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You C, Xu L, Zhu L, Qiu S, Xu N, Wang Y, Yang L. Clinical analysis of five CHD2 gene mutations in Chinese children with epilepsy. Seizure 2024; 121:38-44. [PMID: 39068850 DOI: 10.1016/j.seizure.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
INTRODUCTION Increasing evidence reveals critical roles for CHD2 in children with developmental and epileptic encephalopathy. OBJECTIVES The aim was to present clinical analysis results of five cases with CHD2 mutations and 157 reported cases with non-copy number variations (non-CNV) of CHD2. METHODS This study recruited pediatric epilepsy patients with CHD2 mutations and clinical data from November 2016 to October 2023 in the Linyi People's Hospital, China. Whole-exome and gene panel sequencing were employed to find mutations. The HGMD and PubMed databases were examined for documented cases that had CHD2 mutations. RESULTS This study reports five cases with CHD2 mutations: c.3543T > A, c.1850A > G, c.2536C > T, c.4233_4236del, c.3782G > C. Three novel mutations (c.3543T > A, c.1850A > G, c.2536C > T) have never been reported. c.4233_4236del has been reported in three cases, indicating that this locus may be a mutation hotspot. c.3782G > C has been reported in one case. All five patients had seizures before the age of four. Three patients had varying degrees of developmental delay, and four patients had varying degrees of intellectual disability. All of them had controlled seizures after Valproic acid (VPA) monotherapy or VPA in combination with other medications. Furthermore, we reviewed 157 reported cases having non-CNV mutations of CHD2. Most mutations of these cases were de novo. Epilepsy, developmental delay, and intellectual disability were the typical clinical phenotypes. We also found a significant clustering of the mutations near the C-terminus of the CHD2 protein (P < 0.001). CONCLUSION This study reports new CHD2 genotypes and analyzes reported CHD2 mutation cases. Given its significance in epileptic encephalopathies, research on the CHD2 gene may provide new insights into epileptogenesis.
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Affiliation(s)
- Cuiping You
- Central Laboratory, Linyi People's Hospital, Linyi, Shandong, China
| | - Liyun Xu
- Shandong Medical College, Linyi, China
| | - Liping Zhu
- Department of Pediatrics, Linyi People's Hospital, Linyi, China
| | - Shiyan Qiu
- Department of Pediatrics, Linyi People's Hospital, Linyi, China
| | - Na Xu
- Department of Pediatrics, Linyi People's Hospital, Linyi, China
| | - Yanyan Wang
- Department of Laboratory Medicine, Linyi People's Hospital, Linyi, China; Key Laboratory for Laboratory Medicine of Linyi City, Linyi, China; Shandong Provincial Medicine and Health Key Laboratory for Precise Diagnosis of Hereditary Rare Diseases, Linyi People's Hospital, Linyi, China
| | - Li Yang
- Department of Pediatrics, Linyi People's Hospital, Linyi, China.
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Zhang X, Duan S, Apostolou PE, Wu X, Watanabe J, Gallitto M, Barron T, Taylor KR, Woo PJ, Hua X, Zhou H, Wei HJ, McQuillan N, Kang KD, Friedman GK, Canoll PD, Chang K, Wu CC, Hashizume R, Vakoc CR, Monje M, McKhann GM, Gogos JA, Zhang Z. CHD2 Regulates Neuron-Glioma Interactions in Pediatric Glioma. Cancer Discov 2024; 14:1732-1754. [PMID: 38767413 PMCID: PMC11456263 DOI: 10.1158/2159-8290.cd-23-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/05/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
High-grade gliomas (HGG) are deadly diseases for both adult and pediatric patients. Recently, it has been shown that neuronal activity promotes the progression of multiple subgroups of HGG. However, epigenetic mechanisms that govern this process remain elusive. Here we report that the chromatin remodeler chromodomain helicase DNA-binding protein 2 (CHD2) regulates neuron-glioma interactions in diffuse midline glioma (DMG) characterized by onco-histone H3.1K27M. Depletion of CHD2 in H3.1K27M DMG cells compromises cell viability and neuron-to-glioma synaptic connections in vitro, neuron-induced proliferation of H3.1K27M DMG cells in vitro and in vivo, activity-dependent calcium transients in vivo, and extends the survival of H3.1K27M DMG-bearing mice. Mechanistically, CHD2 coordinates with the transcription factor FOSL1 to control the expression of axon-guidance and synaptic genes in H3.1K27M DMG cells. Together, our study reveals a mechanism whereby CHD2 controls the intrinsic gene program of the H3.1K27M DMG subtype, which in turn regulates the tumor growth-promoting interactions of glioma cells with neurons. Significance: Neurons drive the proliferation and invasion of glioma cells. Here we show that chromatin remodeler chromodomain helicase DNA-binding protein 2 controls the epigenome and expression of axon-guidance and synaptic genes, thereby promoting neuron-induced proliferation of H3.1K27M diffuse midline glioma and the pathogenesis of this deadly disease.
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Affiliation(s)
- Xu Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- These authors contributed equally
| | - Shoufu Duan
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- These authors contributed equally
| | - Panagiota E. Apostolou
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Xiaoping Wu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jun Watanabe
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Matthew Gallitto
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tara Barron
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Kathryn R. Taylor
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Pamelyn J. Woo
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hong-Jian Wei
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nicholas McQuillan
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kyung-Don Kang
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Division of Pediatrics, Neuro-Oncology Section, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gregory K. Friedman
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Division of Pediatrics, Neuro-Oncology Section, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter D. Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Cheng-Chia Wu
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rintaro Hashizume
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | | | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, CA 94305, USA
| | - Guy M. McKhann
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Joseph A. Gogos
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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Wang Y, Liu H, Zhang M, Xu J, Zheng L, Liu P, Chen J, Liu H, Chen C. Epigenetic reprogramming in gastrointestinal cancer: biology and translational perspectives. MedComm (Beijing) 2024; 5:e670. [PMID: 39184862 PMCID: PMC11344282 DOI: 10.1002/mco2.670] [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: 09/16/2023] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/27/2024] Open
Abstract
Gastrointestinal tumors, the second leading cause of human mortality, are characterized by their association with inflammation. Currently, progress in the early diagnosis and effective treatment of gastrointestinal tumors is limited. Recent whole-genome analyses have underscored their profound heterogeneity and extensive genetic and epigenetic reprogramming. Epigenetic reprogramming pertains to dynamic and hereditable alterations in epigenetic patterns, devoid of concurrent modifications in the underlying DNA sequence. Common epigenetic modifications encompass DNA methylation, histone modifications, noncoding RNA, RNA modifications, and chromatin remodeling. These modifications possess the potential to invoke or suppress a multitude of genes associated with cancer, thereby governing the establishment of chromatin configurations characterized by diverse levels of accessibility. This intricate interplay assumes a pivotal and indispensable role in governing the commencement and advancement of gastrointestinal cancer. This article focuses on the impact of epigenetic reprogramming in the initiation and progression of gastric cancer, esophageal cancer, and colorectal cancer, as well as other uncommon gastrointestinal tumors. We elucidate the epigenetic landscape of gastrointestinal tumors, encompassing DNA methylation, histone modifications, chromatin remodeling, and their interrelationships. Besides, this review summarizes the potential diagnostic, therapeutic, and prognostic targets in epigenetic reprogramming, with the aim of assisting clinical treatment strategies.
