 2024; 13:274. [PMID: 38202281 PMCID: PMC10779565 DOI: 10.3390/jcm13010274] [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: 12/04/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
WDR5 is a conserved nuclear protein that scaffolds the assembly of epigenetic regulatory complexes and moonlights in functions ranging from recruiting MYC oncoproteins to chromatin to facilitating the integrity of mitosis. It is also a high-value target for anti-cancer therapies, with small molecule WDR5 inhibitors and degraders undergoing extensive preclinical assessment. WDR5 inhibitors were originally conceived as epigenetic modulators, proposed to inhibit cancer cells by reversing oncogenic patterns of histone H3 lysine 4 methylation-a notion that persists to this day. This premise, however, does not withstand contemporary inspection and establishes expectations for the mechanisms and utility of WDR5 inhibitors that can likely never be met. Here, we highlight salient misconceptions regarding WDR5 inhibitors as epigenetic modulators and provide a unified model for their action as a ribosome-directed anti-cancer therapy that helps focus understanding of when and how the tumor-inhibiting properties of these agents can best be understood and exploited.
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Affiliation(s)
- April M. Weissmiller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 32132, USA;
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - William P. Tansey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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2
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Yan B, Yuan Q, Guryanova OA. Epigenetic Mechanisms in Hematologic Aging and Premalignant Conditions. EPIGENOMES 2023; 7:32. [PMID: 38131904 PMCID: PMC10743085 DOI: 10.3390/epigenomes7040032] [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: 10/26/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Hematopoietic stem cells (HSCs) are essential for maintaining overall health by continuously generating blood cells throughout an individual's lifespan. However, as individuals age, the hematopoietic system undergoes significant functional decline, rendering them more susceptible to age-related diseases. Growing research evidence has highlighted the critical role of epigenetic regulation in this age-associated decline. This review aims to provide an overview of the diverse epigenetic mechanisms involved in the regulation of normal HSCs during the aging process and their implications in aging-related diseases. Understanding the intricate interplay of epigenetic mechanisms that contribute to aging-related changes in the hematopoietic system holds great potential for the development of innovative strategies to delay the aging process. In fact, interventions targeting epigenetic modifications have shown promising outcomes in alleviating aging-related phenotypes and extending lifespan in various animal models. Small molecule-based therapies and reprogramming strategies enabling epigenetic rejuvenation have emerged as effective approaches for ameliorating or even reversing aging-related conditions. By acquiring a deeper understanding of these epigenetic mechanisms, it is anticipated that interventions can be devised to prevent or mitigate the rates of hematologic aging and associated diseases later in life. Ultimately, these advancements have the potential to improve overall health and enhance the quality of life in aging individuals.
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Affiliation(s)
- Bowen Yan
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
| | | | - Olga A. Guryanova
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
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3
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Wallace L, Obeng EA. Noncoding rules of survival: epigenetic regulation of normal and malignant hematopoiesis. Front Mol Biosci 2023; 10:1273046. [PMID: 38028538 PMCID: PMC10644717 DOI: 10.3389/fmolb.2023.1273046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Hematopoiesis is an essential process for organismal development and homeostasis. Epigenetic regulation of gene expression is critical for stem cell self-renewal and differentiation in normal hematopoiesis. Increasing evidence shows that disrupting the balance between self-renewal and cell fate decisions can give rise to hematological diseases such as bone marrow failure and leukemia. Consequently, next-generation sequencing studies have identified various aberrations in histone modifications, DNA methylation, RNA splicing, and RNA modifications in hematologic diseases. Favorable outcomes after targeting epigenetic regulators during disease states have further emphasized their importance in hematological malignancy. However, these targeted therapies are only effective in some patients, suggesting that further research is needed to decipher the complexity of epigenetic regulation during hematopoiesis. In this review, an update on the impact of the epigenome on normal hematopoiesis, disease initiation and progression, and current therapeutic advancements will be discussed.
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Affiliation(s)
| | - Esther A. Obeng
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, United States
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4
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Huang X, Dai Z, Li Q, Lin X, Huang Q, Zeng T. Roles and regulatory mechanisms of KIN17 in cancers (Review). Oncol Lett 2023; 25:137. [PMID: 36909374 PMCID: PMC9996293 DOI: 10.3892/ol.2023.13723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/30/2023] [Indexed: 02/19/2023] Open
Abstract
KIN17, which is known as a DNA and RNA binding protein, is highly expressed in numerous types of human cancers and was discovered to participate in several vital cell behaviors, including DNA replication, damage repair, regulation of cell cycle and RNA processing. Furthermore, KIN17 is associated with cancer cell proliferation, migration, invasion and cell cycle regulation by regulating pathways including the p38 MAPK, NF-κB-Snail and TGF-β/Smad2 signaling pathways. In addition, knockdown of KIN17 was found to enhance the sensitivity of tumor cells to chemotherapeutic agents. Immunohistochemical analysis revealed that there were significant differences in the expression of KIN17 between cancer tissues and adjacent tissues. Both the Kaplan-Meier survival analysis and multivariate Cox regression analysis indicated that KIN17 is aberrantly high expressed in various tumor tissues and is also associated with poor prognosis in patients with various tumor types. Taken together, KIN17 has key roles in tumorigenesis and cancer development. Investigating the relationship between KIN17 and neoplasms will provide a vital theoretical basis for KIN17 to serve as a diagnostic and prognostic biomarker for cancer patients and as a potential target for cancer therapy.
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Affiliation(s)
- Xueran Huang
- Medical Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, P.R. China
| | - Zichang Dai
- Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Qiuyan Li
- Medical Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, P.R. China.,Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Xiaocong Lin
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Qiyuan Huang
- Clinical Biobank Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Tao Zeng
- Medical Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, P.R. China
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5
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Shi D, Shan Y, Zhu X, Wang H, Wu S, Wu Z, Bao W. Histone Methyltransferase MLL1 Mediates Oxidative Stress and Apoptosis upon Deoxynivalenol Exposure in the Intestinal Porcine Epithelial Cells. Antioxidants (Basel) 2022; 11:antiox11102006. [PMID: 36290729 PMCID: PMC9598511 DOI: 10.3390/antiox11102006] [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: 08/21/2022] [Revised: 10/02/2022] [Accepted: 10/04/2022] [Indexed: 11/21/2022] Open
Abstract
Deoxynivalenol (DON), as a secondary metabolite of fungi, is continually detected in livestock feed and has a high risk to animals and humans. Moreover, pigs are very sensitive to DON. Recently, the role of histone modification has drawn people’s attention; however, few studies have elucidated how histone modification participates in the cytotoxicity or genotoxicity induced by mycotoxins. In this study, we used intestinal porcine epithelial cells (IPEC-J2 cells) as a model to DON exposure in vitro. Mixed lineage leukemia 1 (MLL1) regulates gene expression by exerting the role of methyltransferase. Our studies demonstrated that H3K4me3 enrichment was enhanced and MLL1 was highly upregulated upon 1 μg/mL DON exposure in IPEC-J2 cells. We found that the silencing of MLL1 resulted in increasing the apoptosis rate, arresting the cell cycle, and activating the mitogen-activated protein kinases (MAPKs) pathway. An RNA-sequencing analysis proved that differentially expressed genes (DEGs) were enriched in the cell cycle, apoptosis, and tumor necrosis factor (TNF) signaling pathway between the knockdown of MLL1 and negative control groups, which were associated with cytotoxicity induced by DON. In summary, these current results might provide new insight into how MLL1 regulates cytotoxic effects induced by DON via an epigenetic mechanism.
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Affiliation(s)
- Dongfeng Shi
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yiyi Shan
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyang Zhu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Haifei Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhengchang Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Z.W.); (W.B.)
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Z.W.); (W.B.)
