1
|
Tong D, Tang Y, Zhong P. The emerging roles of histone demethylases in cancers. Cancer Metastasis Rev 2024; 43:795-821. [PMID: 38227150 DOI: 10.1007/s10555-023-10160-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Modulation of histone methylation status is regarded as an important mechanism of epigenetic regulation and has substantial clinical potential for the therapy of diseases, including cancer and other disorders. The present study aimed to provide a comprehensive introduction to the enzymology of histone demethylases, as well as their cancerous roles, molecular mechanisms, therapeutic possibilities, and challenges for targeting them, in order to advance drug design for clinical therapy and highlight new insight into the mechanisms of these enzymes in cancer. A series of clinical trials have been performed to explore potential roles of histone demethylases in several cancer types. Numerous targeted inhibitors associated with immunotherapy, chemotherapy, radiotherapy, and targeted therapy have been used to exert anticancer functions. Future studies should evaluate the dynamic transformation of histone demethylases leading to carcinogenesis and explore individual therapy.
Collapse
Affiliation(s)
- Dali Tong
- Department of Urological Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, People's Republic of China.
| | - Ying Tang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China.
| | - Peng Zhong
- Department of Pathology, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, People's Republic of China.
| |
Collapse
|
2
|
Tian M, Wang Z, Su Z, Shibata E, Shibata Y, Dutta A, Zang C. Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap. eLife 2024; 12:RP89548. [PMID: 38567819 PMCID: PMC10990492 DOI: 10.7554/elife.89548] [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] [Indexed: 04/05/2024] Open
Abstract
Based on experimentally determined average inter-origin distances of ~100 kb, DNA replication initiates from ~50,000 origins on human chromosomes in each cell cycle. The origins are believed to be specified by binding of factors like the origin recognition complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and five ORC-binding profiles to critically evaluate whether the most reproducible origins are specified by these features. Out of ~7.5 million union origins identified by all datasets, only 0.27% (20,250 shared origins) were reproducibly obtained in at least 20 independent SNS-seq datasets and contained in initiation zones identified by each of three other techniques, suggesting extensive variability in origin usage and identification. Also, 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF-binding sites, G-quadruplex sites, and activating histone marks, these overlaps are comparable or less than that of known transcription start sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the ~13,000 reproducible ORC-binding sites in human cancer cells, and only 4.5% were within 1 kb of the ~11,000 union MCM2-7-binding sites in contrast to the nearly 100% overlap in the two comparisons in the yeast, Saccharomyces cerevisiae. Thus, in human cancer cell lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and currently known ORC- or MCM-binding sites.
Collapse
Affiliation(s)
- Mengxue Tian
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Etsuko Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Public Health Sciences, University of VirginiaCharlottesvilleUnited States
| |
Collapse
|
3
|
Ahmad H, Chetlangia N, Prasanth SG. Chromatin's Influence on Pre-Replication Complex Assembly and Function. BIOLOGY 2024; 13:152. [PMID: 38534422 DOI: 10.3390/biology13030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
In all eukaryotes, the initiation of DNA replication requires a stepwise assembly of factors onto the origins of DNA replication. This is pioneered by the Origin Recognition Complex, which recruits Cdc6. Together, they bring Cdt1, which shepherds MCM2-7 to form the OCCM complex. Sequentially, a second Cdt1-bound hexamer of MCM2-7 is recruited by ORC-Cdc6 to form an MCM double hexamer, which forms a part of the pre-RC. Although the mechanism of ORC binding to DNA varies across eukaryotes, how ORC is recruited to replication origins in human cells remains an area of intense investigation. This review discusses how the chromatin environment influences pre-RC assembly, function, and, eventually, origin activity.
Collapse
Affiliation(s)
- Hina Ahmad
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Neha Chetlangia
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
4
|
Lee CSK, Weiβ M, Hamperl S. Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes. Nucleus 2023; 14:2229642. [PMID: 37469113 PMCID: PMC10361152 DOI: 10.1080/19491034.2023.2229642] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
In eukaryotic genomes, hundreds to thousands of potential start sites of DNA replication named origins are dispersed across each of the linear chromosomes. During S-phase, only a subset of origins is selected in a stochastic manner to assemble bidirectional replication forks and initiate DNA synthesis. Despite substantial progress in our understanding of this complex process, a comprehensive 'identity code' that defines origins based on specific nucleotide sequences, DNA structural features, the local chromatin environment, or 3D genome architecture is still missing. In this article, we review the genetic and epigenetic features of replication origins in yeast and metazoan chromosomes and highlight recent insights into how this flexibility in origin usage contributes to nuclear organization, cell growth, differentiation, and genome stability.
Collapse
Affiliation(s)
- Clare S K Lee
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Matthias Weiβ
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| |
Collapse
|
5
|
Seidel P, Rubarth A, Zodel K, Peighambari A, Neumann F, Federkiel Y, Huang H, Hoefflin R, Adlesic M, Witt C, Hoffmann DJ, Metzger P, Lindemann RK, Zenke FT, Schell C, Boerries M, von Elverfeldt D, Reichardt W, Follo M, Albers J, Frew IJ. ATR represents a therapeutic vulnerability in clear cell renal cell carcinoma. JCI Insight 2022; 7:156087. [PMID: 36413415 PMCID: PMC9869969 DOI: 10.1172/jci.insight.156087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/10/2022] [Indexed: 11/24/2022] Open
Abstract
Metastatic clear cell renal cell carcinomas (ccRCCs) are resistant to DNA-damaging chemotherapies, limiting therapeutic options for patients whose tumors are resistant to tyrosine kinase inhibitors and/or immune checkpoint therapies. Here we show that mouse and human ccRCCs were frequently characterized by high levels of endogenous DNA damage and that cultured ccRCC cells exhibited intact cellular responses to chemotherapy-induced DNA damage. We identify that pharmacological inhibition of the DNA damage-sensing kinase ataxia telangiectasia and Rad3-related protein (ATR) with the orally administered, potent, and selective drug M4344 (gartisertib) induced antiproliferative effects in ccRCC cells. This effect was due to replication stress and accumulation of DNA damage in S phase. In some cells, DNA damage persisted into subsequent G2/M and G1 phases, leading to the frequent accumulation of micronuclei. Daily single-agent treatment with M4344 inhibited the growth of ccRCC xenograft tumors. M4344 synergized with chemotherapeutic drugs including cisplatin and carboplatin and the poly(ADP-ribose) polymerase inhibitor olaparib in mouse and human ccRCC cells. Weekly M4344 plus cisplatin treatment showed therapeutic synergy in ccRCC xenografts and was efficacious in an autochthonous mouse ccRCC model. These studies identify ATR inhibition as a potential novel therapeutic option for ccRCC.