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Affiliation(s)
- Yingjie Wang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Hongyu Liu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Mengsha Zhang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Jing Xu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Liuxian Zheng
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Pengpeng Liu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Jingyao Chen
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Hongyu Liu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Chong Chen
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
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Hasanlu M, Amiri-Dashatan N, Farahani M, Koushki M, Ahmadi H, Parsamanesh N, Ahmadi NA. Comprehensive Analysis of the Expression, Prognosis, and Immune Infiltrates for Chromodomain-Helicase-DNA-Binding Proteins in Breast Tumor. Asian Pac J Cancer Prev 2024; 25:1547-1558. [PMID: 38809626 PMCID: PMC11318824 DOI: 10.31557/apjcp.2024.25.5.1547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 05/04/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND Several recent studies suggest that chromodomain-helicase -DNA-binding domains (CHDs) are linked with cancers. We explored the association between chromodomain-Helicase-DNA-binding domain proteins and breast cancer (BrCa) and introduced potential prognostic markers using various databases. MATERIALS AND METHODS We analyzed the expression of the CHD family and their prognostic value in BrCa by mining UALCAN, TIMER, and Kaplan-Meier plotter databases. The association of CHD expression and immune infiltrating abundance was studied via the TIMER database. In addition, microRNAs related to the CHD family were identified by using the MirTarBase online database. RESULTS The present study indicated that compared to normal tissues, BrCa tissues showed increased mRNA levels of CHD3/4/7 but decreased CHD2/5/9 expression. Interestingly, We also found a positive correlation between CHD gene expression and the infiltration of macrophage, neutrophil, and dendritic cells in BrCa, except CHD3/5. The Kaplan-Meier Plotter analysis suggested that high expression levels of CHD1/2/3/4/6/8/9 were significantly related to shorter relapse-free survival (RFS), while higher mRNA expression of CHD1, CHD2, CHD8, and CHD9 was significantly associated with longer overall survival of BrCa patients. The miRNAs of hsa-miR-615-3p and hsa-let-7b-5p were identified as being more correlated with the CHD family. CONCLUSION The altered expression of some CHD members was significantly related to clinical cancer outcomes, and CHD1/2/8/9 could serve as potential prognostic biomarkers to improve the survival of BrCa patients. However, to evaluate the studied CHD members in detail are needed further investigations including experimental validation.
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Affiliation(s)
- Masoumeh Hasanlu
- Department of Internal Medicine, Vali-e-Asr Hospital, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Nasrin Amiri-Dashatan
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Masoumeh Farahani
- Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehdi Koushki
- Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Hesameddin Ahmadi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Micro Nano System Laboratory (MNSL), Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran.
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Nayeb Ali Ahmadi
- Proteomics Research Center, Department of Medical Laboratory Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Muhammad T, Pastore SF, Good K, Ausió J, Vincent JB. Chromatin gatekeeper and modifier CHD proteins in development, and in autism and other neurological disorders. Psychiatr Genet 2023; 33:213-232. [PMID: 37851134 DOI: 10.1097/ypg.0000000000000353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and responds to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation. In this review, we first discuss the structural and functional domains of the CHD proteins, and their binding sites, and phosphorylation, acetylation, and methylation sites. The conservation of important amino acids in SWItch/sucrose non-fermenting (SWI/SNF) domains, and their protein and mRNA tissue expression profiles are discussed. Next, we convey the important binding partners of CHD proteins, their protein complexes and activities, and their involvements in epigenetic regulation. We also show the ChIP-seq binding dynamics for CHD1, CHD2, CHD4, and CHD7 proteins at promoter regions of histone genes, as well as several genes that are critical for neurodevelopment. The role of CHD proteins in development is also discussed. Finally, this review provides information about CHD protein mutations reported in autism and neurodevelopmental disorders, and their pathogenicity. Overall, this review provides information on the progress of research into CHD proteins, their structural and functional domains, epigenetics, and their role in stem cell, development, and neurological disorders.
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Affiliation(s)
- Tahir Muhammad
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Stephen F Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Katrina Good
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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Hurwitz LM, Beane Freeman LE, Andreotti G, Hofmann JN, Parks CG, Sandler DP, Lubin JH, Liu J, Jones K, Berndt SI, Koutros S. Joint associations between established genetic susceptibility loci, pesticide exposures, and risk of prostate cancer. ENVIRONMENTAL RESEARCH 2023; 237:117063. [PMID: 37659638 PMCID: PMC10591852 DOI: 10.1016/j.envres.2023.117063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/20/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
More than 200 genetic variants have been independently associated with prostate cancer risk. Studies among farmers have also observed increased prostate cancer risk associated with exposure to specific organophosphate (fonofos, terbufos, malathion, dimethoate) and organochlorine (aldrin, chlordane) insecticides. We examined the joint associations between these pesticides, established prostate cancer loci, and prostate cancer risk among 1,162 cases (588 aggressive) and 2,206 frequency-matched controls nested in the Agricultural Health Study cohort. History of lifetime pesticide use was combined with a polygenic risk score (PRS) generated using 256 established prostate cancer risk variants. Logistic regression models estimated the joint associations of the pesticides, the PRS, and the 256 individual genetic variants with risk of total and aggressive prostate cancer. Likelihood ratio tests assessed multiplicative interaction. We observed interaction between ever use of fonofos and the PRS in relation to total and aggressive prostate cancer risk. Compared to the reference group (never use, PRS < median), men with ever use of fonofos and PRS > median had elevated risks of total (OR 1.35 [1.06-1.73], p-interaction = 0.03) and aggressive (OR 1.49 [1.09-2.04], p-interaction = 0.19) prostate cancer. There was also suggestion of interaction between pesticides and individual genetic variants occurring in regions associated with DNA damage response (CDH3, EMSY genes) and with variants related to altered androgen receptor-driven transcriptional programs critical for prostate cancer. Our study provides evidence that men with greater genetic susceptibility to prostate cancer may be at higher risk if they are also exposed to pesticides and suggests potential mechanisms by which pesticides may increase prostate cancer risk.
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Affiliation(s)
- Lauren M Hurwitz
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA.
| | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - Gabriella Andreotti
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - Jonathan N Hofmann
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - Christine G Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Jay H Lubin
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA; Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA; Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sonja I Berndt
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
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Sun J, Liu F, Yuan L, Pang NN, Zhu B, Yang N. Mechanism studies of the activation of DNA methyltransferase DNMT1 triggered by histone H3 ubiquitination, revealed by multi-scale molecular dynamics simulations. SCIENCE CHINA. LIFE SCIENCES 2023; 66:313-323. [PMID: 36271982 DOI: 10.1007/s11427-021-2179-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/17/2022] [Indexed: 11/05/2022]
Abstract
DNMT1 is a DNA methyltransferase that catalyzes and maintains methylation in CpG dinucleotides. It blocks the entrance of DNA into the catalytic pocket via the replication foci targeting sequence (RFTS) domain. Recent studies have shown that an H3-tail-conjugated two-mono-ubiquitin mark (H3Ub2) activates DNMT1 by binding to the RFTS domain. However, the activation mechanism of DNMT1 remains unclear. In this work, we combine various sampling methods of extensive simulations, including conventional molecular dynamics, Gaussian-accelerated molecular dynamics, and coarse-grained molecular dynamics, to elucidate the activation mechanism of DNMT1. Geometric and energy analyses show that binding of H3Ub2 to the RFTS domain of DNMT1 results in the bending of the α4-helix in the RFTS domain at approximately 30°-35°, and the RFTS domain rotates ∼20° anti-clockwise and moves ∼3 Å away from the target recognition domain (TRD). The hydrogen-bonding network at the RFTS-TRD interface is significantly disrupted, implying that the RFTS domain is dissociated from the catalytic core, which contributes to activating the auto-inhibited conformation of DNMT1. These results provide structural and dynamic evidence for the role of H3Ub2 in regulating the catalytic activity of DNMT1.
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Affiliation(s)
- Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, 300353, China
| | - Fei Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, 300353, China
| | - Longxiao Yuan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, 300353, China
| | - Ning-Ning Pang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, 300353, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, 300353, China.
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8
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Vaicekauskaitė I, Sabaliauskaitė R, Lazutka JR, Jarmalaitė S. The Emerging Role of Chromatin Remodeling Complexes in Ovarian Cancer. Int J Mol Sci 2022; 23:ijms232213670. [PMID: 36430148 PMCID: PMC9697406 DOI: 10.3390/ijms232213670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/31/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Ovarian cancer (OC) is the fifth leading cause of women's death from cancers. The high mortality rate is attributed to the late presence of the disease and the lack of modern diagnostic tools, including molecular biomarkers. Moreover, OC is a highly heterogeneous disease, which contributes to early treatment failure. Thus, exploring OC molecular mechanisms could significantly enhance our understanding of the disease and provide new treatment options. Chromatin remodeling complexes (CRCs) are ATP-dependent molecular machines responsible for chromatin reorganization and involved in many DNA-related processes, including transcriptional regulation, replication, and reparation. Dysregulation of chromatin remodeling machinery may be related to cancer development and chemoresistance in OC. Some forms of OC and other gynecologic diseases have been associated with mutations in specific CRC genes. Most notably, ARID1A in endometriosis-related OC, SMARCA4, and SMARCB1 in hypercalcemic type small cell ovarian carcinoma (SCCOHT), ACTL6A, CHRAC1, RSF1 amplification in high-grade serous OC. Here we review the available literature on CRCs' involvement in OC to improve our understanding of its development and investigate CRCs as possible biomarkers and treatment targets for OC.