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6
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van Dijk AD, Griffen TL, Qiu YH, Hoff FW, Toro E, Ruiz K, Ruvolo PP, Lillard JW, de Bont ESJM, Burger JA, Wierda W, Kornblau SM. RPPA-based proteomics recognizes distinct epigenetic signatures in chronic lymphocytic leukemia with clinical consequences. Leukemia 2022; 36:712-722. [PMID: 34625713 DOI: 10.1038/s41375-021-01438-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/11/2021] [Accepted: 09/21/2021] [Indexed: 11/08/2022]
Abstract
The chronic lymphocytic leukemia (CLL) armamentarium has evolved significantly, with novel therapies that inhibit Bruton Tyrosine Kinase, PI3K delta and/or the BCL2 protein improving outcomes. Still, the clinical course of CLL patients is highly variable and most previously recognized prognostic features lack the capacity to predict response to modern treatments indicating the need for new prognostic markers. In this study, we identified four epigenetically distinct proteomic signatures of a large cohort of CLL and related diseases derived samples (n = 871) using reverse phase protein array technology. These signatures are associated with clinical features including age, cytogenetic abnormalities [trisomy 12, del(13q) and del(17p)], immunoglobulin heavy-chain locus (IGHV) mutational load, ZAP-70 status, Binet and Rai staging as well as with the outcome measures of time to treatment and overall survival. Protein signature membership was identified as predictive marker for overall survival regardless of other clinical features. Among the analyzed epigenetic proteins, EZH2, HDAC6, and loss of H3K27me3 levels were the most independently associated with poor survival. These findings demonstrate that proteomic based epigenetic biomarkers can be used to better classify CLL patients and provide therapeutic guidance.
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Affiliation(s)
- Anneke D van Dijk
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen, the Netherlands.
| | - Ti'ara L Griffen
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Yihua H Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fieke W Hoff
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen, the Netherlands
| | - Endurance Toro
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin Ruiz
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter P Ruvolo
- Department of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James W Lillard
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Eveline S J M de Bont
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen, the Netherlands
| | - Jan A Burger
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William Wierda
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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7
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Zorro Shahidian L, Daujat S. Development and Validation of Antibodies Targeting Site-Specific Histone Methylation. Methods Mol Biol 2022; 2529:171-206. [PMID: 35733016 DOI: 10.1007/978-1-0716-2481-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of specific anti-modification antibodies as research tools has revolutionized the way histone methylation is studied. Lack of stringent quality controls, however, led to the development of nonspecific antibodies, compromising their use. In this chapter, we provide a series of protocols that collectively will help those studying histone methylation to develop and thoroughly validate high-end sequence-specific and methylation-dependent antibodies.
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Affiliation(s)
- Lara Zorro Shahidian
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Santander, Spain
| | - Sylvain Daujat
- Biotechnology and Cell Signaling, CNRS UMR7242, University of Strasbourg, Illkirch Cedex, France.
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8
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Guida N, Sanguigno L, Mascolo L, Calabrese L, Serani A, Molinaro P, Lau CG, Annunziato L, Formisano L. The Transcriptional Complex Sp1/KMT2A by Up-Regulating Restrictive Element 1 Silencing Transcription Factor Accelerates Methylmercury-Induced Cell Death in Motor Neuron-Like NSC34 Cells Overexpressing SOD1-G93A. Front Neurosci 2021; 15:771580. [PMID: 34899171 PMCID: PMC8662822 DOI: 10.3389/fnins.2021.771580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Methylmercury (MeHg) exposure has been related to amyotrophic lateral sclerosis (ALS) pathogenesis and molecular mechanisms of its neurotoxicity has been associated to an overexpression of the Restrictive Element 1 Silencing Transcription factor (REST). Herein, we evaluated the possibility that MeHg could accelerate neuronal death of the motor neuron-like NSC34 cells transiently overexpressing the human Cu2+/Zn2+superoxide dismutase 1 (SOD1) gene mutated at glycine 93 (SOD1-G93A). Indeed, SOD1-G93A cells exposed to 100 nM MeHg for 24 h showed a reduction in cell viability, as compared to cells transfected with empty vector or with unmutated SOD1 construct. Interestingly, cell survival reduction in SOD1-G93A cells was associated with an increase of REST mRNA and protein levels. Furthermore, MeHg increased the expression of the transcriptional factor Sp1 and promoted its binding to REST gene promoter sequence. Notably, Sp1 knockdown reverted MeHg-induced REST increase. Co-immunoprecipitation experiments demonstrated that Sp1 physically interacted with the epigenetic writer Lysine-Methyltransferase-2A (KMT2A). Moreover, knocking-down of KMT2A reduced MeHg-induced REST mRNA and protein increase in SOD1-G93A cells. Finally, we found that MeHg-induced REST up-regulation triggered necropoptotic cell death, monitored by RIPK1 increased protein expression. Interestingly, REST knockdown or treatment with the necroptosis inhibitor Necrostatin-1 (Nec) decelerated MeH-induced cell death in SOD1-G93A cells. Collectively, this study demonstrated that MeHg hastens necroptotic cell death in SOD1-G93A cells via Sp1/KMT2A complex, that by epigenetic mechanisms increases REST gene expression.
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Affiliation(s)
| | - Luca Sanguigno
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, "Federico II" University of Naples, Naples, Italy
| | - Luigi Mascolo
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, "Federico II" University of Naples, Naples, Italy
| | - Lucrezia Calabrese
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, "Federico II" University of Naples, Naples, Italy
| | - Angelo Serani
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, "Federico II" University of Naples, Naples, Italy
| | - Pasquale Molinaro
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, "Federico II" University of Naples, Naples, Italy
| | - C Geoffrey Lau
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China
| | | | - Luigi Formisano
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, "Federico II" University of Naples, Naples, Italy
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9
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MLL1 is required for maintenance of intestinal stem cells. PLoS Genet 2021; 17:e1009250. [PMID: 34860830 PMCID: PMC8641872 DOI: 10.1371/journal.pgen.1009250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/30/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic mechanisms are gatekeepers for the gene expression patterns that establish and maintain cellular identity in mammalian development, stem cells and adult homeostasis. Amongst many epigenetic marks, methylation of histone 3 lysine 4 (H3K4) is one of the most widely conserved and occupies a central position in gene expression. Mixed lineage leukemia 1 (MLL1/KMT2A) is the founding mammalian H3K4 methyltransferase. It was discovered as the causative mutation in early onset leukemia and subsequently found to be required for the establishment of definitive hematopoiesis and the maintenance of adult hematopoietic stem cells. Despite wide expression, the roles of MLL1 in non-hematopoietic tissues remain largely unexplored. To bypass hematopoietic lethality, we used bone marrow transplantation and conditional mutagenesis to discover that the most overt phenotype in adult Mll1-mutant mice is intestinal failure. MLL1 is expressed in intestinal stem cells (ISCs) and transit amplifying (TA) cells but not in the villus. Loss of MLL1 is accompanied by loss of ISCs and a differentiation bias towards the secretory lineage with increased numbers and enlargement of goblet cells. Expression profiling of sorted ISCs revealed that MLL1 is required to promote expression of several definitive intestinal transcription factors including Pitx1, Pitx2, Foxa1, Gata4, Zfp503 and Onecut2, as well as the H3K27me3 binder, Bahcc1. These results were recapitulated using conditional mutagenesis in intestinal organoids. The stem cell niche in the crypt includes ISCs in close association with Paneth cells. Loss of MLL1 from ISCs promoted transcriptional changes in Paneth cells involving metabolic and stress responses. Here we add ISCs to the MLL1 repertoire and observe that all known functions of MLL1 relate to the properties of somatic stem cells, thereby highlighting the suggestion that MLL1 is a master somatic stem cell regulator.