Collapse
Affiliation(s)
- Philipp Seidel
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Anne Rubarth
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Kyra Zodel
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Asin Peighambari
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Felix Neumann
- Translational Innovation Platform Oncology and Immuno-Oncology, the Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Yannick Federkiel
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Hsin Huang
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Rouven Hoefflin
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Mojca Adlesic
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Christian Witt
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - David J. Hoffmann
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | | | - Ralph K. Lindemann
- Translational Innovation Platform Oncology and Immuno-Oncology, the Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Frank T. Zenke
- Translational Innovation Platform Oncology and Immuno-Oncology, the Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Christoph Schell
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Freiburg, Freiburg, Germany.,Comprehensive Cancer Center Freiburg (CCCF) and
| | | | - Wilfried Reichardt
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Freiburg, Freiburg, Germany.,Medical Physics, Department of Radiology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Marie Follo
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| | - Joachim Albers
- Translational Innovation Platform Oncology and Immuno-Oncology, the Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Ian J. Frew
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Freiburg, Freiburg, Germany.,Comprehensive Cancer Center Freiburg (CCCF) and,Medical Physics, Department of Radiology, Faculty of Medicine, Medical Center – University of Freiburg, Freiburg, Germany
| |
Collapse
|
6
|
Millán-Zambrano G, Burton A, Bannister AJ, Schneider R. Histone post-translational modifications - cause and consequence of genome function. Nat Rev Genet 2022; 23:563-580. [PMID: 35338361 DOI: 10.1038/s41576-022-00468-7] [Citation(s) in RCA: 282] [Impact Index Per Article: 141.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2022] [Indexed: 12/16/2022]
Abstract
Much has been learned since the early 1960s about histone post-translational modifications (PTMs) and how they affect DNA-templated processes at the molecular level. This understanding has been bolstered in the past decade by the identification of new types of histone PTM, the advent of new genome-wide mapping approaches and methods to deposit or remove PTMs in a locally and temporally controlled manner. Now, with the availability of vast amounts of data across various biological systems, the functional role of PTMs in important processes (such as transcription, recombination, replication, DNA repair and the modulation of genomic architecture) is slowly emerging. This Review explores the contribution of histone PTMs to the regulation of genome function by discussing when these modifications play a causative (or instructive) role in DNA-templated processes and when they are deposited as a consequence of such processes, to reinforce and record the event. Important advances in the field showing that histone PTMs can exert both direct and indirect effects on genome function are also presented.
Collapse
Affiliation(s)
- Gonzalo Millán-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Adam Burton
- Institute of Epigenetics and Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Andrew J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Center Munich, Munich, Germany.
- Faculty of Biology, Ludwig Maximilian University (LMU) of Munich, Munich, Germany.
| |
Collapse
|
7
|
Kaempferol antagonizes adipogenesis by repressing histone H3K4 methylation at PPARγ target genes. Biochem Biophys Res Commun 2022; 617:48-54. [DOI: 10.1016/j.bbrc.2022.05.098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 01/13/2023]
|
8
|
Pavlenko E, Ruengeler T, Engel P, Poepsel S. Functions and Interactions of Mammalian KDM5 Demethylases. Front Genet 2022; 13:906662. [PMID: 35899196 PMCID: PMC9309374 DOI: 10.3389/fgene.2022.906662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/06/2022] [Indexed: 12/26/2022] Open
Abstract
Mammalian histone demethylases of the KDM5 family are mediators of gene expression dynamics during developmental, cellular differentiation, and other nuclear processes. They belong to the large group of JmjC domain containing, 2-oxoglutarate (2-OG) dependent oxygenases and target methylated lysine 4 of histone H3 (H3K4me1/2/3), an epigenetic mark associated with active transcription. In recent years, KDM5 demethylases have gained increasing attention due to their misregulation in many cancer entities and are intensively explored as therapeutic targets. Despite these implications, the molecular basis of KDM5 function has so far remained only poorly understood. Little is known about mechanisms of nucleosome recognition, the recruitment to genomic targets, as well as the local regulation of demethylase activity. Experimental evidence suggests close physical and functional interactions with epigenetic regulators such as histone deacetylase (HDAC) containing complexes, as well as the retinoblastoma protein (RB). To understand the regulation of KDM5 proteins in the context of chromatin, these interactions have to be taken into account. Here, we review the current state of knowledge on KDM5 function, with a particular emphasis on molecular interactions and their potential implications. We will discuss and outline open questions that need to be addressed to better understand histone demethylation and potential demethylation-independent functions of KDM5s. Addressing these questions will increase our understanding of histone demethylation and allow us to develop strategies to target individual KDM5 enzymes in specific biological and disease contexts.
Collapse
Affiliation(s)
- Egor Pavlenko
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Till Ruengeler
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Paulina Engel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Simon Poepsel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- *Correspondence: Simon Poepsel,
| |
Collapse
|
9
|
LSD1 is required for euchromatic origin firing and replication timing. Signal Transduct Target Ther 2022; 7:102. [PMID: 35414135 PMCID: PMC9005705 DOI: 10.1038/s41392-022-00927-x] [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: 04/12/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 11/08/2022] Open
Abstract
The chromatin-based rule governing the selection and activation of replication origins remains to be elucidated. It is believed that DNA replication initiates from open chromatin domains; thus, replication origins reside in open and active chromatin. However, we report here that lysine-specific demethylase 1 (LSD1), which biochemically catalyzes H3K4me1/2 demethylation favoring chromatin condensation, interacts with the DNA replication machinery in human cells. We find that LSD1 level peaks in early S phase, when it is required for DNA replication by facilitating origin firing in euchromatic regions. Indeed, euchromatic zones enriched in H3K4me2 are the preferred sites for the pre-replicative complex (pre-RC) binding. Remarkably, LSD1 deficiency leads to a genome-wide switch of replication from early to late. We show that LSD1-engaged DNA replication is mechanistically linked to the loading of TopBP1-Interacting Checkpoint and Replication Regulator (TICRR) onto the pre-RC and subsequent recruitment of CDC45 during origin firing. Together, these results reveal an unexpected role for LSD1 in euchromatic origin firing and replication timing, highlighting the importance of epigenetic regulation in the activation of replication origins. As selective inhibitors of LSD1 are being exploited as potential cancer therapeutics, our study supports the importance of leveraging an appropriate level of LSD1 to curb the side effects of anti-LSD1 therapy.
Collapse
|
10
|
Tedesco M, Giannese F, Lazarević D, Giansanti V, Rosano D, Monzani S, Catalano I, Grassi E, Zanella ER, Botrugno OA, Morelli L, Panina Bordignon P, Caravagna G, Bertotti A, Martino G, Aldrighetti L, Pasqualato S, Trusolino L, Cittaro D, Tonon G. Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin. Nat Biotechnol 2022; 40:235-244. [PMID: 34635836 DOI: 10.1038/s41587-021-01031-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 07/22/2021] [Indexed: 02/08/2023]
Abstract
Recent efforts have succeeded in surveying open chromatin at the single-cell level, but high-throughput, single-cell assessment of heterochromatin and its underlying genomic determinants remains challenging. We engineered a hybrid transposase including the chromodomain (CD) of the heterochromatin protein-1α (HP-1α), which is involved in heterochromatin assembly and maintenance through its binding to trimethylation of the lysine 9 on histone 3 (H3K9me3), and developed a single-cell method, single-cell genome and epigenome by transposases sequencing (scGET-seq), that, unlike single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), comprehensively probes both open and closed chromatin and concomitantly records the underlying genomic sequences. We tested scGET-seq in cancer-derived organoids and human-derived xenograft (PDX) models and identified genetic events and plasticity-driven mechanisms contributing to cancer drug resistance. Next, building upon the differential enrichment of closed and open chromatin, we devised a method, Chromatin Velocity, that identifies the trajectories of epigenetic modifications at the single-cell level. Chromatin Velocity uncovered paths of epigenetic reorganization during stem cell reprogramming and identified key transcription factors driving these developmental processes. scGET-seq reveals the dynamics of genomic and epigenetic landscapes underlying any cellular processes.