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Affiliation(s)
- Ieva Vaicekauskaitė
- Laboratory of Genetic Diagnostic, National Cancer Institute, Santariškių 1, LT-08406 Vilnius, Lithuania
- Institute of Biosciences, Vilnius University, Sauletekio Avenue 7, LT-10222 Vilnius, Lithuania
| | - Rasa Sabaliauskaitė
- Laboratory of Genetic Diagnostic, National Cancer Institute, Santariškių 1, LT-08406 Vilnius, Lithuania
| | - Juozas Rimantas Lazutka
- Institute of Biosciences, Vilnius University, Sauletekio Avenue 7, LT-10222 Vilnius, Lithuania
| | - Sonata Jarmalaitė
- Institute of Biosciences, Vilnius University, Sauletekio Avenue 7, LT-10222 Vilnius, Lithuania
- Laboratory of Clinical Oncology, National Cancer Institute, Santariškių 1, LT-08406 Vilnius, Lithuania
- Correspondence:
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9
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Bonczek O, Wang L, Gnanasundram SV, Chen S, Haronikova L, Zavadil-Kokas F, Vojtesek B. DNA and RNA Binding Proteins: From Motifs to Roles in Cancer. Int J Mol Sci 2022; 23:ijms23169329. [PMID: 36012592 PMCID: PMC9408909 DOI: 10.3390/ijms23169329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
DNA and RNA binding proteins (DRBPs) are a broad class of molecules that regulate numerous cellular processes across all living organisms, creating intricate dynamic multilevel networks to control nucleotide metabolism and gene expression. These interactions are highly regulated, and dysregulation contributes to the development of a variety of diseases, including cancer. An increasing number of proteins with DNA and/or RNA binding activities have been identified in recent years, and it is important to understand how their activities are related to the molecular mechanisms of cancer. In addition, many of these proteins have overlapping functions, and it is therefore essential to analyze not only the loss of function of individual factors, but also to group abnormalities into specific types of activities in regard to particular cancer types. In this review, we summarize the classes of DNA-binding, RNA-binding, and DRBPs, drawing particular attention to the similarities and differences between these protein classes. We also perform a cross-search analysis of relevant protein databases, together with our own pipeline, to identify DRBPs involved in cancer. We discuss the most common DRBPs and how they are related to specific cancers, reviewing their biochemical, molecular biological, and cellular properties to highlight their functions and potential as targets for treatment.
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Affiliation(s)
- Ondrej Bonczek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
- Correspondence: (O.B.); (B.V.)
| | - Lixiao Wang
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | - Lucia Haronikova
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Filip Zavadil-Kokas
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Correspondence: (O.B.); (B.V.)
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10
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Nihous H, Baud J, Azmani R, Michot A, Perret R, Mayeur L, de Pinieux G, Milin S, Angot E, Duquenne S, Geneste D, Lucchesi C, Le Loarer F, Bouvier C. Clinicopathologic and Molecular Study of Hybrid Nerve Sheath Tumors Reveals Their Common Association With Fusions Involving VGLL3. Am J Surg Pathol 2022; 46:591-602. [PMID: 35256555 DOI: 10.1097/pas.0000000000001858] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A subset of benign peripheral nerve sheath tumors are "hybrid" combining several lines of differentiation, most often schwannian and perineurial features. The pathogenesis of these tumors was poorly described until the recent discovery of recurrent VGLL3 rearrangements in hybrid schwannoma/perineuriomas, supporting the hypothesis that this entity represents a distinct subgroup of tumors and not only a morphologic variation of other peripheral nerve sheath tumors. Following this finding, we investigated 10 cases of hybrid peripheral nerve sheath tumors with immunohistochemistry, RNA sequencing, and array comparative genomic hybridization. By light microscopy, 7 tumors were hybrid schwannoma/perineurioma tumors, and 3 were hybrid schwannoma/neurofibroma. Most cases of hybrid schwannoma/perineuriomas displayed VGLL3 rearrangements fused in 5' either to CHD7 or CHD9 (n=6/7) and had simple diploid genetic profiles with few copy number alterations. Compared with a control group composed of 28 tumors associated with varied neural phenotypes, all VGLL3-fused tumors clustered together by transcriptomic analysis. In contrast, 1 case of hybrid schwannoma/perineurioma tumor harbored a CDH9-ZFHX3 fusion, a prominent perineurial component identified by immunohistochemistry and clustered with perineuriomas. No recurrent genetic alteration was seen in the 3 hybrid schwannoma/neurofibromas. To summarize, this study confirms and expands the recent findings on hybrid schwannoma/perineurioma, highlighting the predominance of VGLL3 fusions in these tumors.
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Affiliation(s)
- Hugo Nihous
- Department of Pathology, AP-HM La Timone, Marseille
| | - Jessica Baud
- INSERM U1218, ACTION, Comprehensive Cancer Center of Bordeaux, Bergonie Institute
- Department of Pathology, University of Bordeaux, Talence, France
| | | | - Audrey Michot
- INSERM U1218, ACTION, Comprehensive Cancer Center of Bordeaux, Bergonie Institute
- Surgery
| | | | - Laetitia Mayeur
- Molecular Pathology, Comprehensive Cancer Center of Bordeaux, Bordeaux
| | | | - Serge Milin
- Department of Pathology, Poitiers University Hospital, Poitiers
| | - Emilie Angot
- Department of Pathology, Rouen University Hospital, Rouen
| | | | | | - Carlo Lucchesi
- INSERM U1218, ACTION, Comprehensive Cancer Center of Bordeaux, Bergonie Institute
- Departments of Bioinformatics
| | - Francois Le Loarer
- INSERM U1218, ACTION, Comprehensive Cancer Center of Bordeaux, Bergonie Institute
- Pathology
- Department of Pathology, University of Bordeaux, Talence, France
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11
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Cardoso AR, Lopes-Marques M, Oliveira M, Amorim A, Prata MJ, Azevedo L. Genetic Variability of the Functional Domains of Chromodomains Helicase DNA-Binding (CHD) Proteins. Genes (Basel) 2021; 12:genes12111827. [PMID: 34828433 PMCID: PMC8623811 DOI: 10.3390/genes12111827] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
In the past few years, there has been an increasing neuroscientific interest in understanding the function of mammalian chromodomains helicase DNA-binding (CHD) proteins due to their association with severe developmental syndromes. Mammalian CHDs include nine members (CHD1 to CHD9), grouped into subfamilies according to the presence of specific functional domains, generally highly conserved in evolutionary terms. Mutations affecting these domains hold great potential to disrupt protein function, leading to meaningful pathogenic scenarios, such as embryonic defects incompatible with life. Here, we analysed the evolution of CHD proteins by performing a comparative study of the functional domains of CHD proteins between orthologous and paralogous protein sequences. Our findings show that the highest degree of inter-species conservation was observed at Group II (CHD3, CHD4, and CHD5) and that most of the pathological variations documented in humans involve amino acid residues that are conserved not only between species but also between paralogs. The parallel analysis of both orthologous and paralogous proteins, in cases where gene duplications have occurred, provided extra information showing patterns of flexibility as well as interchangeability between amino acid positions. This added complexity needs to be considered when the impact of novel mutations is assessed in terms of evolutionary conservation.