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10
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Klonou A, Chlamydas S, Piperi C. Structure, Activity and Function of the MLL2 (KMT2B) Protein Lysine Methyltransferase. Life (Basel) 2021; 11:823. [PMID: 34440566 PMCID: PMC8401916 DOI: 10.3390/life11080823] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 12/31/2022] Open
Abstract
The Mixed Lineage Leukemia 2 (MLL2) protein, also known as KMT2B, belongs to the family of mammalian histone H3 lysine 4 (H3K4) methyltransferases. It is a large protein of 2715 amino acids, widely expressed in adult human tissues and a paralog of the MLL1 protein. MLL2 contains a characteristic C-terminal SET domain responsible for methyltransferase activity and forms a protein complex with WRAD (WDR5, RbBP5, ASH2L and DPY30), host cell factors 1/2 (HCF 1/2) and Menin. The MLL2 complex is responsible for H3K4 trimethylation (H3K4me3) on specific gene promoters and nearby cis-regulatory sites, regulating bivalent developmental genes as well as stem cell and germinal cell differentiation gene sets. Moreover, MLL2 plays a critical role in development and germ line deletions of Mll2 have been associated with early growth retardation, neural tube defects and apoptosis that leads to embryonic death. It has also been involved in the control of voluntary movement and the pathogenesis of early stage childhood dystonia. Additionally, tumor-promoting functions of MLL2 have been detected in several cancer types, including colorectal, hepatocellular, follicular cancer and gliomas. In this review, we discuss the main structural and functional aspects of the MLL2 methyltransferase with particular emphasis on transcriptional mechanisms, gene regulation and association with diseases.
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Affiliation(s)
- Alexia Klonou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.K.); (S.C.)
| | - Sarantis Chlamydas
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.K.); (S.C.)
- Research and Development Department, Active Motif, Inc., Carlsbad, CA 92008, USA
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.K.); (S.C.)
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11
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Yuan M, Wu B, Zhang L, Wang H, Yang Y. CD40L/CD40 regulates adipokines and cytokines by H3K4me3 modification in epicardial adipocytes. J Cardiovasc Pharmacol 2021; 78:228-234. [PMID: 34029270 DOI: 10.1097/fjc.0000000000001060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/28/2021] [Indexed: 11/25/2022]
Abstract
ABSTRACT Epicardial adipose tissue (EAT) dysfunction mediates chronic inflammation by regulating inflammation-related adipokines and cytokines, and further promotes coronary artery disease (CAD) development. CD40L/CD40 is involved in multiple inflammatory pathways that contribute to various pathophysiological processes. However, the function of CD40L/CD40 in adipokine and cytokine expression and production in epicardial adipocytes remains unclear. The purpose of the present study was to explore the role and underlying mechanisms of CD40L/CD40 in adipokine and cytokine expression and production. We isolated adipocytes from EAT tissues of CAD and non-CAD patients. We noticed that CD40 was dramatically increased in EAT tissues of CAD patients. Loss-of-function and gain-of-function studies were performed. The results showed that CD40 silencing reduced recombinant CD40 ligand (rCD40L)-induced up-regulation of plasminogen activator inhibitor-1 (PAI-1), leptin, interleukin-6 (IL-6) and monocyte chemotactic protein-1 (MCP-1) mRNA levels and secretion. Overexpression of CD40 displayed the opposite results. In addition, rCD40L triggered mixed lineage leukemia protein-1 (MLL1) expression both in mRNA and protein levels. CD40 depletion apparently blocked MLL1 expression, whereas gain of function of CD40 resulted in augmentation of MLL1 levels. Interestingly, ChIP-qCPR analysis revealed that CD40 elimination dampened histone H3 lysine 4 trimethylation (H3K4me3) enrichment at PAI-1, leptin, IL-6 and MCP-1 promoter regions in the presence of rCD40L. The reverse pattern was observed upon ectopic expression of CD40. Most important, MLL1 silencing effectively reversed the promotive effects of CD40 on adipokine and cytokine secretion. Taken together, our findings suggest that CD40L/CD40 regulates adipokine and cytokine expression by H3K4me3 modification in adipocytes.
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Affiliation(s)
- Ming Yuan
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi, P.R. China
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12
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The Role of H3K4 Trimethylation in CpG Islands Hypermethylation in Cancer. Biomolecules 2021; 11:biom11020143. [PMID: 33499170 PMCID: PMC7912453 DOI: 10.3390/biom11020143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/30/2020] [Accepted: 01/15/2021] [Indexed: 01/01/2023] Open
Abstract
CpG methylation in transposons, exons, introns and intergenic regions is important for long-term silencing, silencing of parasitic sequences and alternative promoters, regulating imprinted gene expression and determining X chromosome inactivation. Promoter CpG islands, although rich in CpG dinucleotides, are unmethylated and remain so during all phases of mammalian embryogenesis and development, except in specific cases. The biological mechanisms that contribute to the maintenance of the unmethylated state of CpG islands remain elusive, but the modification of established DNA methylation patterns is a common feature in all types of tumors and is considered as an event that intrinsically, or in association with genetic lesions, feeds carcinogenesis. In this review, we focus on the latest results describing the role that the levels of H3K4 trimethylation may have in determining the aberrant hypermethylation of CpG islands in tumors.
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13
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Abstract
Sequence analyses highlight a massive peptide sharing between immunoreactive Epstein-Barr virus (EBV) epitopes and human proteins that—when mutated, deficient or improperly functioning—associate with tumorigenesis, diabetes, lupus, multiple sclerosis, rheumatoid arthritis, and immunodeficiencies, among others. Peptide commonality appears to be the molecular platform capable of linking EBV infection to the vast EBV-associated diseasome via cross-reactivity and questions the hypothesis of the “negative selection” of self-reactive lymphocytes. Of utmost importance, this study warns that using entire antigens in anti-EBV immunotherapies can associate with autoimmune manifestations and further supports the concept of peptide uniqueness for designing safe and effective anti-EBV immunotherapies.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, Bari, Italy
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Aviv University School of Medicine, Tel-Hashomer, Israel.,I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, Sechenov University, Moscow, Russia
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14
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Kwon M, Park K, Hyun K, Lee JH, Zhou L, Cho YW, Ge K, Skalnik DG, Muir TW, Kim J. H2B ubiquitylation enhances H3K4 methylation activities of human KMT2 family complexes. Nucleic Acids Res 2020; 48:5442-5456. [PMID: 32365172 PMCID: PMC7261165 DOI: 10.1093/nar/gkaa317] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/27/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
In mammalian cells, distinct H3K4 methylation states are created by deposition of methyl groups by multiple complexes of histone lysine methyltransferase 2 (KMT2) family proteins. For comprehensive analyses that directly compare the catalytic properties of all six human KMT2 complexes, we employed a biochemically defined system reconstituted with recombinant KMT2 core complexes (KMT2CoreCs) containing minimal components required for nucleosomal H3K4 methylation activity. We found that each KMT2CoreC generates distinct states and different levels of H3K4 methylation, and except for MLL3 all are stimulated by H2Bub. Notably, SET1BCoreC exhibited the strongest H3K4 methylation activity and, to our surprise, did not require H2B ubiquitylation (H2Bub); in contrast, H2Bub was required for the H3K4me2/3 activity of the paralog SET1ACoreC. We also found that WDR5, RbBP5, ASH2L and DPY30 are required for efficient H3K4 methyltransferase activities of all KMT2CoreCs except MLL3, which could produce H3K4me1 in the absence of WDR5. Importantly, deletion of the PHD2 domain of CFP1 led to complete loss of the H3K4me2/3 activities of SET1A/BCoreCs in the presence of H2Bub, indicating a critical role for this domain in the H2Bub-stimulated H3K4 methylation. Collectively, our results suggest that each KMT2 complex methylates H3K4 through distinct mechanisms in which individual subunits differentially participate.