Collapse
Affiliation(s)
- Martina Tedesco
- Università Vita-Salute San Raffaele, Milano, Italy
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | | | - Dejan Lazarević
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Valentina Giansanti
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
| | - Dalia Rosano
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Silvia Monzani
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IEO, IRCCS European Institute of Oncology, Milano, Italy
| | - Irene Catalano
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Elena Grassi
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | | | - Oronza A Botrugno
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Leonardo Morelli
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Paola Panina Bordignon
- Università Vita-Salute San Raffaele, Milano, Italy
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
| | - Andrea Bertotti
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Gianvito Martino
- Università Vita-Salute San Raffaele, Milano, Italy
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Luca Aldrighetti
- Hepatobiliary Surgery Division, IRCCS San Raffaele Hospital, Milano, Italy
| | - Sebastiano Pasqualato
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IEO, IRCCS European Institute of Oncology, Milano, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy.
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy.
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy.
| |
Collapse
|
11
|
The genetic architecture of DNA replication timing in human pluripotent stem cells. Nat Commun 2021; 12:6746. [PMID: 34799581 PMCID: PMC8604924 DOI: 10.1038/s41467-021-27115-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022] Open
Abstract
DNA replication follows a strict spatiotemporal program that intersects with chromatin structure but has a poorly understood genetic basis. To systematically identify genetic regulators of replication timing, we exploited inter-individual variation in human pluripotent stem cells from 349 individuals. We show that the human genome's replication program is broadly encoded in DNA and identify 1,617 cis-acting replication timing quantitative trait loci (rtQTLs) - sequence determinants of replication initiation. rtQTLs function individually, or in combinations of proximal and distal regulators, and are enriched at sites of histone H3 trimethylation of lysines 4, 9, and 36 together with histone hyperacetylation. H3 trimethylation marks are individually repressive yet synergistically associate with early replication. We identify pluripotency-related transcription factors and boundary elements as positive and negative regulators of replication timing, respectively. Taken together, human replication timing is controlled by a multi-layered mechanism with dozens of effectors working combinatorially and following principles analogous to transcription regulation.
Collapse
|
12
|
Hao F. Systemic Profiling of KDM5 Subfamily Signature in Non-Small-Cell Lung Cancer. Int J Gen Med 2021; 14:7259-7275. [PMID: 34737620 PMCID: PMC8558507 DOI: 10.2147/ijgm.s329733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/14/2021] [Indexed: 11/23/2022] Open
Abstract
Background Despite improvements in diagnosis and treatment, lung cancer is one of the most lethal human diseases, with a dismal 5-year relative survival rate of only 5% for patients diagnosed with advanced metastatic disease. Accumulating evidence supports that epigenetic aberration of histone demethylase-KDM5 subfamily is linked to human pan-cancer. However, the detailed functions of KDM5 proteins in lung cancer, especially in non-small-cell lung cancer (NSCLC), remain poorly understand. Methods UALCAN, GEPIA, Kaplan-Meier plotter, cBioPortal, TIMER, TISIDB, and STRING databases were utilized in this investigation. Results We detected varying degrees of gene mutations of KDM5 subfamily members and found that KDM5B/C were remarkably overexpressed in LUAD and LUSC compared to normal tissues. Different from KDM5D, positive relationship was shown between overall survival and mRNA expression of KDM5A/B/C in lung cancer. We determined that KDM5A/B/C expression levels were positively correlated with CD4+ T cells infiltration, especially immunological markers of Tregs and Th17 cells. Moreover, LUAD and LUSC were separately rich in inflammatory and wound healing subtypes after immunogenomics analyzing with respect to KDM5 subfamily overexpression. And with their 120 co-expressed genes, we revealed that nucleocytoplasmic transport and cellular protein localization-related genes were closely connected to KDM5 subfamily alterations, next to chromatin remodeling genes. Conclusion We formulated the immune-infiltrating and prognostic value of KDM5 subfamily and highlighted its promising role in immune-inflammatory interaction with tumour microenvironment in NSCLC.
Collapse
Affiliation(s)
- Fang Hao
- Department of Oncology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| |
Collapse
|
13
|
Hsu CL, Lo YC, Kao CF. H3K4 Methylation in Aging and Metabolism. EPIGENOMES 2021; 5:14. [PMID: 34968301 PMCID: PMC8594702 DOI: 10.3390/epigenomes5020014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 02/03/2023] Open
Abstract
During the process of aging, extensive epigenetic alterations are made in response to both exogenous and endogenous stimuli. Here, we summarize the current state of knowledge regarding one such alteration, H3K4 methylation (H3K4me), as it relates to aging in different species. We especially highlight emerging evidence that links this modification with metabolic pathways, which may provide a mechanistic link to explain its role in aging. H3K4me is a widely recognized marker of active transcription, and it appears to play an evolutionarily conserved role in determining organism longevity, though its influence is context specific and requires further clarification. Interestingly, the modulation of H3K4me dynamics may occur as a result of nutritional status, such as methionine restriction. Methionine status appears to influence H3K4me via changes in the level of S-adenosyl methionine (SAM, the universal methyl donor) or the regulation of H3K4-modifying enzyme activities. Since methionine restriction is widely known to extend lifespan, the mechanistic link between methionine metabolic flux, the sensing of methionine concentrations and H3K4me status may provide a cogent explanation for several seemingly disparate observations in aging organisms, including age-dependent H3K4me dynamics, gene expression changes, and physiological aberrations. These connections are not yet entirely understood, especially at a molecular level, and will require further elucidation. To conclude, we discuss some potential H3K4me-mediated molecular mechanisms that may link metabolic status to the aging process.
Collapse
Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Yi-Chen Lo
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan;
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| |
Collapse
|
14
|
de La Roche Saint-André C, Géli V. Set1-dependent H3K4 methylation becomes critical for limiting DNA damage in response to changes in S-phase dynamics in Saccharomyces cerevisiae. DNA Repair (Amst) 2021; 105:103159. [PMID: 34174709 DOI: 10.1016/j.dnarep.2021.103159] [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: 02/10/2021] [Revised: 05/27/2021] [Accepted: 06/13/2021] [Indexed: 11/29/2022]
Abstract
DNA replication is a highly regulated process that occurs in the context of chromatin structure and is sensitive to several histone post-translational modifications. In Saccharomyces cerevisiae, the histone methylase Set1 is responsible for the transcription-dependent deposition of H3K4 methylation (H3K4me) throughout the genome. Here we show that a combination of a hypomorphic replication mutation (orc5-1) with the absence of Set1 (set1Δ) compromises the progression through S-phase, and this is associated with a large increase in DNA damage. The ensuing DNA damage checkpoint activation, in addition to that of the spindle assembly checkpoint, restricts the growth of orc5-1 set1Δ. The opposite effects of the lack of RNase H activity and the reduction of histone levels on orc5-1 set1Δ viability are in agreement with their expected effects on replication fork progression. We propose that the role of H3K4 methylation during DNA replication becomes critical when the replication forks acceleration due to decreased origin firing in the orc5-1 background increases the risk for transcription replication conflicts. Furthermore, we show that an increase of reactive oxygen species levels, likely a consequence of the elevated DNA damage, is partly responsible for the lethality in orc5-1 set1Δ.