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Affiliation(s)
- Ana R. Cardoso
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Mónica Lopes-Marques
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Manuela Oliveira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - António Amorim
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Prata
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Luísa Azevedo
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
- Correspondence:
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12
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Trakadis Y, Accogli A, Qi B, Bloom D, Joober R, Levy E, Tabbane K. Next-generation gene panel testing in adolescents and adults in a medical neuropsychiatric genetics clinic. Neurogenetics 2021; 22:313-322. [PMID: 34363551 DOI: 10.1007/s10048-021-00664-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/21/2021] [Indexed: 01/04/2023]
Abstract
Intellectual disability (ID) encompasses a clinically and genetically heterogeneous group of neurodevelopmental disorders that may present with psychiatric illness in up to 40% of cases. Despite the evidence for clinical utility of genetic panels in pediatrics, there are no published studies in adolescents/adults with ID or autism spectrum disorder (ASD). This study was approved by our institutional research ethics board. We retrospectively reviewed the medical charts of all patients evaluated between January 2017 and December 2019 in our adult neuropsychiatric genetics clinic at the McGill University Health Centre (MUHC), who had undergone a comprehensive ID/ASD gene panel. Thirty-four patients aged > 16 years, affected by ID/ASD and/or other neuropsychiatric/behavioral disorders, were identified. Pathogenic or likely pathogenic variants were identified in one-third of our cohort (32%): 8 single-nucleotide variants in 8 genes (CASK, SHANK3, IQSEC2, CHD2, ZBTB20, TREX1, SON, and TUBB2A) and 3 copy number variants (17p13.3, 16p13.12p13.11, and 9p24.3p24.1). The presence of psychiatric/behavioral disorders, regardless of the co-occurrence of ID, and, at a borderline level, the presence of ID alone were associated with positive genetic findings (p = 0.024 and p = 0.054, respectively). Moreover, seizures were associated with positive genetic results (p = 0.024). One-third of individuals presenting with psychiatric illness who met our red flags for Mendelian diseases have pathogenic or likely pathogenic variants which can be identified using a comprehensive ID/ASD gene panel (~ 2500 genes) performed on an exome backbone.
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Affiliation(s)
- Y Trakadis
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Room A04.3140, 1001 Boul. Décarie, Montreal, QC, H4A 3J1, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada. .,Douglas Mental Health Institute/Hospital, Montreal, Canada. .,Department of Psychiatry, McGill University, Montreal, Canada.
| | - A Accogli
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Room A04.3140, 1001 Boul. Décarie, Montreal, QC, H4A 3J1, Canada
| | - B Qi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - D Bloom
- Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
| | - R Joober
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
| | - E Levy
- Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
| | - K Tabbane
- Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
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13
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McMahon KA, Stroud DA, Gambin Y, Tillu V, Bastiani M, Sierecki E, Polinkovsky ME, Hall TE, Gomez GA, Wu Y, Parat MO, Martel N, Lo HP, Khanna KK, Alexandrov K, Daly R, Yap A, Ryan MT, Parton RG. Cavin3 released from caveolae interacts with BRCA1 to regulate the cellular stress response. eLife 2021; 10:61407. [PMID: 34142659 PMCID: PMC8279762 DOI: 10.7554/elife.61407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 06/11/2021] [Indexed: 12/13/2022] Open
Abstract
Caveolae-associated protein 3 (cavin3) is inactivated in most cancers. We characterized how cavin3 affects the cellular proteome using genome-edited cells together with label-free quantitative proteomics. These studies revealed a prominent role for cavin3 in DNA repair, with BRCA1 and BRCA1 A-complex components being downregulated on cavin3 deletion. Cellular and cell-free expression assays revealed a direct interaction between BRCA1 and cavin3 that occurs when cavin3 is released from caveolae that are disassembled in response to UV and mechanical stress. Overexpression and RNAi-depletion revealed that cavin3 sensitized various cancer cells to UV-induced apoptosis. Supporting a role in DNA repair, cavin3-deficient cells were sensitive to PARP inhibition, where concomitant depletion of 53BP1 restored BRCA1-dependent sensitivity to PARP inhibition. We conclude that cavin3 functions together with BRCA1 in multiple cancer-related pathways. The loss of cavin3 function may provide tumor cell survival by attenuating apoptotic sensitivity and hindering DNA repair under chronic stress conditions.
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Affiliation(s)
- Kerrie-Ann McMahon
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Yann Gambin
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Vikas Tillu
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Michele Bastiani
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Emma Sierecki
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Mark E Polinkovsky
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Thomas E Hall
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Guillermo A Gomez
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Yeping Wu
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Marie-Odile Parat
- School of Pharmacy, The University of Queensland, Woolloongabba, Australia
| | - Nick Martel
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Harriet P Lo
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Kum Kum Khanna
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Roger Daly
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Melbourne, Australia
| | - Alpha Yap
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Michael T Ryan
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Melbourne, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Queensland, Australia
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14
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Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity. Sci Rep 2021; 11:10571. [PMID: 34011996 PMCID: PMC8134446 DOI: 10.1038/s41598-021-90170-1] [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: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 11/08/2022] Open
Abstract
Breast cancers exhibit intratumoral heterogeneity associated with disease progression and therapeutic resistance. To define the sources and the extent of heterogeneity, we performed an in-depth analysis of the genomic architecture of three chemoradiation-naïve breast cancers with well-defined clinical features including variable ER, PR, ERBB2 receptor expression and two distinct pathogenic BRCA2mut genotypes. The latter included a germ line carrier and a patient with a somatic variant. In each case we combined DNA content-based flow cytometry with whole exome sequencing and genome wide copy number variant (CNV) analysis of distinct populations sorted from multiple (4–18) mapped biopsies within the tumors and involved lymph nodes. Interrogating flow-sorted tumor populations from each biopsy provided an objective method to distinguish fixed and variable genomic lesions in each tumor. Notably we show that tumors exploit CNVs to fix mutations and deletions in distinct populations throughout each tumor. The identification of fixed genomic lesions that are shared or unique within each tumor, has broad implications for the study of tumor heterogeneity including the presence of tumor markers and therapeutic targets, and of candidate neoepitopes in breast and other solid tumors that can advance more effective treatment and clinical management of patients with disease.
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15
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Lettieri A, Oleari R, Paganoni AJJ, Gervasini C, Massa V, Fantin A, Cariboni A. Semaphorin Regulation by the Chromatin Remodeler CHD7: An Emerging Genetic Interaction Shaping Neural Cells and Neural Crest in Development and Cancer. Front Cell Dev Biol 2021; 9:638674. [PMID: 33869187 PMCID: PMC8047133 DOI: 10.3389/fcell.2021.638674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
CHD7 is a chromatin remodeler protein that controls gene expression via the formation of multi-protein complexes with specific transcription factors. During development, CHD7 controls several differentiation programs, mainly by acting on neural progenitors and neural crest (NC) cells. Thus, its roles range from the central nervous system to the peripheral nervous system and the organs colonized by NC cells, including the heart. Accordingly, mutated CHD7 is linked to CHARGE syndrome, which is characterized by several neuronal dysfunctions and by malformations of NC-derived/populated organs. Altered CHD7 has also been associated with different neoplastic transformations. Interestingly, recent evidence revealed that semaphorins, a class of molecules involved in developmental and pathological processes similar to those controlled by CHD7, are regulated by CHD7 in a context-specific manner. In this article, we will review the recent insights that support the existence of genetic interactions between these pathways, both during developmental processes and cancer progression.
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Affiliation(s)
- Antonella Lettieri
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Roberto Oleari
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Alyssa J J Paganoni
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Cristina Gervasini
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valentina Massa
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Fantin
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Anna Cariboni
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
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16
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Kuehn HS, Niemela JE, Stoddard J, Mannurita SC, Shahin T, Goel S, Hintermeyer M, Heredia RJ, Garofalo M, Lucas L, Singh S, Tondo A, Jacobs Z, Gahl WA, Latour S, Verbsky J, Routes J, Cunningham-Rundles C, Boztug K, Gambineri E, Fleisher TA, Chandrakasan S, Rosenzweig SD. Germline IKAROS dimerization haploinsufficiency causes hematologic cytopenias and malignancies. Blood 2021; 137:349-363. [PMID: 32845957 PMCID: PMC7819759 DOI: 10.1182/blood.2020007292] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
IKAROS is a transcription factor forming homo- and heterodimers and regulating lymphocyte development and function. Germline mutations affecting the IKAROS N-terminal DNA binding domain, acting in a haploinsufficient or dominant-negative manner, cause immunodeficiency. Herein, we describe 4 germline heterozygous IKAROS variants affecting its C-terminal dimerization domain, via haploinsufficiency, in 4 unrelated families. Index patients presented with hematologic disease consisting of cytopenias (thrombocytopenia, anemia, neutropenia)/Evans syndrome and malignancies (T-cell acute lymphoblastic leukemia, Burkitt lymphoma). These dimerization defective mutants disrupt homo- and heterodimerization in a complete or partial manner, but they do not affect the wild-type allele function. Moreover, they alter key mechanisms of IKAROS gene regulation, including sumoylation, protein stability, and the recruitment of the nucleosome remodeling and deacetylase complex; none affected in N-terminal DNA binding defects. These C-terminal dimerization mutations are largely associated with hematologic disorders, display dimerization haploinsufficiency and incomplete clinical penetrance, and differ from previously reported allelic variants in their mechanism of action. Dimerization mutants contribute to the growing spectrum of IKAROS-associated diseases displaying a genotype-phenotype correlation.