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Affiliation(s)
- Minjung Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Kihyun Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Kwangbeom Hyun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jeong-Heon Lee
- Biology Department, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Linjiao Zhou
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, NJ 08544, USA
| | - Young-Wook Cho
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David G Skalnik
- Biology Department, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, NJ 08544, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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15
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Feng Z, Jie L, Guimin L, Xi W. Mixed Lineage Leukemia 1 Promoted Neuron Apoptosis in Ischemic Penumbra via Regulating ASK-1/TNF-α Complex. Front Neuroanat 2020; 14:36. [PMID: 32792914 PMCID: PMC7394220 DOI: 10.3389/fnana.2020.00036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 06/03/2020] [Indexed: 12/26/2022] Open
Abstract
Neuron apoptosis in ischemic penumbra was proved to be involved in ischemic stroke (IS) development and contributed to the poor prognosis of IS. Recent studies showed that aberrant trimethylation of histone H3 lysine 4 (H3K4me3) level was associated with cell apoptosis. This study aimed to explore the underlying mechanism of neuron apoptosis in ischemic penumbra via histone methyltransferase (HMT) mixed lineage leukemia 1 (MLL1) mediated epigenetic pathway. Mouse IS model was established by middle cerebral artery occlusion (MCAO). Mouse primary cortical mixed cells were cultured and treated with oxygen–glucose deprivation (OGD) to simulate IS process. The expressions of apoptosis signal regulating kinase-1 (ASK-1), pASK-1, cleaved caspase-3, ASK-1/serine–threonine kinase receptor-associated protein (STRAP)/14-3-3 complex, ASK-1/tumor necrosis factor-α (TNF-α) complex, and MLL1 in mouse brain tissue and mouse primary cortical mixed cells were analyzed. The function of MLL1 was investigated using small interfering RNA (siRNA) targeting MLL1 and vector overexpressing MLL1. In vivo inhibition of MLL1 was conducted to explore its value as a therapeutic target. The prognostic value of MLL1 was investigated in IS patients. Results showed that the expressions of ASK-1, pASK-1, cleaved caspase-3, ASK-1/TNF-α complex, and MLL1 increased significantly in ischemic penumbra compared to brain tissue from the control group (P < 0.05). MCAO and OGD significantly upregulated the H3K4me3 level in ASK-1 promoter region and promoted the recruitment of MLL1 to this region (P < 0.05). siMLL1 significantly reversed the proapoptosis effects of OGD in primary cortical mixed cells, while MLL1 overexpression induced apoptosis of cells (P < 0.05). In vivo inhibition of MLL1 significantly reduced the infarct volume and the neurological score of MCAO mice (P < 0.05). Serum MLL1 level had a positive association with that in ischemic core and penumbra in mouse model and was positively correlated with the infarct volume and neurological score (P < 0.05). Besides, serum MLL1 level was also significantly correlated with the severity of IS (P < 0.05), and high serum MLL1 level indicated poor prognosis of IS patients (P < 0.05). These results revealed that MLL1 contributed to neuron cell apoptosis in ischemic penumbra after IS onset by promoting the formation of ASK-1/TNF-α complex, and its serum level was associated with poor prognosis of IS.
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Affiliation(s)
- Zhang Feng
- Department of Neurology, Shandong Provincial Western Hospital, Shandong Provincial ENT Hospital, Jinan, China
| | - Liu Jie
- Department of Neurology, The Fourth Hospital of Jinan City, Jinan, China
| | - Lv Guimin
- Department of Neurology, Zibo Integrated Traditional Chinese and Western Medicine Hospital, Zibo, China
| | - Wang Xi
- Department of Neurology, Chongqing Wulong Hospital of Traditional Chinese Medicine, Wulong, China
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16
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Meitern R, Fort J, Giraudeau M, Rattiste K, Sild E, Sepp T. Age-dependent expression of cancer-related genes in a long-lived seabird. Evol Appl 2020; 13:1708-1718. [PMID: 32821278 PMCID: PMC7428815 DOI: 10.1111/eva.13024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/21/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
Studies of model animals like mice and rats have led to great advances in our understanding of the process of tumorigenesis, but this line of study has less to offer for understanding the mechanisms of cancer resistance. Increasing the diversity of nonmodel species from the perspective of molecular mechanisms of natural cancer resistance can lead to new insights into the evolution of protective mechanisms against neoplastic processes and to a wider understanding of natural cancer defense mechanisms. Such knowledge could then eventually be harnessed for the development of human cancer therapies. We suggest here that seabirds are promising, albeit currently completely ignored candidates for studying cancer defense mechanisms, as they have a longer maximum life span than expected from their body size and rates of energy metabolism and may have thus evolved mechanisms to limit neoplasia progression, especially at older ages. We here apply a novel, intraspecific approach of comparing old and young seabirds for improving our understanding of aging and neoplastic processes in natural settings. We used the long-lived common gulls (Larus canus) for studying the age-related pattern of expression of cancer-related genes, based on transcriptome analysis and databases of orthologues of human cancer genes. The analysis of differently expressed cancer-related genes between young and old gulls indicated that similarly to humans, age is potentially affecting cancer risk in this species. Out of eleven differentially expressed cancer-related genes between the groups, three were likely artifactually linked to cancer. The remaining eight were downregulated in old gulls compared to young ones. The downregulation of five of them could be interpreted as a mechanism suppressing neoplasia risk and three as increasing the risk. Based on these results, we suggest that old gulls differ from young ones both from the aspect of cancer susceptibility and tumor suppression at the genetic level.
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Affiliation(s)
- Richard Meitern
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Jérôme Fort
- Littoral Environnement et Sociétés (LIENSs)UMR 7266 CNRS‐La Rochelle UniversitéLa RochelleFrance
| | | | - Kalev Rattiste
- Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartuEstonia
| | - Elin Sild
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Tuul Sepp
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
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17
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Imuta H, Fujita D, Oba S, Kiyosue A, Nishimatsu H, Yudo K, Suzuki E. Histone methylation and demethylation are implicated in the transient and sustained activation of the interleukin-1β gene in murine macrophages. Heart Vessels 2020; 35:1746-1754. [PMID: 32676696 DOI: 10.1007/s00380-020-01670-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
Macrophages play a crucial role in the development of atherosclerosis. To explore the mechanism by which macrophages attain a proinflammatory phenotype for a sustained period, we stimulated macrophages with lipopolysaccharide (LPS) and interferon-γ (IFN-γ) and measured the interleukin-1β (IL-1β) expression. The IL-1β expression increased transiently, and its expression lasted for, at least, 1 week after the cessation of LPS and IFN-γ stimulation. At the promoter region of the IL-1β gene, the demethylation of histone H3 lysine 27 (H3K27) was significantly induced for 1 week after transient stimulation with LPS and IFN-γ. The expression of H3K27 demethylases ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX) and jumonji domain-containing 3 (JMJD3) increased significantly for 1 week after transient stimulation with LPS and IFN-γ. When the UTX expression was inhibited by using small interfering RNA (siRNA) for UTX, the IL-1β expression was significantly suppressed in both transient and sustained phases, whereas siRNA for JMJD3 significantly inhibited only the sustained phase of the IL-1β expression. These results suggested that H3K27 demethylation was implicated in the transient and sustained increase in the IL-1β expression after LPS and IFN-γ stimulation.
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Affiliation(s)
- Hiroyuki Imuta
- Division of Cardiovascular Medicine, Faculty of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Daishi Fujita
- Division of Cardiovascular Medicine, Faculty of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shigeyoshi Oba
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Arihiro Kiyosue
- Division of Cardiovascular Medicine, Faculty of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hiroaki Nishimatsu
- Department of Urology, Fraternity Memorial Hospital, 2-1-11 Yokozuna, Sumida-ku, Tokyo, 130-8587, Japan
| | - Kazuo Yudo
- Institute of Medical Science, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, 216-8512, Japan
| | - Etsu Suzuki
- Institute of Medical Science, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, 216-8512, Japan.