Collapse
Affiliation(s)
- Christophe de La Roche Saint-André
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes, Marseille, France.
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes, Marseille, France
| |
Collapse
|
15
|
Gaillard S, Charasson V, Ribeyre C, Salifou K, Pillaire MJ, Hoffmann JS, Constantinou A, Trouche D, Vandromme M. KDM5A and KDM5B histone-demethylases contribute to HU-induced replication stress response and tolerance. Biol Open 2021; 10:268370. [PMID: 34184733 PMCID: PMC8181900 DOI: 10.1242/bio.057729] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/20/2021] [Indexed: 12/25/2022] Open
Abstract
KDM5A and KDM5B histone-demethylases are overexpressed in many cancers and have been involved in drug tolerance. Here, we describe that KDM5A, together with KDM5B, contribute to replication stress (RS) response and tolerance. First, they positively regulate RRM2, the regulatory subunit of ribonucleotide reductase. Second, they are required for optimal levels of activated Chk1, a major player of the intra-S phase checkpoint that protects cells from RS. We also found that KDM5A is enriched at ongoing replication forks and associates with both PCNA and Chk1. Because RRM2 is a major determinant of replication stress tolerance, we developed cells resistant to HU, and show that KDM5A/B proteins are required for both RRM2 overexpression and tolerance to HU. Altogether, our results indicate that KDM5A/B are major players of RS management. They also show that drugs targeting the enzymatic activity of KDM5 proteins may not affect all cancer-related consequences of KDM5A/B overexpression.
Collapse
Affiliation(s)
- Solenne Gaillard
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Virginie Charasson
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Cyril Ribeyre
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Kader Salifou
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Marie-Jeanne Pillaire
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037 Toulouse, France
| | - Jean-Sebastien Hoffmann
- Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 avenue Irène-Joliot-Curie, 31059 Toulouse cedex, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Didier Trouche
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Marie Vandromme
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| |
Collapse
|
16
|
Kumagai A, Dunphy WG. Binding of the Treslin-MTBP Complex to Specific Regions of the Human Genome Promotes the Initiation of DNA Replication. Cell Rep 2021; 32:108178. [PMID: 32966791 PMCID: PMC7523632 DOI: 10.1016/j.celrep.2020.108178] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/12/2020] [Accepted: 08/31/2020] [Indexed: 12/16/2022] Open
Abstract
The processes that control where higher eukaryotic cells initiate DNA replication throughout the genome are not understood clearly. In metazoans, the Treslin-MTBP complex mediates critical final steps in formation of the activated replicative helicase prior to initiation of replication. Here, we map the genome-wide distribution of the MTBP subunit of this complex in human cells. Our results indicate that MTBP binds to at least 30,000 sites in the genome. A majority of these sites reside in regions of open chromatin that contain transcriptional-regulatory elements (e.g., promoters, enhancers, and super-enhancers), which are known to be preferred areas for initiation of replication. Furthermore, many binding sites encompass two genomic features: a nucleosome-free DNA sequence (e.g., G-quadruplex DNA or AP-1 motif) and a nucleosome bearing histone marks characteristic of open chromatin, such as H3K4me2. Taken together, these findings indicate that Treslin-MTBP associates coordinately with multiple genomic signals to promote initiation of replication. Kumagai and Dunphy show that Treslin-MTBP, activator of the replicative helicase, binds to at least 30,000 sites in the human genome. Many sites contain a nucleosome with active chromatin marks and nucleosome-free DNA (G-quadruplex or AP-1 site). Thus, Treslin-MTBP associates with multiple genomic elements to promote initiation of DNA replication.
Collapse
Affiliation(s)
- Akiko Kumagai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - William G Dunphy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| |
Collapse
|
17
|
Chen XJ, Ren AQ, Zheng L, Zheng ED. Predictive Value of KDM5C Alterations for Immune Checkpoint Inhibitors Treatment Outcomes in Patients With Cancer. Front Immunol 2021; 12:664847. [PMID: 33953726 PMCID: PMC8089485 DOI: 10.3389/fimmu.2021.664847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022] Open
Abstract
Lysine (K)-specific demethylase 5C (KDM5C) plays a significant role in the tumor cell proliferation, invasion, drug resistance and the regulation of tumor-related gene expression. Here, we aimed to investigate its predictive value in patients with cancers received immune checkpoint inhibitors (ICIs). We explored the predictive value of KDM5C alterations and the association between KDM5C alteration and immune landscape by using published cohort with clinical outcome and sequenced data from online database. The frequency of KDM5C alterations was 2.1% across 48045 tumor samples with different cancers from 185 studies. KDM5C alterations were correlated with markedly inferior overall survival (OS, 53 vs. 102 months, P<0.0001) than those without. However, in ICI-treated group, patients with KDM5C alterations had a substantially prolonged OS than the wild-type group (not reached vs. 18 months, P=0.0041). The predictive value of KDM5C alterations for ICI treatment outcome was not observed in patients with microsatellite-stable tumors (P=0.2875). Intriguingly, patients with non-small-cell lung cancer and KDM5C alterations receiving ICI had the better progression-free survival than wild type group (13.2 vs. 3.2 months, P=0.0762). Mechanistically, KDM5C altered tumors had dramatically higher TMB level and was associated with significantly higher level of CD8+ T cell infiltration and T effector signature. In conclusion, KDM5C alterations was correlated with enhanced tumor immunogenicity and inflamed anti-tumor immunity, thus resulting in better treatment outcome in cancer patients receiving ICIs.
Collapse
Affiliation(s)
- Xiao-Juan Chen
- Department of Clinical Medicine, Graduate School, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Gastroenterology, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Ai-Qun Ren
- Department of Gastroenterology, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Liang Zheng
- Department of Gastroenterology, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| | - En-Dian Zheng
- Department of Gastroenterology, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
18
|
Qi S, Al Mamun A, Ngwa C, Romana S, Ritzel R, Arnold AP, McCullough LD, Liu F. X chromosome escapee genes are involved in ischemic sexual dimorphism through epigenetic modification of inflammatory signals. J Neuroinflammation 2021; 18:70. [PMID: 33712031 PMCID: PMC7953638 DOI: 10.1186/s12974-021-02120-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/24/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Stroke is a sexually dimorphic disease. Previous studies have found that young females are protected against ischemia compared to males, partially due to the protective effect of ovarian hormones, particularly estrogen (E2). However, there are also genetic and epigenetic effects of X chromosome dosage that contribute to stroke sensitivity and neuroinflammation after injury, especially in the aged. Genes that escape from X chromosome inactivation (XCI) contribute to sex-specific phenotypes in many disorders. Kdm5c and kdm6a are X escapee genes that demethylate H3K4me3 and H3K27me3, respectively. We hypothesized that the two demethylases play critical roles in mediating the stroke sensitivity. METHODS To identify the X escapee genes involved in stroke, we performed RNA-seq in flow-sorted microglia from aged male and female wild type (WT) mice subjected to middle cerebral artery occlusion (MCAO). The expression of these genes (kdm5c/kdm6a) were confirmed in four core genotypes (FCG) mice and in post-mortem human stroke brains by immunohistochemistry (IHC), Western blot, and RT-PCR. Chromatin immunoprecipitation (ChIP) assays were conducted to detect DNA levels of inflammatory interferon regulatory factor (IRF) 4/5 precipitated by histone H3K4 and H3K27 antibodies. Manipulation of kdm5c/kdm6a expression with siRNA or lentivirus was performed in microglial culture, to determine downstream pathways and examine the regulatory roles in inflammatory cytokine production. RESULTS Kdm5c and kdm6a mRNA levels were significantly higher in aged WT female vs. male microglia, and the sex difference also existed in ischemic brains from FCG mice and human stroke patients. The ChIP assay showed the IRF 4/5 had higher binding levels to demethylated H3K4 or H3K27, respectively, in female vs. male ischemic microglia. Knockdown or over expression of kdm5c/kdm6a with siRNA or lentivirus altered the methylation of H3K4 or H3K27 at the IRF4/5 genes, which in turn, impacted the production of inflammatory cytokines. CONCLUSIONS The KDM-Histone-IRF pathways are suggested to mediate sex differences in cerebral ischemia. Epigenetic modification of stroke-related genes constitutes an important mechanism underlying the ischemic sexual dimorphism.