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Affiliation(s)
- Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Julie E Niemela
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Sara Ciullini Mannurita
- Department of Neuroscience, Psychology, Pharmaceutical Area and Child Health (NEUROFARBA)/Paediatric Haemato-Oncology Laboratory, Anna Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Tala Shahin
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Shubham Goel
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Mary Hintermeyer
- Division of Asthma, Allergy, and Clinical Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Raul Jimenez Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Mary Garofalo
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Laura Lucas
- Immunedysregulation and Immuno-Hematology Program, Division of Bone Marrow Transplant, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, and
| | - Smriti Singh
- Genetic Counseling Program, Emory School of Medicine, Atlanta, GA
| | - Annalisa Tondo
- Hematology/Oncology Department, Anna Meyer Children's Hospital, Florence, Italy
| | - Zachary Jacobs
- Department of Internal Medicine, University of Missouri School of Medicine, Colombia, MO
| | - William A Gahl
- Section on Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to Epstein-Barr Virus (EBV) Infection, INSERM Unité Mixte de Recherche (UMR) 1163, Paris, France
| | - James Verbsky
- Division of Asthma, Allergy, and Clinical Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - John Routes
- Division of Asthma, Allergy, and Clinical Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Charlotte Cunningham-Rundles
- Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY; and
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- St Anna Children's Cancer Research Institute, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Eleonora Gambineri
- Department of Neuroscience, Psychology, Pharmaceutical Area and Child Health (NEUROFARBA)/Paediatric Haemato-Oncology Laboratory, Anna Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Thomas A Fleisher
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Shanmuganathan Chandrakasan
- Immunedysregulation and Immuno-Hematology Program, Division of Bone Marrow Transplant, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, and
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
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17
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Wilson MM, Henshall DC, Byrne SM, Brennan GP. CHD2-Related CNS Pathologies. Int J Mol Sci 2021; 22:E588. [PMID: 33435571 PMCID: PMC7827033 DOI: 10.3390/ijms22020588] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/08/2023] Open
Abstract
Epileptic encephalopathies (EE) are severe epilepsy syndromes characterized by multiple seizure types, developmental delay and even regression. This class of disorders are increasingly being identified as resulting from de novo genetic mutations including many identified mutations in the family of chromodomain helicase DNA binding (CHD) proteins. In particular, several de novo pathogenic mutations have been identified in the gene encoding chromodomain helicase DNA binding protein 2 (CHD2), a member of the sucrose nonfermenting (SNF-2) protein family of epigenetic regulators. These mutations in the CHD2 gene are causative of early onset epileptic encephalopathy, abnormal brain function, and intellectual disability. Our understanding of the mechanisms by which modification or loss of CHD2 cause this condition remains poorly understood. Here, we review what is known and still to be elucidated as regards the structure and function of CHD2 and how its dysregulation leads to a highly variable range of phenotypic presentations.
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Affiliation(s)
- Marc-Michel Wilson
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland; (M.-M.W.); (D.C.H.)
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
| | - David C. Henshall
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland; (M.-M.W.); (D.C.H.)
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
| | - Susan M. Byrne
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
- Department of Paediatrics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland
- Department of Paediatric Neurology, Our Ladies Children’s Hospital Crumlin, Dublin 12, Ireland
| | - Gary P. Brennan
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 04, Ireland
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18
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Abstract
As primary carriers of epigenetic information and gatekeepers of genomic DNA, nucleosomes are essential for proper growth and development of all eukaryotic cells. Although they are intrinsically dynamic, nucleosomes are actively reorganized by ATP-dependent chromatin remodelers. Chromatin remodelers contain helicase-like ATPase motor domains that can translocate along DNA, and a long-standing question in the field is how this activity is used to reposition or slide nucleosomes. In addition to ratcheting along DNA like their helicase ancestors, remodeler ATPases appear to dictate specific alternating geometries of the DNA duplex, providing an unexpected means for moving DNA past the histone core. Emerging evidence supports twist-based mechanisms for ATP-driven repositioning of nucleosomes along DNA. In this review, we discuss core experimental findings and ideas that have shaped the view of how nucleosome sliding may be achieved.
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Affiliation(s)
- Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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19
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Blessing C, Knobloch G, Ladurner AG. Restraining and unleashing chromatin remodelers - structural information guides chromatin plasticity. Curr Opin Struct Biol 2020; 65:130-138. [PMID: 32693313 DOI: 10.1016/j.sbi.2020.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/06/2020] [Accepted: 06/16/2020] [Indexed: 12/21/2022]
Abstract
Chromatin remodeling enzymes are large molecular machines that guard the genome by reorganizing chromatin structure. They can reposition, space and evict nucleosomes and thus control gene expression, DNA replication and repair. Recent cryo-electron microscopy (cryo-EM) analyses have captured snapshots of various chromatin remodelers as they interact with nucleosomes. In this review, we summarize and discuss the advances made in our understanding of the regulation of chromatin remodelers, the mode of DNA translocation, as well as the influence of associated protein domains and remodeler subunits on the specific functions of chromatin remodeling complexes. The emerging structural information will help our understanding of disease mechanisms and guide our knowledge toward innovative therapeutic interventions.
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Affiliation(s)
- Charlotte Blessing
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular Life Sciences, Am Klopferspitz 18, 82152 Planegg-Martinsried, Germany
| | - Gunnar Knobloch
- Eisbach Bio GmbH, Am Klopferspitz 19, 82152, Planegg-Martinsried, Germany
| | - Andreas G Ladurner
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular Life Sciences, Am Klopferspitz 18, 82152 Planegg-Martinsried, Germany; Eisbach Bio GmbH, Am Klopferspitz 19, 82152, Planegg-Martinsried, Germany.
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20
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Yu Y, Andreu-Agullo C, Liu BF, Barboza L, Toth M, Lai EC. Regulation of embryonic and adult neurogenesis by Ars2. Development 2020; 147:147/2/dev180018. [PMID: 31969356 DOI: 10.1242/dev.180018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/20/2019] [Indexed: 11/20/2022]
Abstract
Neural development is controlled at multiple levels to orchestrate appropriate choices of cell fate and differentiation. Although more attention has been paid to the roles of neural-restricted factors, broadly expressed factors can have compelling impacts on tissue-specific development. Here, we describe in vivo conditional knockout analyses of murine Ars2, which has mostly been studied as a general RNA-processing factor in yeast and cultured cells. Ars2 protein expression is regulated during neural lineage progression, and is required for embryonic neural stem cell (NSC) proliferation. In addition, Ars2 null NSCs can still transition into post-mitotic neurons, but fail to undergo terminal differentiation. Similarly, adult-specific deletion of Ars2 compromises hippocampal neurogenesis and results in specific behavioral defects. To broaden evidence for Ars2 as a chromatin regulator in neural development, we generated Ars2 ChIP-seq data. Notably, Ars2 preferentially occupies DNA enhancers in NSCs, where it colocalizes broadly with NSC regulator SOX2. Ars2 association with chromatin is markedly reduced following NSC differentiation. Altogether, Ars2 is an essential neural regulator that interacts dynamically with DNA and controls neural lineage development.
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Affiliation(s)
- Yang Yu
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Celia Andreu-Agullo
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Bing Fang Liu
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | - Luendreo Barboza
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | - Miklos Toth
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | - Eric C Lai
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 252, New York, NY 10065, USA
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21
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Wang ZL, Wang Z, Li GZ, Wang QW, Bao ZS, Zhang CB, Jiang T. Immune Cytolytic Activity Is Associated With Genetic and Clinical Properties of Glioma. Front Immunol 2019; 10:1756. [PMID: 31428092 PMCID: PMC6688525 DOI: 10.3389/fimmu.2019.01756] [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: 08/16/2018] [Accepted: 07/11/2019] [Indexed: 12/30/2022] Open
Abstract
Background: Immunotherapy provided unprecedented advances in the treatment of several previously untreated cancers. However, these immunomodulatory maneuvers showed limited response to patients with glioma in clinical trials. Our aim was to depict the immune characteristics of glioma with immune cytolytic activity at genetic and transcriptome levels. Methods: In total, 325 gliomas from CGGA dataset as training cohort and 699 gliomas from TCGA dataset as validation cohort were enrolled in our analysis. We calculated the immune cytolytic activity for 1,000 of gliomas. The characteristics of immune cytolytic activity in gliomas were interpreted by the corresponding clinical, molecular genetics and radiological information. Results: We found that immune cytolytic activity was highly associated with molecular, clinical, and edema extent. High cytolytic activity gliomas were more likely to be diagnosed as glioblastoma and might be a potential marker of mesenchymal subtype. Moreover, those gliomas exhibited significantly increased copy number alterations including recurrent focal amplifications of PDGFA and EGFR, as well as recurrent deletions of CDKN2A/B. Subsequent biological function analysis revealed that the immune response and immune checkpoints expression were significantly correlated with the cytolytic activity of gliomas. Immune cytolytic activity was significantly positively associated with the extent of peri-tumor edema and was independently correlated with reduced survival time. Conclusion: Our results highlighted the immunoregulatory mechanism heterogeneity of gliomas. Cytolytic activity, indirectly reflected by the extent of peri-tumor edema, may provide a potential index to evaluate the status of immune microenvironment and immune checkpoints in glioma, which should be fully valued for precision classification and immunotherapy.