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18
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Zraly CB, Zakkar A, Perez JH, Ng J, White KP, Slattery M, Dingwall AK. The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development. Nucleic Acids Res 2020; 48:3476-3495. [PMID: 32052053 PMCID: PMC7144903 DOI: 10.1093/nar/gkaa082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/17/2020] [Accepted: 01/30/2020] [Indexed: 12/29/2022] Open
Abstract
The MLR COMPASS complex monomethylates H3K4 that serves to epigenetically mark transcriptional enhancers to drive proper gene expression during animal development. Chromatin enrichment analyses of the Drosophila MLR complex reveals dynamic association with promoters and enhancers in embryos with late stage enrichments biased toward both active and poised enhancers. RNAi depletion of the Cmi (also known as Lpt) subunit that contains the chromatin binding PHD finger domains attenuates enhancer functions, but unexpectedly results in inappropriate enhancer activation during stages when hormone responsive enhancers are poised, revealing critical epigenetic roles involved in both the activation and repression of enhancers depending on developmental context. Cmi is necessary for robust H3K4 monomethylation and H3K27 acetylation that mark active enhancers, but not for the chromatin binding of Trr, the MLR methyltransferase. Our data reveal two likely major regulatory modes of MLR function, contributions to enhancer commissioning in early embryogenesis and bookmarking enhancers to enable rapid transcriptional re-activation at subsequent developmental stages.
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Affiliation(s)
- Claudia B Zraly
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Abdul Zakkar
- Department of Biology, Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - John Hertenstein Perez
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Jeffrey Ng
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.,Department of Biology, Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Matthew Slattery
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.,Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Andrew K Dingwall
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.,Department of Pathology & Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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19
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Park K, Kim JA, Kim J. Transcriptional regulation by the KMT2 histone H3K4 methyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194545. [DOI: 10.1016/j.bbagrm.2020.194545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/21/2020] [Accepted: 03/13/2020] [Indexed: 01/09/2023]
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20
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Roston A, Evans D, Gill H, McKinnon M, Isidor B, Cogné B, Mwenifumbo J, van Karnebeek C, An J, Jones SJM, Farrer M, Demos M, Connolly M, Gibson WT. SETD1B-associated neurodevelopmental disorder. J Med Genet 2020; 58:196-204. [PMID: 32546566 DOI: 10.1136/jmedgenet-2019-106756] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/11/2020] [Accepted: 04/14/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Dysfunction of histone methyltransferases and chromatin modifiers has been implicated in complex neurodevelopmental syndromes and cancers. SETD1B encodes a lysine-specific methyltransferase that assists in transcriptional activation of genes by depositing H3K4 methyl marks. Previous reports of patients with rare variants in SETD1B describe a distinctive phenotype that includes seizures, global developmental delay and intellectual disability. METHODS Two of the patients described herein were identified via genome-wide and exome-wide testing, with microarray and research-based exome, through the CAUSES (Clinical Assessment of the Utility of Sequencing and Evaluation as a Service) Research Clinic at the University of British Columbia. The third Vancouver patient had clinical trio exome sequencing through Blueprint Genetics. The fourth patient underwent singleton exome sequencing in Nantes, with subsequent recruitment to this cohort through GeneMatcher. RESULTS Here we present clinical reports of four patients with rare coding variants in SETD1B that demonstrate a shared phenotype, including intellectual disability, language delay, conserved musculoskeletal findings and seizures that may be treatment-refractory. We include supporting evidence from next-generation sequencing among a cohort of paediatric patients with epilepsy. CONCLUSION Rare coding variants in SETD1B can cause a diagnosable syndrome and could contribute as a risk factor for epilepsy, autism and other neurodevelopmental phenotypes. In the long term, some patients may also be at increased risk for cancers and other complex diseases. Thus, longitudinal studies are required to further elucidate the precise role of SETD1B in neurodevelopmental disorders and other systemic disease.
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Affiliation(s)
- Alexandra Roston
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Dan Evans
- Centre for Applied Neurogenetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Harinder Gill
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,Provincial Medical Genetics Program, BC Women's Hospital and Health Centre, Vancouver, British Columbia, Canada
| | - Margaret McKinnon
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Bertrand Isidor
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, Pays de la Loire, France
| | - Benjamin Cogné
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, Pays de la Loire, France.,INSERM, CNRS, UNIV Nantes, l'institut du thorax, Nantes, Frances
| | - Jill Mwenifumbo
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Emma Children's Hospital, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, Netherlands.,Department of Pediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Jianghong An
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Matthew Farrer
- Centre for Applied Neurogenetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Demos
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mary Connolly
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - William T Gibson
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
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21
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Hematopoietic regeneration under the spell of epigenetic-epitranscriptomic factors and transposable elements. Curr Opin Hematol 2020; 27:264-272. [DOI: 10.1097/moh.0000000000000585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Enhancing Hematopoiesis from Murine Embryonic Stem Cells through MLL1-Induced Activation of a Rac/Rho/Integrin Signaling Axis. Stem Cell Reports 2020; 14:285-299. [PMID: 31951812 PMCID: PMC7013201 DOI: 10.1016/j.stemcr.2019.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
The Mixed Lineage Leukemia (MLL1, KMT2A) gene is critical for development and maintenance of hematopoietic stem cells (HSCs), however, whether this protein is limiting for HSC development is unknown due to lack of physiologic model systems. Here, we develop an MLL1-inducible embryonic stem cell (ESC) system and show that induction of wild-type MLL1 during ESC differentiation selectively increases hematopoietic potential from a transitional c-Kit+/Cd41+ population in the embryoid body and also at sites of hematopoiesis in embryos. Single-cell sequencing analysis illustrates inherent heterogeneity of the c-Kit+/Cd41+ population and demonstrates that MLL1 induction shifts its composition toward multilineage hematopoietic identities. Surprisingly, this does not occur through increasing Hox or other canonical MLL1 targets but through an enhanced Rac/Rho/integrin signaling state, which increases responsiveness to Vla4 ligands and enhances hematopoietic commitment. Together, our data implicate a Rac/Rho/integrin signaling axis in the endothelial to hematopoietic transition and demonstrate that MLL1 actives this axis. Increasing MLL1 enhances hematopoietic potential in vitro and in vivo scRNA sequencing illustrates the heterogeneity of an EMP-like population from EBs MLL1 activates Rac/Rho/integrin signaling during hematopoietic specification MLL1-induced HSPCs are primed for hematopoiesis via integrin-mediated adhesion
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23
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Epigenetic Regulation of p21 cip1/waf1 in Human Cancer. Cancers (Basel) 2019; 11:cancers11091343. [PMID: 31514410 PMCID: PMC6769618 DOI: 10.3390/cancers11091343] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023] Open
Abstract
p21cip1/waf1 is a central regulator of cell cycle control and survival. While mutations are rare, it is commonly dysregulated in several human cancers due to epigenetic mechanisms influencing its transcriptional control. These mechanisms include promoter hypermethylation as well as additional pathways such as histone acetylation or methylation. The epigenetic regulators include writers, such as DNA methyltransferases (DNMTs); histone acetyltransferases (HATs) and histone lysine methyltransferases; erasers, such as histone deacetylases (HDACs); histone lysine demethylases [e.g., the Lysine Demethylase (KDM) family]; DNA hydroxylases; readers, such as the methyl-CpG-binding proteins (MBPs); and bromodomain-containing proteins, including the bromo- and extraterminal domain (BET) family. We further discuss the roles that long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) play in the epigenetic control of p21cip1/waf1 expression and its function in human cancers.