Collapse
Affiliation(s)
- Shaohua Qi
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Abdullah Al Mamun
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Conelius Ngwa
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Sharmeen Romana
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Rodney Ritzel
- Department of Anesthesiology, Center for Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Arthur P Arnold
- Department of Integrative Biology and Physiology, UCLA, 610 Charles Young Drive South, Los Angeles, CA, 90095, USA
| | - Louise D McCullough
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Fudong Liu
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| |
Collapse
|
19
|
Yang GJ, Zhu MH, Lu XJ, Liu YJ, Lu JF, Leung CH, Ma DL, Chen J. The emerging role of KDM5A in human cancer. J Hematol Oncol 2021; 14:30. [PMID: 33596982 PMCID: PMC7888121 DOI: 10.1186/s13045-021-01041-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Histone methylation is a key posttranslational modification of chromatin, and its dysregulation affects a wide array of nuclear activities including the maintenance of genome integrity, transcriptional regulation, and epigenetic inheritance. Variations in the pattern of histone methylation influence both physiological and pathological events. Lysine-specific demethylase 5A (KDM5A, also known as JARID1A or RBP2) is a KDM5 Jumonji histone demethylase subfamily member that erases di- and tri-methyl groups from lysine 4 of histone H3. Emerging studies indicate that KDM5A is responsible for driving multiple human diseases, particularly cancers. In this review, we summarize the roles of KDM5A in human cancers, survey the field of KDM5A inhibitors including their anticancer activity and modes of action, and the current challenges and potential opportunities of this field.
Collapse
Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.,Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, People's Republic of China
| | - Ming-Hui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Xin-Jiang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Yan-Jun Liu
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, 210046, People's Republic of China
| | - Jian-Fei Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Chung-Hang Leung
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, People's Republic of China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, People's Republic of China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China. .,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China. .,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.
| |
Collapse
|
20
|
Kawano-Matsuda F, Maeda T, Kaname T, Yanagi K, Ihara K. X-linked mental retardation and severe short stature with a novel mutation of the KDM5C gene. Clin Pediatr Endocrinol 2021; 30:61-64. [PMID: 33446955 PMCID: PMC7783125 DOI: 10.1297/cpe.30.61] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/13/2020] [Indexed: 11/18/2022] Open
Abstract
Many monogenetic disorders of short stature have autosomal recessive/dominant form of
inheritance. However, X-linked short stature has not been well recognized. Herein, we
report a case of a boy from a family with familial severe short stature and mental
retardation, who displayed an X-linked recessive trait. The boy at the age of 4 yr and 6
mo presented with remarkable growth failure (height: 76.5 cm [–6.3 SD]) and mental
retardation (IQ: 30) and cerebellar volume loss and without an external anomaly or
microcephaly to our hospital. A careful interview to determine the family history
suggested a genetic background of familial mental retardation and short stature. His
mother had mild intellectual disability with normal stature and his maternal uncle had
severe mental retardation with remarkably short stature. Whole-exome sequencing identified
a pathogenic variant in the KDM5C gene, NM_004187: exon 23:
c.3874_3875del: (p.Ala1292Glnfs*7). He presented with a novel frameshift mutation. His
mother was a heterozygous carrier of the variant. This case suggests that a disorder
associated with the KDM5C gene should be considered when patients present
with remarkably short stature and X-linked mental retardation.
Collapse
Affiliation(s)
| | - Tomoki Maeda
- Department of Pediatrics, Oita University Faculty of Medicine, Oita, Japan
| | - Tadashi Kaname
- National Center for Child Health and Development, Tokyo, Japan
| | - Kumiko Yanagi
- National Center for Child Health and Development, Tokyo, Japan
| | - Kenji Ihara
- Department of Pediatrics, Oita University Faculty of Medicine, Oita, Japan
| |
Collapse
|
21
|
Ding Q, Koren A. Positive and Negative Regulation of DNA Replication Initiation. Trends Genet 2020; 36:868-879. [PMID: 32739030 PMCID: PMC7572746 DOI: 10.1016/j.tig.2020.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
Genomic DNA is replicated every cell cycle by the programmed activation of replication origins at specific times and chromosomal locations. The factors that define the locations of replication origins and their typical activation times in eukaryotic cells are poorly understood. Previous studies highlighted the role of activating factors and epigenetic modifications in regulating replication initiation. Here, we review the role that repressive pathways - and their alleviation - play in establishing the genomic landscape of replication initiation. Several factors mediate this repression, in particular, factors associated with inactive chromatin. Repression can support organized, yet stochastic, replication initiation, and its absence could explain instances of rapid and random replication or re-replication.
Collapse
Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
22
|
Mu MD, Qian ZM, Yang SX, Rong KL, Yung WH, Ke Y. Therapeutic effect of a histone demethylase inhibitor in Parkinson's disease. Cell Death Dis 2020; 11:927. [PMID: 33116116 PMCID: PMC7595123 DOI: 10.1038/s41419-020-03105-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 12/30/2022]
Abstract
Iron accumulation in the substantia nigra is recognized as a hallmark of Parkinson's disease (PD). Therefore, reducing accumulated iron and associated oxidative stress is considered a promising therapeutic strategy for PD. However, current iron chelators have poor membrane permeability and lack cell-type specificity. Here we identified GSK-J4, a histone demethylase inhibitor with the ability to cross blood brain barrier, as a potent iron suppressor. Only a trace amount of GSK-J4 significantly and selectively reduced intracellular labile iron in dopaminergic neurons, and suppressed H2O2 and 6-OHDA-induced cell death in vitro. The iron-suppressive effect was mainly mediated by inducing an increase in the expression of the iron exporter ferroportin-1. In parallel, GSK-J4 rescued dopaminergic neuron loss and motor defects in 6-OHDA-induced PD rats, which was accompanied by reduction of oxidative stress. Importantly, GSK-J4 rescued the abnormal changes of histone methylation, H3K4me3 and H3K27me3 during 6-OHDA treatment although the iron-suppressive and neuroprotective effects were sensitive to H3K4me3 inhibition only. Also, upregulating H3K4me3 increased ferroportin-1 expression and neuroprotection. Taken together, we demonstrate a previously unappreciated action of GSK-J4 on cell-specific iron suppression and neuroprotection via epigenetic mechanism. Compared with conventional iron chelators, this compound has a stronger therapeutic potential for PD.