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Affiliation(s)
- Zhi-Liang Wang
- Department of Molecular Pathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zheng Wang
- Department of Molecular Pathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Guan-Zhang Li
- Department of Molecular Pathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Qiang-Wei Wang
- Department of Molecular Pathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhao-Shi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chuan-Bao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Tao Jiang
- Department of Molecular Pathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
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22
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Investigating the structural features of chromodomain proteins in the human genome and predictive impacts of their mutations in cancers. Int J Biol Macromol 2019; 131:1101-1116. [PMID: 30917913 DOI: 10.1016/j.ijbiomac.2019.03.162] [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: 01/15/2019] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 11/22/2022]
Abstract
Epigenetic readers are specific proteins which recognize histone marks and represents the underlying mechanism for chromatin regulation. Histone H3 lysine methylation is a potential epigenetic code for the chromatin organization and transcriptional control. Recognition of histone methylation is achieved by evolutionary conserved reader modules known as chromodomain, identified in several proteins, and is involved in transcriptional silencing and chromatin remodelling. Genetic perturbations within the structurally conserved chromodomain could potentially mistarget the reader protein and impair their regulatory pathways, ultimately leading to cellular chaos by setting the stage for tumor development and progression. Here, we report the structural conservations associated with diverse functions, prognostic significance and functional consequences of mutations within chromodomain of human proteins in distinct cancers. We have extensively analysed chromodomain containing human proteins in terms of their structural-functional ability to act as a molecular switch in the recognition of methyl-lysine recognition. We further investigated the combinatorial potential, target promiscuity and binding specificity associated with their underlying mechanisms. Indeed, the molecular mechanism of epigenetic silencing significantly underlies a newer cancer therapy approach. We hope that a critical understanding of chromodomains will pave the way for novel paths of research providing newer insights into the designing of effective anti-cancer therapies.
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23
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Harwood JC, Kent NA, Allen ND, Harwood AJ. Nucleosome dynamics of human iPSC during neural differentiation. EMBO Rep 2019; 20:embr.201846960. [PMID: 31036712 PMCID: PMC6549019 DOI: 10.15252/embr.201846960] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 01/07/2023] Open
Abstract
Nucleosome positioning is important for neurodevelopment, and genes mediating chromatin remodelling are strongly associated with human neurodevelopmental disorders. To investigate changes in nucleosome positioning during neural differentiation, we generate genome‐wide nucleosome maps from an undifferentiated human‐induced pluripotent stem cell (hiPSC) line and after its differentiation to the neural progenitor cell (NPC) stage. We find that nearly 3% of nucleosomes are highly positioned in NPC, but significantly, there are eightfold fewer positioned nucleosomes in pluripotent cells, indicating increased positioning during cell differentiation. Positioned nucleosomes do not strongly correlate with active chromatin marks or gene transcription. Unexpectedly, we find a small population of nucleosomes that occupy similar positions in pluripotent and neural progenitor cells and are found at binding sites of the key gene regulators NRSF/REST and CTCF. Remarkably, the presence of these nucleosomes appears to be independent of the associated regulatory complexes. Together, these results present a scenario in human cells, where positioned nucleosomes are sparse and dynamic, but may act to alter gene expression at a distance via the structural conformation at sites of chromatin regulation.
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Affiliation(s)
- Janet C Harwood
- MRC Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | | | | | - Adrian J Harwood
- School of Biosciences, Cardiff University, Cardiff, UK .,Neuroscience and Mental Health Research Institute (NMHRI), Cardiff University, Cardiff, UK
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24
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Guan B, Ran XG, Du YQ, Ren F, Tian Y, Wang Y, Chen MM. High CHD9 expression is associated with poor prognosis in clear cell renal cell carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3697-3702. [PMID: 31949752 PMCID: PMC6962849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/22/2018] [Indexed: 06/10/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma. The chromo-helicase-DNA binding proteins (CHDs), containing nine members named CHD1-9, act as regulators of the chromatin remodeling process and gene expression. To determine the correlation between CHD9 expression and ccRCC, we performed an immunohistochemical staining in a tissue microarray (TMAs) containing tissue samples from 88 ccRCC patients. The results showed that cytoplasm CHD9 expression was statistically decreased in tumor tissues compared to adjacent tissues (8.54±2.90 vs 12.61±2.05, P=0.000), while nuclear CHD9 expression was upregulated in the tumor tissues (1.47±2.93 vs 0.29±1.24, P=0.000). A univariate analysis found that cytoplasm CHD9 expression in cancer tissues was correlated with the patients' pathological grading (P=0.002, r=0.330), the clinical stages (P=0.02, r=0.250) and the T grading (P=0.024, r=0.241) significantly. In addition, cytoplasm CHD9 expression in non-tumor tissues was correlated with the ccRCC patients' pathological grading (P=0.031, r=-0.231) significantly. Patients with high cytoplasm CHD9 expression had a significantly worse prognosis than those with low cytoplasm CHD9 expression levels (59.7% vs 85.7%, P=0. 042). In conclusion, our study indicated the important role of CHD9 in ccRCC and suggested CHD9 may be a potential biomarker for prognostic prediction and a new target for therapy.
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Affiliation(s)
- Bo Guan
- Department of Urology, Capital Medical University, Beijing Friendship HospitalBeijing, P. R. China
- Department of Urology, Fuyang People’s HospitalYingzhou District, Fuyang, Anhui Province, P. R. China
| | - Xian-Gui Ran
- Department of Respiratory and Critical Care Medicine, Fuyang People’s HospitalYingzhou District, Fuyang, Anhui Province, P. R. China
| | - Yong-Qiang Du
- Department of Urology, Fuyang People’s HospitalYingzhou District, Fuyang, Anhui Province, P. R. China
| | - Feng Ren
- Youan Hospital, Capital Medical UniversityBeijing, P. R. China
| | - Ye Tian
- Department of Urology, Capital Medical University, Beijing Friendship HospitalBeijing, P. R. China
| | - Ying Wang
- Shanghai Outdo Biotech Co., Ltd.Shanghai, P. R. China
| | - Ming-Min Chen
- Shanghai Outdo Biotech Co., Ltd.Shanghai, P. R. China
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25
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Covalent Modifications of Histone H3K9 Promote Binding of CHD3. Cell Rep 2018; 21:455-466. [PMID: 29020631 DOI: 10.1016/j.celrep.2017.09.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/12/2017] [Accepted: 09/15/2017] [Indexed: 12/15/2022] Open
Abstract
Chromatin remodeling is required for genome function and is facilitated by ATP-dependent complexes, such as nucleosome remodeling and deacetylase (NuRD). Among its core components is the chromodomain helicase DNA binding protein 3 (CHD3) whose functional significance is not well established. Here, we show that CHD3 co-localizes with the other NuRD subunits, including HDAC1, near the H3K9ac-enriched promoters of the NuRD target genes. The tandem PHD fingers of CHD3 bind histone H3 tails and posttranslational modifications that increase hydrophobicity of H3K9-methylation or acetylation (H3K9me3 or H3K9ac)-enhance this interaction. Binding of CHD3 PHDs promotes H3K9Cme3-nucleosome unwrapping in vitro and perturbs the pericentric heterochromatin structure in vivo. Methylation or acetylation of H3K9 uniquely alleviates the intra-nucleosomal interaction of histone H3 tails, increasing H3K9 accessibility. Collectively, our data suggest that the targeting of covalently modified H3K9 by CHD3 might be essential in diverse functions of NuRD.