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24
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Lu J, Xu J, Li J, Pan T, Bai J, Wang L, Jin X, Lin X, Zhang Y, Li Y, Sahni N, Li X. FACER: comprehensive molecular and functional characterization of epigenetic chromatin regulators. Nucleic Acids Res 2019; 46:10019-10033. [PMID: 30102398 PMCID: PMC6212842 DOI: 10.1093/nar/gky679] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 08/04/2018] [Indexed: 01/09/2023] Open
Abstract
Epigenetic alterations, a well-recognized cancer hallmark, are driven by chromatin regulators (CRs). However, little is known about the extent of CR deregulation in cancer, and less is known about their common and specialized roles across various cancers. Here, we performed genome-wide analyses and constructed molecular signatures and network profiles of functional CRs in over 10 000 tumors across 33 cancer types. By integration of DNA mutation, genome-wide methylation, transcriptional/post-transcriptional regulation, and protein interaction networks with clinical outcomes, we identified CRs associated with cancer subtypes and clinical prognosis as potential oncogenic drivers. Comparative network analysis revealed principles of CR regulatory specificity and functionality. In addition, we identified common and specific CRs by assessing their prevalence across cancer types. Common CRs tend to be histone modifiers and chromatin remodelers with fundamental roles, whereas specialized CRs are involved in context-dependent functions. Finally, we have made a user-friendly web interface-FACER (Functional Atlas of Chromatin Epigenetic Regulators) available for exploring clinically relevant CRs for the development of CR biomarkers and therapeutic targets. Our integrative analysis reveals specific determinants of CRs across cancer types and presents a resource for investigating disease-associated CRs.
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Affiliation(s)
- Jianping Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang 150086, China
| | - Junyi Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tao Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Liqiang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiyun Jin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiaoyu Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang 150086, China.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang 150086, China
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25
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Hematopoietic stem and progenitor cell proliferation and differentiation requires the trithorax protein Ash2l. Sci Rep 2019; 9:8262. [PMID: 31164666 PMCID: PMC6547667 DOI: 10.1038/s41598-019-44720-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 05/20/2019] [Indexed: 12/18/2022] Open
Abstract
Post-translational modifications of core histones participate in controlling the expression of genes. Methylation of lysine 4 of histone H3 (H3K4), together with acetylation of H3K27, is closely associated with open chromatin and gene transcription. H3K4 methylation is catalyzed by KMT2 lysine methyltransferases that include the mixed-lineage leukemia 1–4 (MLL1-4) and SET1A and B enzymes. For efficient catalysis, all six require a core complex of four proteins, WDR5, RBBP5, ASH2L, and DPY30. We report that targeted disruption of Ash2l in the murine hematopoietic system results in the death of the mice due to a rapid loss of mature hematopoietic cells. However, lin−Sca1+Kit+ (LSK) cells, which are highly enriched in hematopoietic stem and multi-potent progenitor cells, accumulated in the bone marrow. The loss of Ash2l resulted in global reduction of H3K4 methylation and deregulated gene expression, including down-regulation of many mitosis-associated genes. As a consequence, LSK cells accumulated in the G2-phase of the cell cycle and were unable to proliferate and differentiate. In conclusion, Ash2l is essential for balanced gene expression and for hematopoietic stem and multi-potent progenitor cell physiology.
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26
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Fagan RJ, Dingwall AK. COMPASS Ascending: Emerging clues regarding the roles of MLL3/KMT2C and MLL2/KMT2D proteins in cancer. Cancer Lett 2019; 458:56-65. [PMID: 31128216 DOI: 10.1016/j.canlet.2019.05.024] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/16/2019] [Accepted: 05/19/2019] [Indexed: 12/12/2022]
Abstract
The KMT2 (lysine methyltransferase) family of histone modifying proteins play essential roles in regulating developmental pathways, and mutations in the genes encoding these proteins have been strongly linked to many blood and solid tumor cancers. The KMT2A-D proteins are histone 3 lysine 4 (H3K4) methyltransferases embedded in large COMPASS-like complexes important for RNA Polymerase II-dependent transcription. KMT2 mutations were initially associated with pediatric Mixed Lineage Leukemias (MLL) and found to be the result of rearrangements of the MLL1/KMT2A gene at 11q23. Over the past several years, large-scale tumor DNA sequencing studies have revealed the potential involvement of other KMT2 family genes, including heterozygous somatic mutations in the paralogous MLL3/KMT2C and MLL2(4)/KMT2D genes that are now among the most frequently associated with human cancer. Recent studies have provided a better understanding of the potential roles of disrupted KMT2C and KMT2D family proteins in cell growth aberrancy. These findings, together with an examination of cancer genomics databases provide new insights into the contribution of KMT2C/D proteins in epigenetic gene regulation and links to carcinogenesis.
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Affiliation(s)
- Richard J Fagan
- Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60521, USA
| | - Andrew K Dingwall
- Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60521, USA; Department of Cancer Biology and Pathology & Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60521, USA.
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27
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Yang P, Huang X, Lai C, Li L, Li T, Huang P, Ouyang S, Yan J, Cheng S, Lei G, Wang Z, Yu L, Hong Z, Li R, Dong H, Wang C, Yu Y, Wang X, Li X, Wang L, Lv F, Yin Y, Yang H, Song J, Gao Q, Wang X, Zhang S. SET domain containing 1B gene is mutated in primary hepatic neuroendocrine tumors. Int J Cancer 2019; 145:2986-2995. [PMID: 30977120 DOI: 10.1002/ijc.32334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/27/2019] [Indexed: 11/09/2022]
Abstract
Primary hepatic neuroendocrine tumors (PHNETs) are extremely rare NETs originating from the liver. These tumors are associated with heterogeneous prognosis, and few treatment targets for PHNETs have been identified. Because the major genetic alterations in PHNET are still largely unknown, we performed whole-exome sequencing of 22 paired tissues from PHNET patients and identified 22 recurring mutations of somatic genes involved in the following activities: epigenetic modification (BPTF, MECP2 and WDR5), cell cycle (TP53, ATM, MED12, DIDO1 and ATAD5) and neural development (UBR4, MEN1, GLUL and GIGYF2). Here, we show that TP53 and the SET domain containing the 1B gene (SETD1B) are the most frequently mutated genes in this set of samples (3/22 subjects, 13.6%). A biological analysis suggests that one of the three SETD1B mutants, A1054del, promotes cell proliferation, migration and invasion compared to wild-type SETD1B. Our work unveils that SETD1B A1054del mutant is functional in PHNET and implicates genes including TP53 in the disease. Our findings thus characterize the mutational landscapes of PHNET and implicate novel gene mutations linked to PHNET pathogenesis and potential therapeutic targets.
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Affiliation(s)
- Penghui Yang
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China.,State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | - Chengcai Lai
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- BGI-Shenzhen, Shenzhen, China.,Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Tieling Li
- Chinese PLA General Hospital, Beijing, China
| | - Peide Huang
- BGI-Shenzhen, Shenzhen, China.,Section of Molecular Disease Biology, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jin Yan
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Sijie Cheng
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Guanglin Lei
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Zhaohai Wang
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Linxiang Yu
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Zhixian Hong
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Ruisheng Li
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Hui Dong
- Eastern Hepatobiliary Surgery Institute/Hospital, Shanghai, China
| | - Cheng Wang
- Chinese PLA General Hospital, Beijing, China.,Beijing 307 Hospital Affiliated with the Academy of Medical Sciences, Beijing, China
| | - Yinghao Yu
- Fuzhou General Hospital of Nanjing Military Command of Chinese PLA, Fuzhou, China
| | - Xuan Wang
- The 81st Hospital of PLA, Nanjing, China
| | - Xianghong Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Liming Wang
- Cancer Hospital Chinese Academy of Medical Science, Beijing, China
| | - Fudong Lv
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Ye Yin
- BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jianxun Song
- Microbial pathogenesis and Immunology, Texas A&M University College of Medicine, Bryan, TX
| | | | - Xiliang Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shaogeng Zhang
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
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28
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Kim SH, Park WS, Chung J. SETD2, GIGYF2, FGFR3, BCR, KMT2C, and TSC2 as candidate genes for differentiating multilocular cystic renal neoplasm of low malignant potential from clear cell renal cell carcinoma with cystic change. Investig Clin Urol 2019; 60:148-155. [PMID: 31098421 PMCID: PMC6495037 DOI: 10.4111/icu.2019.60.3.148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/24/2019] [Indexed: 01/06/2023] Open
Abstract
Purpose Multilocular cystic renal neoplasm of low malignant potential (MCRNLMP) and clear cell renal cell carcinoma with cystic change (MCRCC) have different prognoses despite similar histologic characteristics. The aim of this study was to identify differentially mutated genes in resected tumor specimens from patients diagnosed with MCRNLMP and MCRCC using a kidney cancer gene panel. Materials and Methods Between 2009 and 2016, 13 MCRNLMP and 17 MCRCC cases were selected. Tumor tissues from 5 MCRNLMP and 16 MCRCC cases were subjected to gene sequencing to detect mutations among 88 genes selected from a kidney cancer gene panel after quality control. Fisher's exact test was used to compare gene mutation profiles between the two diseases. Genes were considered to be positive for mutation according to the presence of an in-frame/frameshift deletion or insertion, missense/nonsense mutation, or multi-hit mutation. Results During a median follow-up period of 66.2 months, there was only one case of MCRCC recurrence among all 30 patients. Target gene sequencing showed that 35 genes tended to be more frequently positive in either disease group, with six genes showing a significantly different frequency of mutation between the groups: GIGYF2 (odds ratio [OR], 5.735), FGFR3 (OR, 6.787), SETD2 (OR, 4.588), BCR (OR, 6.266), KMT2C (OR, 8.167), and TSC2 (OR, 4.474). Conclusions Six candidate genes showed significantly different mutation patterns between MCRNLMP and MCRCC, providing insight into their pathogenic mechanisms and differential prognoses.