Collapse
Affiliation(s)
- Ming-Dao Mu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
- Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Zhong-Ming Qian
- Institute of Translational and Precision Medicine, Nantong University, Nantong 226001, China
| | - Sheng-Xi Yang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
- Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Kang-Lin Rong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
- Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Wing-Ho Yung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
- Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
| | - Ya Ke
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
- Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
| |
Collapse
|
23
|
Mongelli A, Atlante S, Barbi V, Bachetti T, Martelli F, Farsetti A, Gaetano C. Treating Senescence like Cancer: Novel Perspectives in Senotherapy of Chronic Diseases. Int J Mol Sci 2020; 21:ijms21217984. [PMID: 33121118 PMCID: PMC7663758 DOI: 10.3390/ijms21217984] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022] Open
Abstract
The WHO estimated around 41 million deaths worldwide each year for age-related non-communicable chronic diseases. Hence, developing strategies to control the accumulation of cell senescence in living organisms and the overall aging process is an urgently needed problem of social relevance. During aging, many biological processes are altered, which globally induce the dysfunction of the whole organism. Cell senescence is one of the causes of this modification. Nowadays, several drugs approved for anticancer therapy have been repurposed to treat senescence, and others are under scrutiny in vitro and in vivo to establish their senomorphic or senolytic properties. In some cases, this research led to a significant increase in cell survival or to a prolonged lifespan in animal models, at least. Senomorphics can act to interfere with a specific pathway in order to restore the appropriate cellular function, preserve viability, and to prolong the lifespan. On the other hand, senolytics induce apoptosis in senescent cells allowing the remaining non–senescent population to preserve or restore tissue function. A large number of research articles and reviews recently addressed this topic. Herein, we would like to focus attention on those chemical agents with senomorphic or senolytic properties that perspectively, according to literature, suggest a potential application as senotherapeutics for chronic diseases.
Collapse
Affiliation(s)
- Alessia Mongelli
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy; (A.M.); (S.A.); (V.B.)
| | - Sandra Atlante
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy; (A.M.); (S.A.); (V.B.)
| | - Veronica Barbi
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy; (A.M.); (S.A.); (V.B.)
| | - Tiziana Bachetti
- Direzione Scientifica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy;
| | - Fabio Martelli
- Laboratorio di Cardiologia Molecolare, Policlinico San Donato IRCCS, San Donato Milanese, 20097 Milano; Italy,
| | - Antonella Farsetti
- Institute for Systems Analysis and Computer Science “A. Ruberti” (IASI), National Research Council (CNR), 00185 Rome, Italy
- Correspondence: (A.F.); (C.G.)
| | - Carlo Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy; (A.M.); (S.A.); (V.B.)
- Correspondence: (A.F.); (C.G.)
| |
Collapse
|
24
|
Gardea-Resendez M, Kucuker MU, Blacker CJ, Ho AMC, Croarkin PE, Frye MA, Veldic M. Dissecting the Epigenetic Changes Induced by Non-Antipsychotic Mood Stabilizers on Schizophrenia and Affective Disorders: A Systematic Review. Front Pharmacol 2020; 11:467. [PMID: 32390836 PMCID: PMC7189731 DOI: 10.3389/fphar.2020.00467] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/25/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Epimutations secondary to gene-environment interactions have a key role in the pathophysiology of major psychiatric disorders. In vivo and in vitro evidence suggest that mood stabilizers can potentially reverse epigenetic deregulations found in patients with schizophrenia or mood disorders through mechanisms that are not yet fully understood. However, their activity on epigenetic processes has made them a research target for therapeutic approaches. METHODS We conducted a comprehensive literature search of PubMed and EMBASE for studies investigating the specific epigenetic changes induced by non-antipsychotic mood stabilizers (valproate, lithium, lamotrigine, and carbamazepine) in animal models, human cell lines, or patients with schizophrenia, bipolar disorder, or major depressive disorder. Each paper was reviewed for the nature of research, the species and tissue examined, sample size, mood stabilizer, targeted gene, epigenetic changes found, and associated psychiatric disorder. Every article was appraised for quality using a modified published process and those who met a quality score of moderate or high were included. RESULTS A total of 2,429 records were identified; 1,956 records remained after duplicates were removed and were screened via title, abstract and keywords; 129 records were selected for full-text screening and a remaining of 38 articles were included in the qualitative synthesis. Valproate and lithium were found to induce broader epigenetic changes through different mechanisms, mainly DNA demethylation and histones acetylation. There was less literature and hence smaller effects attributable to lamotrigine and carbamazepine could be associated overall with the small number of studies on these agents. Findings were congruent across sample types. CONCLUSIONS An advanced understanding of the specific epigenetic changes induced by classic mood stabilizers in patients with major psychiatric disorders will facilitate personalized interventions. Further related drug discovery should target the induction of selective chromatin remodeling and gene-specific expression effects.
Collapse
Affiliation(s)
| | - Mehmet Utku Kucuker
- Department of Psychiatry and Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States
| | - Caren J. Blacker
- Department of Psychiatry and Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States
| | - Ada M.-C. Ho
- Department of Psychiatry and Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States
| | - Paul E. Croarkin
- Department of Psychiatry and Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States
| | - Mark A. Frye
- Department of Psychiatry and Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States
| | - Marin Veldic
- Department of Psychiatry and Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States
| |
Collapse
|
25
|
Meyfour A, Pahlavan S, Ansari H, Baharvand H, Salekdeh GH. Down-Regulation of a Male-Specific H3K4 Demethylase, KDM5D, Impairs Cardiomyocyte Differentiation. J Proteome Res 2019; 18:4277-4282. [PMID: 31560558 DOI: 10.1021/acs.jproteome.9b00395] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Despite the small number of Y chromosome genes, their adequate expression is required for regulation of transcription, translation, and protein stability in males, not just for sex determination. In addition to the role in male fertility, the Y chromosome has a significant role in the development and sexual dimorphism of healthy and disease phenotypes. We observed that KDM5D along with its X-counterpart, KDM5C, are up-regulated during the cardiac mesoderm stage of development. Down-regulation of KDM5D using siRNA resulted in accumulation of differentiating cells in the S-phase of the cell cycle and impaired progression to cardiomyocytes as reflected by an altered expression pattern of cardiac progenitor specific markers. Furthermore, while control cells started spontaneous beating at a normal physiological range on day 7 of differentiation induction, no spontaneous beating was observed in KDM5D down-regulated cells. Interestingly, the knockdown of KDM5D had no significant effect on the expression level of its X-counterpart, KDM5C. Thus, we suggest that KDM5D, in cooperation with its X homologue as a dose-sensitive gene, may have an important role in cardiomyocyte differentiation. Our study presents further evidence on the contribution of Y chromosome genes to sex-dependent development outside of sex determination.