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26
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Peña-Llopis S, Wan Y, Martinez ED. Unique epigenetic gene profiles define human breast cancers with poor prognosis. Oncotarget 2018; 7:85819-85831. [PMID: 27863398 PMCID: PMC5349877 DOI: 10.18632/oncotarget.13334] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 10/29/2016] [Indexed: 01/09/2023] Open
Abstract
Epigenetic enzymes are at the nexus of cellular regulatory cascades and can drive cancer-specific deregulation at all stages of the oncogenic process, yet little is known about their prognostic value in human patients. Here, we used qRT-PCR to profile at high resolution the expression of fifty-five epigenetic genes in over one hundred human breast cancer samples and patient-matched benign tissues. We correlated expression patterns with clinical and histological parameters and validated our findings in two independent large patient cohorts (TCGA and METABRIC). We found that human breast malignancies have unique epigenetic profiles and cluster into epigenetic subgroups. A subset of epigenetic genes defined an Epigenetic Signature as an independent predictor of patient survival that outperforms triple negative status and other clinical variables. Our results also suggest that breast cancer grade, but not stage, is driven by transcriptional alterations of epigenetic modifiers. Overall, this study uncovers the presence of epigenetic subtypes within human mammary malignancies and identifies tumor subgroups with specific pharmacologically targetable epigenetic susceptibilities not yet therapeutically exploited.
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Affiliation(s)
- Samuel Peña-Llopis
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Yihong Wan
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
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27
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Accessibility of the histone H3 tail in the nucleosome for binding of paired readers. Nat Commun 2017; 8:1489. [PMID: 29138400 PMCID: PMC5686127 DOI: 10.1038/s41467-017-01598-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 10/03/2017] [Indexed: 12/03/2022] Open
Abstract
Combinatorial polyvalent contacts of histone-binding domains or readers commonly mediate localization and activities of chromatin-associated proteins. A pair of readers, the PHD fingers of the protein CHD4, has been shown to bivalently recognize histone H3 tails. Here we describe a mechanism by which these linked but independent readers bind to the intact nucleosome core particle (NCP). Comprehensive NMR, chemical reactivity, molecular dynamics, and fluorescence analyses point to the critical roles of intra-nucleosomal histone-DNA interactions that reduce the accessibility of H3 tails in NCP, the nucleosomal DNA, and the linker between readers in modulating nucleosome- and/or histone-binding activities of the readers. We show that the second PHD finger of CHD4 initiates recruitment to the nucleosome, however both PHDs are required to alter the NCP dynamics. Our findings reveal a distinctive regulatory mechanism for the association of paired readers with the nucleosome that provides an intricate balance between cooperative and individual activities of the readers. The chromatin remodeller CHD4 contains two PHD finger reader domains that have been shown to bivalently recognize H3 histone tails. Here, the authors describe a mechanism by which the PHD fingers bind to the intact nucleosome core particle, revealing both cooperative and individual interactions.
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28
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Ribich S, Harvey D, Copeland RA. Drug Discovery and Chemical Biology of Cancer Epigenetics. Cell Chem Biol 2017; 24:1120-1147. [PMID: 28938089 DOI: 10.1016/j.chembiol.2017.08.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/11/2017] [Accepted: 08/28/2017] [Indexed: 12/24/2022]
Abstract
Comprehensive whole-exome sequencing, DNA copy-number determination, and transcriptomic analyses of diverse cancers have greatly expanded our understanding of the biology of many tumor types. In addition to mutations in the common cell-of-origin specific driver mutations, these studies have also revealed a large number of loss-of-function and gain-of-function mutations in chromatin-modifying proteins (CMPs). This has revealed that epigenetic dysregulation is a common feature of most pediatric and adult cancers. Many specific and potent inhibitors have been developed for multiple CMP classes, which have assisted in elucidating the role of epigenetics as well as epigenetic vulnerabilities in these cancer types. Clinical trials with numerous CMP inhibitors are also currently in progress to evaluate the therapeutic potential of epigenetic inhibitors. In this review, we aim to provide a summary of genetic mutations in epigenetic genes and a review of CMP inhibitors suitable for preclinical studies or currently in clinical trials. Additionally, we highlight the CMPs for which potent inhibitors have not been developed and additional research focus should be dedicated.
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Affiliation(s)
- Scott Ribich
- Epizyme, Inc., 400 Technology Square, Cambridge, MA 02139, USA
| | - Darren Harvey
- Epizyme, Inc., 400 Technology Square, Cambridge, MA 02139, USA
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29
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Chu X, Guo X, Jiang Y, Yu H, Liu L, Shan W, Yang Z. Genotranscriptomic meta-analysis of the CHD family chromatin remodelers in human cancers - initial evidence of an oncogenic role for CHD7. Mol Oncol 2017; 11:1348-1360. [PMID: 28649742 PMCID: PMC5623824 DOI: 10.1002/1878-0261.12104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/27/2017] [Accepted: 06/10/2017] [Indexed: 12/14/2022] Open
Abstract
Chromodomain helicase DNA binding proteins (CHDs) are characterized by N-terminal tandem chromodomains and a central adenosine triphosphate-dependent helicase domain. CHDs govern the cellular machinery's access to DNA, thereby playing critical roles in various cellular processes including transcription, proliferation, and DNA damage repair. Accumulating evidence demonstrates that mutation and dysregulation of CHDs are implicated in the pathogenesis of developmental disorders and cancer. However, we know little about genomic and transcriptomic alterations and the clinical significance of most CHDs in human cancer. We used TCGA and METABRIC datasets to perform integrated genomic and transcriptomic analyses of nine CHD genes in more than 10 000 primary cancer specimens from 32 tumor types, focusing on breast cancers. We identified associations among recurrent copy number alteration, gene expression, clinicopathological features, and patient survival. We found that CHD7 was the most commonly gained/amplified and mutated, whereas CHD3 was the most deleted across the majority of tumor types, including breast cancer. Overexpression of CHD7 was more prevalent in aggressive subtypes of breast cancer and was significantly correlated with high tumor grade and poor prognosis. CHD7 is required to maintain open, accessible chromatin, thus providing fine-tuning of transcriptional regulation of certain classes of genes. We found that CHD7 expression was positively correlated with a small subset of classical oncogenes, notably NRAS, in breast cancer. Knockdown of CHD7 inhibits cell proliferation and decreases gene expression of several CHD7 targets, including NRAS, in breast cancer cell lines. Thus, our results demonstrate the oncogenic potential of CHD7 and its association with poor prognostic parameters in human cancer.
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Affiliation(s)
- Xiaofang Chu
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Xuhui Guo
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
- Department of Breast SurgeryAffiliated Cancer Hospital of Zhengzhou UniversityHenanChina
| | - Yuanyuan Jiang
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Huimei Yu
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
- College of Basic MedicineJilin UniversityChangchunChina
| | - Lanxin Liu
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Wenqi Shan
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Zeng‐Quan Yang
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
- Molecular Therapeutics ProgramBarbara Ann Karmanos Cancer InstituteDetroitMIUSA
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30
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Abstract
In the past few years, it has become clear that mutations in epigenetic regulatory genes are common in human cancers. Therapeutic strategies are now being developed to target cancers with mutations in these genes using specific chemical inhibitors. In addition, a complementary approach based on the concept of synthetic lethality, which allows exploitation of loss-of-function mutations in cancers that are not targetable by conventional methods, has gained traction. Both of these approaches are now being tested in several clinical trials. In this Review, we present recent advances in epigenetic drug discovery and development, and suggest possible future avenues of investigation to drive progress in this area.