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Affiliation(s)
- Sung Han Kim
- Department of Urology, Center for Prostate Cancer, Research Institute and National Cancer Center, Goyang, Korea
| | - Weon Seo Park
- Department of Pathology, Center for Prostate Cancer, Research Institute and National Cancer Center, Goyang, Korea
| | - Jinsoo Chung
- Department of Urology, Center for Prostate Cancer, Research Institute and National Cancer Center, Goyang, Korea
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29
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Chen D, Li T, Wang C, Lei G, Wang R, Wang Z, Yu L, Yan J, Zhang P, Wang X, Zhang S, Yang P. High‑level SETD1B gene expression is associated with unfavorable prognosis in hepatocellular carcinoma. Mol Med Rep 2019; 19:1587-1594. [PMID: 30628696 PMCID: PMC6390067 DOI: 10.3892/mmr.2019.9832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 11/23/2018] [Indexed: 12/12/2022] Open
Abstract
The SET domain-containing 1B (SETD1B) gene is involved in multiple biological processes, including tumor development and progression. However, the role of SETD1B in hepatocellular carcinoma (HCC) is largely unexplored. The present study, examined the expression of SETD1B in patients with HCC and assessed its clinical significance. Reverse transcriptase quantitative polymerase chain reaction and western blot analysis results revealed that the expression levels of SETD1B mRNA and protein were significantly increased in HCC tumor tissues compared with the adjacent normal tissues. In addition, an analysis of the patient clinical factors indicated that increased levels of SETD1B expression were associated with tumor size, clinical stage and liver cirrhosis. Patients with HCC with decreased levels of SETD1B expression exhibited longer survival times compared with those with increased levels of SETD1B expression. In addition, Cox's regression analysis results implied that the upregulation of SETD1B was an independent prognostic marker in patients with HCC. Taken together, the results demonstrated that SETD1B is essential in the progression of HCC and may be used as a potential prognostic marker and therapeutic target in HCC.
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Affiliation(s)
- Dong Chen
- Hepatobiliary Department, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Tieling Li
- Department of Cardiology, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Cheng Wang
- Department of Cardiology, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Guanglin Lei
- Hepatobiliary Department, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Ruilan Wang
- Hepatobiliary Department, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Zhaohai Wang
- Hepatobiliary Department, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Linxiang Yu
- Hepatobiliary Department, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Jin Yan
- Hepatobiliary Department, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Peirui Zhang
- Hepatobiliary Department, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Xiliang Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Shaogeng Zhang
- Hepatobiliary Department, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Penghui Yang
- Hepatobiliary Department, Beijing 302 Hospital, Beijing 100039, P.R. China
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30
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Gurumurthy A, Shen Y, Gunn E, Bungert J. Phase Separation and Transcription Regulation: Are Super-Enhancers and Locus Control Regions Primary Sites of Transcription Complex Assembly? Bioessays 2019; 41:e1800164. [PMID: 30500078 PMCID: PMC6484441 DOI: 10.1002/bies.201800164] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/31/2018] [Indexed: 01/10/2023]
Abstract
It is proposed that the multiple enhancer elements associated with locus control regions and super-enhancers recruit RNA polymerase II and efficiently assemble elongation competent transcription complexes that are transferred to target genes by transcription termination and transient looping mechanisms. It is well established that transcription complexes are recruited not only to promoters but also to enhancers, where they generate enhancer RNAs. Transcription at enhancers is unstable and frequently aborted. Furthermore, the Integrator and WD-domain containing protein 82 mediate transcription termination at enhancers. Abortion and termination of transcription at the multiple enhancers of locus control regions and super-enhancers provide a large pool of elongation competent transcription complexes. These are efficiently captured by strong basal promoter elements at target genes during transient looping interactions.
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Affiliation(s)
- Aishwarya Gurumurthy
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
| | - Yong Shen
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
| | - Eliot Gunn
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
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31
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Neilsen BK, Chakraborty B, McCall JL, Frodyma DE, Sleightholm RL, Fisher KW, Lewis RE. WDR5 supports colon cancer cells by promoting methylation of H3K4 and suppressing DNA damage. BMC Cancer 2018; 18:673. [PMID: 29925347 PMCID: PMC6011590 DOI: 10.1186/s12885-018-4580-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/08/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND KMT2/MLL proteins are commonly overexpressed or mutated in cancer and have been shown to support cancer maintenance. These proteins are responsible for methylating histone 3 at lysine 4 and promoting transcription and DNA synthesis; however, they are inactive outside of a multi-protein complex that requires WDR5. WDR5 has been implicated in cancer for its role in the COMPASS complex and its interaction with Myc; however, the role of WDR5 in colon cancer has not yet been elucidated. METHODS WDR5 expression was evaluated using RT-qPCR and western blot analysis. Cell viability and colony forming assays were utilized to evaluate the effects of WDR5 depletion or inhibition in colon cancer cells. Downstream effects of WDR5 depletion and inhibition were observed by western blot. RESULTS WDR5 is overexpressed in colon tumors and colon cancer cell lines at the mRNA and protein level. WDR5 depletion reduces cell viability in HCT116, LoVo, RKO, HCT15, SW480, SW620, and T84 colon cancer cells. Inhibition of the WDR5:KMT2/MLL interaction using OICR-9429 reduces cell viability in the same panel of cell lines albeit not to the same extent as RNAi-mediated WDR5 depletion. WDR5 depletion reduced H3K4Me3 and increased phosphorylation of H2AX in HCT116, SW620, and RKO colon cancer cells; however, OICR-9429 treatment did not recapitulate these effects in all cell lines potentially explaining the reduced toxicity of OICR-9429 treatment as compared to WDR5 depletion. WDR5 depletion also sensitized colon cancer cells to radiation-induced DNA damage. CONCLUSIONS These data demonstrate a clear role for WDR5 in colon cancer and future studies should examine its potential to serve as a therapeutic target in cancer. Additional studies are needed to fully elucidate if the requirement for WDR5 is independent of or consistent with its role within the COMPASS complex. OICR-9429 treatment was particularly toxic to SW620 and T84 colon cancer cells, two cell lines without mutations in WDR5 and KMT2/MLL proteins suggesting COMPASS complex inhibition may be particularly effective in tumors lacking KMT2 mutations. Additionally, the ability of WDR5 depletion to amplify the toxic effects of radiation presents the possibility of targeting WDR5 to sensitize cells to DNA-damaging therapies.