Collapse
Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases , Shahid Beheshti University of Medical Sciences , Tehran 19839-63113 , Iran.,Department of Molecular Systems Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran 16635-148 , Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran 16635-148 , Iran
| | - Hassan Ansari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran 16635-148 , Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran 16635-148 , Iran.,Department of Developmental Biology , University of Science and Culture , Tehran 13145-871 , Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran 16635-148 , Iran.,Department of Systems and Synthetic Biology , Agricultural Biotechnology Research Institute of Iran , Karaj 313593315 , Iran.,Department of Molecular Science , Macquarie University , Sydney , NSW 2109 , Australia
| |
Collapse
|
26
|
Zhang Q, Wang HY, Liu X, Roth MH, Shestov AA, Lee SC, Jain K, Soderquist C, Xiong QB, Ruella M, Strauser H, Glickson JD, Schuster SJ, Ptasznik A, Wasik MA. Dynamic Changes in Gene Mutational Landscape With Preservation of Core Mutations in Mantle Cell Lymphoma Cells. Front Oncol 2019; 9:568. [PMID: 31334109 PMCID: PMC6617136 DOI: 10.3389/fonc.2019.00568] [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: 02/01/2019] [Accepted: 06/11/2019] [Indexed: 01/20/2023] Open
Abstract
While studies have identified a number of mutations in mantle cell lymphoma (MCL), the list may still be incomplete and contribution to the pathogenesis remains unclear. We analyzed the mutational landscape of four mantle cell lymphoma biopsies obtained during an 8-year period from the same patient with his normal cells serving as control; we also established a cell line from the final stage of the disease. Numerous mutations with high allelic burden have been identified in all four biopsies. While a large subset of mutations was seen only in individual biopsies, the core of 21 mutations persisted throughout the disease. This mutational core is also maintained in the cell line that also displays DNA-methylation and cytokine secretion profiles of the primary mantle cell lymphoma cells. This cell line is uniquely sensitive to clinically relevant inhibitors of Bruton's Tyrosine Kinase. The response to Bruton Tyrosine Kinase's inhibition is enhanced by inhibitors of CDK4/6 and mTOR. Among the mutations seen in the primary and cultured MCL cells, mutations of three genes are involved in the control of H3K4 methylation: demethylase KDM5C, present already in the early disease, and methyltransferase KMT2D and cofactor BCOR, both of which are seen late in the disease and are novel and predicted to be pathogenic. The presence of these mutations was associated with hypermethylation of H3K4. Restoration of KDM5C expression affected expression of numerous genes involved in cell proliferation, adherence/movement, and invasiveness.
Collapse
Affiliation(s)
- Qian Zhang
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Hong Y Wang
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Xiaobin Liu
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Michael H Roth
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Alex A Shestov
- Department of Radiology, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Seung-Cheol Lee
- Department of Radiology, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Kanika Jain
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Craig Soderquist
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Qun-Bin Xiong
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Marco Ruella
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Honore Strauser
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Jerry D Glickson
- Department of Radiology, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Stephen J Schuster
- Department of Lymphoma Program, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States
| | - Andrzej Ptasznik
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States.,Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Mariusz A Wasik
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States.,Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, United States
| |
Collapse
|
27
|
The cancer driver genes IDH1/2, JARID1C/ KDM5C, and UTX/ KDM6A: crosstalk between histone demethylation and hypoxic reprogramming in cancer metabolism. Exp Mol Med 2019; 51:1-17. [PMID: 31221981 PMCID: PMC6586683 DOI: 10.1038/s12276-019-0230-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/12/2018] [Indexed: 12/16/2022] Open
Abstract
Recent studies on mutations in cancer genomes have distinguished driver mutations from passenger mutations, which occur as byproducts of cancer development. The cancer genome atlas (TCGA) project identified 299 genes and 24 pathways/biological processes that drive tumor progression (Cell 173: 371-385 e318, 2018). Of the 299 driver genes, 12 genes are involved in histones, histone methylation, and demethylation. Among these 12 genes, those encoding the histone demethylases JARID1C/KDM5C and UTX/KDM6A were identified as cancer driver genes. Furthermore, gain-of-function mutations in genes encoding metabolic enzymes, such as isocitrate dehydrogenases (IDH)1/2, drive tumor progression by producing an oncometabolite, D-2-hydroxyglutarate (D-2HG), which is a competitive inhibitor of α-ketoglutarate, O2-dependent dioxygenases such as Jumonji domain-containing histone demethylases, and DNA demethylases. Studies on oncometabolites suggest that histone demethylases mediate metabolic changes in chromatin structure. We have reviewed the most recent findings regarding cancer-specific metabolic reprogramming and the tumor-suppressive roles of JARID1C/KDM5C and UTX/KDM6A. We have also discussed mutations in other isoforms such as the JARID1A, 1B, 1D of KDM5 subfamilies and the JMJD3/KDM6B of KDM6 subfamilies, which play opposing roles in tumor progression as oncogenes or tumor suppressors depending on the cancer cell type. Genes involved in the removal of methyl groups from histones associated with DNA can promote or suppress tumor growth depending on the metabolic status of the cancer cell. Hyunsung Park and colleagues at the University of Seoul, South Korea, review current knowledge of two genes encoding histone demethylases which have been identified by The Cancer Genome Atlas (TCGA) project as cancer driver genes. Because these demethylase enzymes rely on cellular metabolites to function, their effect is influenced by metabolic conditions in the tumor microenvironment such as low oxygen. The mechanisms through which changes in histone methylation affect the expression of genes involved in tumor progression remain unknown. Further understanding of how cancer metabolism affects the modification of histones will help guide the development of more effective cancer treatments.
Collapse
|
28
|
Abstract
DNA replication starts with the opening of DNA at sites called DNA replication origins. From the single sequence-specific DNA replication origin of the small Escherichia coli genome, up to thousands of origins that are necessary to replicate the large human genome, strict sequence specificity has been lost. Nevertheless, genome-wide analyses performed in the recent years, using different mapping methods, demonstrated that there are precise locations along the metazoan genome from which replication initiates. These sites contain relaxed sequence consensus and epigenetic features. There is flexibility in the choice of origins to be used during a given cell cycle, probably imposed by evolution and developmental constraints. Here, we will briefly describe their main features.
Collapse
|
29
|
Zhang YX, Akumuo RC, España RA, Yan CX, Gao WJ, Li YC. The histone demethylase KDM6B in the medial prefrontal cortex epigenetically regulates cocaine reward memory. Neuropharmacology 2018; 141:113-125. [PMID: 30165076 PMCID: PMC6170674 DOI: 10.1016/j.neuropharm.2018.08.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 02/07/2023]
Abstract
Epigenetic remodeling contributes to synaptic plasticity via modification of gene expression, which underlies cocaine-induced long-term memory. A prevailing hypothesis in drug addiction is that drugs of abuse rejuvenate developmental machinery to render reward circuitry highly plastic and thus engender drug memories to be highly stable. Identification and reversal of these pathological pathways are therefore critical for cocaine abuse treatment. Previous studies revealed an interesting finding in which the mRNA of histone lysine demethylase, KDM6B, is upregulated in the medial prefrontal cortex (mPFC) during early cocaine withdrawal. However, whether and how it contributes to drug-seeking behavior remain unknown. Here we used a conditioned place preference paradigm to investigate the potential role of KDM6B in drug-associated memory. We found that KDM6B protein levels selectively increased in the mPFC during cocaine withdrawal. Notably, systemic injection of KDM6B inhibitor, GSK-J4, disrupted both reconsolidation of cocaine-conditioned memory and cocaine-primed reinstatement, suggesting dual effects of KDM6B in cocaine reward memory. In addition, we found that NMDAR expression and function were both enhanced during early cocaine withdrawal in mPFC. Injection of GSK-J4 selectively reversed this cocaine-induced increase of NR2A expression and synaptic function, suggesting that mal-adaptation of cocaine-induced synaptic plasticity in mPFC largely underlies KDM6B-mediated cocaine-associated memory. Altogether, these data suggest that KDM6B plays an essential role in cocaine-associated memory, which mainly acts through enhancing cocaine-induced synaptic plasticity in the mPFC. Our findings revealed a novel role of KDM6B in cocaine-associated memory and inhibition of KDM6B is a potential strategy to alleviate drug-seeking behavior.