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31
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Yu H, Jiang Y, Liu L, Shan W, Chu X, Yang Z, Yang ZQ. Integrative genomic and transcriptomic analysis for pinpointing recurrent alterations of plant homeodomain genes and their clinical significance in breast cancer. Oncotarget 2017; 8:13099-13115. [PMID: 28055972 PMCID: PMC5355080 DOI: 10.18632/oncotarget.14402] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 12/05/2016] [Indexed: 11/29/2022] Open
Abstract
A wide range of the epigenetic effectors that regulate chromatin modification, gene expression, genomic stability, and DNA repair contain structurally conserved domains called plant homeodomain (PHD) fingers. Alternations of several PHD finger-containing proteins (PHFs) due to genomic amplification, mutations, deletions, and translocations have been linked directly to various types of cancer. However, little is known about the genomic landscape and the clinical significance of PHFs in breast cancer. Hence, we performed a large-scale genomic and transcriptomic analysis of 98 PHF genes in breast cancer using TCGA and METABRIC datasets and correlated the recurrent alterations with clinicopathological features and survival of patients. Different subtypes of breast cancer had different patterns of copy number and expression for each PHF. We identified a subset of PHF genes that was recurrently altered with high prevalence, including PYGO2 (pygopus family PHD finger 2), ZMYND8 (zinc finger, MYND-type containing 8), ASXL1 (additional sex combs like 1) and CHD3 (chromodomain helicase DNA binding protein 3). Copy number increase and overexpression of ZMYND8 were more prevalent in Luminal B subtypes and were significantly associated with shorter survival of breast cancer patients. ZMYND8 was also involved in a positive feedback circuit of the estrogen receptor (ER) pathway, and the expression of ZMYND8 was repressed by the bromodomain and extra terminal (BET) inhibitor in breast cancer. Our findings suggest a promising avenue for future research-to focus on a subset of PHFs to better understand the molecular mechanisms and to identify therapeutic targets in breast cancer.
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Affiliation(s)
- Huimei Yu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- College of Basic Medicine, Jilin University, Changchun, China
| | - Yuanyuan Jiang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Lanxin Liu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Wenqi Shan
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Xiaofang Chu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Zhe Yang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Zeng-Quan Yang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI 48201, USA
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Abstract
Macrophage migration inhibitory factor (MIF) plays an important role in supporting the proliferation and/or survival of murine neural stem/progenitor cells (NSPCs); however, the downstream effectors of this factor remain unknown. Here, we show that MIF increases the expression of Pax6 and Chd7 in NSPCs in vitro. During neural development, the chromatin remodeling factor Chd7 (chromatin helicase-DNA-binding protein 7) is expressed in the ventricular zone of the telencephalon of mouse brain at embryonic day 14.5, as well as in cultured NSPCs. Retroviral overexpression of Pax6 in NSPCs increased Chd7 gene expression. Lentivirally-expressed Chd7 shRNA suppressed cell proliferation and neurosphere formation, and inhibited neurogenesis in vitro, while decreasing gene expression of Hes5 and N-myc. In addition, CHD7 overexpression increased cell proliferation in human embryonic stem cell-derived NSPCs (ES-NSPCs). In Chd7 mutant fetal mouse brains, there were fewer intermediate progenitor cells (IPCs) compared to wildtype littermates, indicating that Chd7 contributes to neurogenesis in the early developmental mouse brain. Furthermore, in silico database analysis showed that, among members of the CHD family, CHD7 is highly expressed in human gliomas. Interestingly, high levels of CHD7 gene expression in human glioma initiating cells (GICs) compared to normal astrocytes were revealed and gene silencing of CHD7 decreased GIC proliferation. Collectively, our data demonstrate that CHD7 is an important factor in the proliferation and stemness maintenance of NSPCs, and CHD7 is a promising therapeutic target for the treatment of gliomas.
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Functional Insights into Chromatin Remodelling from Studies on CHARGE Syndrome. Trends Genet 2015; 31:600-611. [PMID: 26411921 PMCID: PMC4604214 DOI: 10.1016/j.tig.2015.05.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/25/2015] [Accepted: 05/26/2015] [Indexed: 12/27/2022]
Abstract
CHARGE syndrome is a rare genetic syndrome characterised by a unique combination of multiple organ anomalies. Dominant loss-of-function mutations in the gene encoding chromodomain helicase DNA binding protein 7 (CHD7), which is an ATP-dependent chromatin remodeller, have been identified as the cause of CHARGE syndrome. Here, we review recent work aimed at understanding the mechanism of CHD7 function in normal and pathological states, highlighting results from biochemical and in vivo studies. The emerging picture from this work suggests that the mechanisms by which CHD7 fine-tunes gene expression are context specific, consistent with the pleiotropic nature of CHARGE syndrome.
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Micucci JA, Sperry ED, Martin DM. Chromodomain helicase DNA-binding proteins in stem cells and human developmental diseases. Stem Cells Dev 2015; 24:917-26. [PMID: 25567374 DOI: 10.1089/scd.2014.0544] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Dynamic regulation of gene expression is vital for proper cellular development and maintenance of differentiated states. Over the past 20 years, chromatin remodeling and epigenetic modifications of histones have emerged as key controllers of rapid reversible changes in gene expression. Mutations in genes encoding enzymes that modify chromatin have also been identified in a variety of human neurodevelopmental disorders, ranging from isolated intellectual disability and autism spectrum disorder to multiple congenital anomaly conditions that affect major organ systems and cause severe morbidity and mortality. In this study, we review recent evidence that chromodomain helicase DNA-binding (CHD) proteins regulate stem cell proliferation, fate, and differentiation in a wide variety of tissues and organs. We also highlight known roles of CHD proteins in human developmental diseases and present current unanswered questions about the pleiotropic effects of CHD protein complexes, their genetic targets, nucleosome sliding functions, and enzymatic effects in cells and tissues.
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Affiliation(s)
- Joseph A Micucci
- 1 Division of Hematology, Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
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Iourov IY, Vorsanova SG, Yurov YB. In silico molecular cytogenetics: a bioinformatic approach to prioritization of candidate genes and copy number variations for basic and clinical genome research. Mol Cytogenet 2014; 7:98. [PMID: 25525469 PMCID: PMC4269961 DOI: 10.1186/s13039-014-0098-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 12/02/2014] [Indexed: 01/08/2023] Open
Abstract
Background The availability of multiple in silico tools for prioritizing genetic variants widens the possibilities for converting genomic data into biological knowledge. However, in molecular cytogenetics, bioinformatic analyses are generally limited to result visualization or database mining for finding similar cytogenetic data. Obviously, the potential of bioinformatics might go beyond these applications. On the other hand, the requirements for performing successful in silico analyses (i.e. deep knowledge of computer science, statistics etc.) can hinder the implementation of bioinformatics in clinical and basic molecular cytogenetic research. Here, we propose a bioinformatic approach to prioritization of genomic variations that is able to solve these problems. Results Selecting gene expression as an initial criterion, we have proposed a bioinformatic approach combining filtering and ranking prioritization strategies, which includes analyzing metabolome and interactome data on proteins encoded by candidate genes. To finalize the prioritization of genetic variants, genomic, epigenomic, interactomic and metabolomic data fusion has been made. Structural abnormalities and aneuploidy revealed by array CGH and FISH have been evaluated to test the approach through determining genotype-phenotype correlations, which have been found similar to those of previous studies. Additionally, we have been able to prioritize copy number variations (CNV) (i.e. differentiate between benign CNV and CNV with phenotypic outcome). Finally, the approach has been applied to prioritize genetic variants in cases of somatic mosaicism (including tissue-specific mosaicism). Conclusions In order to provide for an in silico evaluation of molecular cytogenetic data, we have proposed a bioinformatic approach to prioritization of candidate genes and CNV. While having the disadvantage of possible unavailability of gene expression data or lack of expression variability between genes of interest, the approach provides several advantages. These are (i) the versatility due to independence from specific databases/tools or software, (ii) relative algorithm simplicity (possibility to avoid sophisticated computational/statistical methodology) and (iii) applicability to molecular cytogenetic data because of the chromosome-centric nature. In conclusion, the approach is able to become useful for increasing the yield of molecular cytogenetic techniques.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, Russian Academy of Medical Sciences, 117152 Moscow, Russia ; Russian National Research Medical University named after N.I. Pirogov, Separated Structural Unit "Clinical Research Institute of Pediatrics", Ministry of Health of Russian Federation, 125412 Moscow, Russia ; Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, Moscow, 123995 Russia
| | - Svetlana G Vorsanova
- Mental Health Research Center, Russian Academy of Medical Sciences, 117152 Moscow, Russia ; Russian National Research Medical University named after N.I. Pirogov, Separated Structural Unit "Clinical Research Institute of Pediatrics", Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | - Yuri B Yurov
- Mental Health Research Center, Russian Academy of Medical Sciences, 117152 Moscow, Russia ; Russian National Research Medical University named after N.I. Pirogov, Separated Structural Unit "Clinical Research Institute of Pediatrics", Ministry of Health of Russian Federation, 125412 Moscow, Russia
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