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Affiliation(s)
- Beth K Neilsen
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Binita Chakraborty
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Present address: Department of Pharmacology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jamie L McCall
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Present address: Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Danielle E Frodyma
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Richard L Sleightholm
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kurt W Fisher
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Robert E Lewis
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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32
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Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin. Cells 2018; 7:cells7030017. [PMID: 29498679 PMCID: PMC5870349 DOI: 10.3390/cells7030017] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. Here we discuss recent findings that try to elucidate the important question of how KMT2 complexes are recruited to specific sites on chromatin. This is embedded into short overviews of the biological functions of KMT2 complexes and the consequences of H3K4 methylation.
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33
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Liu L, Wan X, Zhou P, Zhou X, Zhang W, Hui X, Yuan X, Ding X, Zhu R, Meng G, Xiao H, Ma F, Huang H, Song X, Zhou B, Xiong S, Zhang Y. The chromatin remodeling subunit Baf200 promotes normal hematopoiesis and inhibits leukemogenesis. J Hematol Oncol 2018; 11:27. [PMID: 29482581 PMCID: PMC5828314 DOI: 10.1186/s13045-018-0567-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/05/2018] [Indexed: 11/10/2022] Open
Abstract
Background Adenosine triphosphate (ATP)-dependent chromatin remodeling SWI/SNF-like BAF and PBAF complexes have been implicated in the regulation of stem cell function and cancers. Several subunits of BAF or PBAF, including BRG1, BAF53a, BAF45a, BAF180, and BAF250a, are known to be involved in hematopoiesis. Baf200, a subunit of PBAF complex, plays a pivotal role in heart morphogenesis and coronary artery angiogenesis. However, little is known on the importance of Baf200 in normal and malignant hematopoiesis. Methods Utilizing Tie2-Cre-, Vav-iCre-, and Mx1-Cre-mediated Baf200 gene deletion combined with fetal liver/bone marrow transplantation, we investigated the function of Baf200 in fetal and adult hematopoiesis. In addition, a mouse model of MLL-AF9-driven leukemogenesis was used to study the role of Baf200 in malignant hematopoiesis. We also explored the potential mechanism by using RNA-seq, RT-qPCR, cell cycle, and apoptosis assays. Results Tie2-Cre-mediated loss of Baf200 causes perinatal death due to defective erythropoiesis and impaired hematopoietic stem cell expansion in the fetal liver. Vav-iCre-mediated loss of Baf200 causes only mild anemia and enhanced extramedullary hematopoiesis. Fetal liver hematopoietic stem cells from Tie2-Cre+, Baf200f/f or Vav-iCre+, Baf200f/f embryos and bone marrow hematopoietic stem cells from Vav-iCre+, Baf200f/f mice exhibited impaired long-term reconstitution potential in vivo. A cell-autonomous requirement of Baf200 for hematopoietic stem cell function was confirmed utilizing the interferon-inducible Mx1-Cre mouse strain. Transcriptomes analysis revealed that expression of several erythropoiesis- and hematopoiesis-associated genes were regulated by Baf200. In addition, loss of Baf200 in a mouse model of MLL-AF9-driven leukemogenesis accelerates the tumor burden and shortens the host survival. Conclusion Our current studies uncover critical roles of Baf200 in both normal and malignant hematopoiesis and provide a potential therapeutic target for suppressing the progression of leukemia without interfering with normal hematopoiesis. Electronic supplementary material The online version of this article (10.1186/s13045-018-0567-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lulu Liu
- Institute of Biology and Medical Sciences, Soochow University, No. 199 Ren'ai Rd, Suzhou, China.,Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China
| | - Xiaoling Wan
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peipei Zhou
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyuan Zhou
- University of Chinese Academy of Sciences, Beijing, China.,CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Zhang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,School of Life Sciences, Shanghai University, Shanghai, China
| | - Xinhui Hui
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,School of Life Sciences, Shanghai University, Shanghai, China
| | - Xiujie Yuan
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaodan Ding
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ruihong Zhu
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangxun Meng
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hui Xiao
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Feng Ma
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - He Huang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianmin Song
- Department of Hematology, Shanghai Jiao Tong University Affiliated Shanghai General Hospital, Shanghai, China
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.
| | - Sidong Xiong
- Institute of Biology and Medical Sciences, Soochow University, No. 199 Ren'ai Rd, Suzhou, China.
| | - Yan Zhang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China. .,University of Chinese Academy of Sciences, Beijing, China.
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34
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Gan T, Li BE, Mishra BP, Jones KL, Ernst P. MLL1 Promotes IL-7 Responsiveness and Survival during B Cell Differentiation. THE JOURNAL OF IMMUNOLOGY 2018; 200:1682-1691. [PMID: 29351999 DOI: 10.4049/jimmunol.1701572] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/18/2017] [Indexed: 12/15/2022]
Abstract
B lymphocyte differentiation is an exquisitely regulated homeostatic process resulting in continuous production of appropriately selected B cells. Relatively small changes in gene expression can result in deregulation of this process, leading to acute lymphocytic leukemia (ALL), immune deficiency, or autoimmunity. Translocation of MLL1 (KMT2A) often results in a pro-B cell ALL, but little is known about its role in normal B cell differentiation. Using a Rag1-cre mouse knock-in to selectively delete Mll1 in developing lymphocytes, we show that B cell, but not T cell, homeostasis depends on MLL1. Mll1-/- B progenitors fail to differentiate efficiently through the pro- to pre-B cell transition, resulting in a persistent reduction in B cell populations. Cells inefficiently transit the pre-BCR checkpoint, despite normal to higher levels of pre-BCR components, and rearranged IgH expression fails to rescue this differentiation block. Instead of IgH-rearrangement defects, we find that Mll1-/- pre-B cells exhibit attenuated RAS/MAPK signaling downstream of the pre-BCR, which results in reduced survival in physiologic levels of IL-7. Genome-wide expression data illustrate that MLL1 is connected to B cell differentiation and IL-7-dependent survival through a complex transcriptional network. Overall, our data demonstrate that wild-type MLL1 is a regulator of pre-BCR signaling and B cell differentiation and further suggest that targeting its function in pro-B cell ALL may be more broadly effective than previously anticipated.
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Affiliation(s)
- Tao Gan
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Bin E Li
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Bibhu P Mishra
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Kenneth L Jones
- Hematology/Oncology/Bone Marrow Transplant Section, Department of Pediatrics, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045; and.,Department of Pharmacology, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045
| | - Patricia Ernst
- Hematology/Oncology/Bone Marrow Transplant Section, Department of Pediatrics, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045; and .,Department of Pharmacology, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045
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CALR mutational status identifies different disease subtypes of essential thrombocythemia showing distinct expression profiles. Blood Cancer J 2017; 7:638. [PMID: 29217833 PMCID: PMC5802509 DOI: 10.1038/s41408-017-0010-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 09/05/2017] [Indexed: 12/21/2022] Open
Abstract
Polycythemia vera (PV) and essential thrombocythemia (ET) are Philadelphia-negative myeloproliferative neoplasms (MPNs) characterized by erythrocytosis and thrombocytosis, respectively. Approximately 95% of PV and 50–70% of ET patients harbor the V617F mutation in the exon 14 of JAK2 gene, while about 20–30% of ET patients carry CALRins5 or CALRdel52 mutations. These ET CALR-mutated subjects show higher platelet count and lower thrombotic risk compared to JAK2-mutated patients. Here, we showed that CALR-mutated and JAK2V617F-positive CD34+ cells display different gene and miRNA expression profiles. Indeed, we highlighted several pathways differentially activated between JAK2V617F- and CALR-mutated progenitors, i.e., mTOR, MAPK/PI3K, and MYC pathways. Furthermore, we unveiled that the expression of several genes involved in DNA repair, chromatin remodeling, splicing, and chromatid cohesion are decreased in CALR-mutated cells. According to the low risk of thrombosis in CALR-mutated patients, we also found the downregulation of several genes involved in thrombin signaling and platelet activation. As a whole, these data support the model that CALR-mutated ET could be considered as a distinct disease entity from JAK2V617F-positive MPNs and may provide the molecular basis supporting the different clinical features of these patients.
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