Collapse
Affiliation(s)
- Yu-Xiang Zhang
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China; Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Rita C Akumuo
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Rodrigo A España
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Chun-Xia Yan
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China.
| | - Wen-Jun Gao
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, 19129, USA.
| | - Yan-Chun Li
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, 19129, USA.
| |
Collapse
|
30
|
Aze A, Maiorano D. Recent advances in understanding DNA replication: cell type-specific adaptation of the DNA replication program. F1000Res 2018; 7. [PMID: 30228862 PMCID: PMC6117848 DOI: 10.12688/f1000research.15408.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2018] [Indexed: 12/11/2022] Open
Abstract
DNA replication is an essential process occurring prior to cell division. Cell division coupled to proliferation ensures the growth and renewal of a large variety of specialized cell types generated during embryonic development. Changes in the DNA replication program occur during development. Embryonic undifferentiated cells show a high replication rate and fast proliferation, whereas more differentiated cells are characterized by reduced DNA synthesis and a low proliferation rate. Hence, the DNA replication program must adapt to the specific features of cells committed to different fates. Recent findings on DNA synthesis regulation in different cell types open new perspectives for developing efficient and more adapted therapies to treat various diseases such as genetic diseases and cancer. This review will put the emphasis on recent progress made in this field.
Collapse
Affiliation(s)
- Antoine Aze
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, Montpellier, 34396 Cedex 5, France
| | - Domenico Maiorano
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, Montpellier, 34396 Cedex 5, France
| |
Collapse
|
31
|
Mishra S, Van Rechem C, Pal S, Clarke TL, Chakraborty D, Mahan SD, Black JC, Murphy SE, Lawrence MS, Daniels DL, Whetstine JR. Cross-talk between Lysine-Modifying Enzymes Controls Site-Specific DNA Amplifications. Cell 2018; 174:803-817.e16. [PMID: 30057114 PMCID: PMC6212369 DOI: 10.1016/j.cell.2018.06.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/02/2018] [Accepted: 06/08/2018] [Indexed: 12/28/2022]
Abstract
Acquired chromosomal DNA amplifications are features of many tumors. Although overexpression and stabilization of the histone H3 lysine 9/36 (H3K9/36) tri-demethylase KDM4A generates transient site-specific copy number gains (TSSGs), additional mechanisms directly controlling site-specific DNA copy gains are not well defined. In this study, we uncover a collection of H3K4-modifying chromatin regulators that function with H3K9 and H3K36 regulators to orchestrate TSSGs. Specifically, the H3K4 tri-demethylase KDM5A and specific COMPASS/KMT2 H3K4 methyltransferases modulate different TSSG loci through H3K4 methylation states and KDM4A recruitment. Furthermore, a distinct chromatin modifier network, MLL1-KDM4B-KDM5B, controls copy number regulation at a specific genomic locus in a KDM4A-independent manner. These pathways comprise an epigenetic addressing system for defining site-specific DNA rereplication and amplifications.
Collapse
Affiliation(s)
- Sweta Mishra
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sangita Pal
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Thomas L Clarke
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Damayanti Chakraborty
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sarah D Mahan
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Joshua C Black
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sedona E Murphy
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Department of Pathology, Harvard Medical School, 13th Street, Charlestown, MA 02129, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA.
| |
Collapse
|
32
|
Zhao PA, Rivera-Mulia JC, Gilbert DM. Replication Domains: Genome Compartmentalization into Functional Replication Units. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:229-257. [DOI: 10.1007/978-981-10-6955-0_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
33
|
Epigenome Aberrations: Emerging Driving Factors of the Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2017; 18:ijms18081774. [PMID: 28812986 PMCID: PMC5578163 DOI: 10.3390/ijms18081774] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/29/2017] [Accepted: 08/12/2017] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC), the most common form of Kidney cancer, is characterized by frequent mutations of the von Hippel-Lindau (VHL) tumor suppressor gene in ~85% of sporadic cases. Loss of pVHL function affects multiple cellular processes, among which the activation of hypoxia inducible factor (HIF) pathway is the best-known function. Constitutive activation of HIF signaling in turn activates hundreds of genes involved in numerous oncogenic pathways, which contribute to the development or progression of ccRCC. Although VHL mutations are considered as drivers of ccRCC, they are not sufficient to cause the disease. Recent genome-wide sequencing studies of ccRCC have revealed that mutations of genes coding for epigenome modifiers and chromatin remodelers, including PBRM1, SETD2 and BAP1, are the most common somatic genetic abnormalities after VHL mutations in these tumors. Moreover, recent research has shed light on the extent of abnormal epigenome alterations in ccRCC tumors, including aberrant DNA methylation patterns, abnormal histone modifications and deregulated expression of non-coding RNAs. In this review, we discuss the epigenetic modifiers that are commonly mutated in ccRCC, and our growing knowledge of the cellular processes that are impacted by them. Furthermore, we explore new avenues for developing therapeutic approaches based on our knowledge of epigenome aberrations of ccRCC.
Collapse
|
34
|
Abstract
In this review, Prioleau and MacAlpine summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages.
Collapse
Affiliation(s)
- Marie-Noëlle Prioleau
- Institut Jacques Monod, UMR7592, Centre National de la Recherche Scientifique, Universite Paris Diderot, Equipe Labellisee Association pour la Recherche sur le Cancer, Paris 75013, France
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710. USA
| |
Collapse
|
35
|
Xu J, Zheng X, Cheng KK, Chang X, Shen G, Liu M, Wang Y, Shen J, Zhang Y, He Q, Dong J, Yang Z. NMR-based metabolomics Reveals Alterations of Electro-acupuncture Stimulations on Chronic Atrophic Gastritis Rats. Sci Rep 2017; 7:45580. [PMID: 28358020 PMCID: PMC5372362 DOI: 10.1038/srep45580] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/28/2017] [Indexed: 12/15/2022] Open
Abstract
Chronic atrophic gastritis (CAG) is a common gastrointestinal disease which has been considered as precancerous lesions of gastric carcinoma. Previously, electro-acupuncture stimulation has been shown to be effective in ameliorating symptoms of CAG. However the underlying mechanism of this beneficial treatment is yet to be established. In the present study, an integrated histopathological examination along with molecular biological assay, as well as 1H NMR analysis of multiple biological samples (urine, serum, stomach, cortex and medulla) were employed to systematically assess the pathology of CAG and therapeutic effect of electro-acupuncture stimulation at Sibai (ST 2), Liangmen (ST 21), and Zusanli (ST 36) acupoints located in the stomach meridian using a rat model of CAG. The current results showed that CAG caused comprehensive metabolic alterations including the TCA cycle, glycolysis, membrane metabolism and catabolism, gut microbiota-related metabolism. On the other hand, electro-acupuncture treatment was found able to normalize a number of CAG-induced metabolomics changes by alleviating membrane catabolism, restoring function of neurotransmitter in brain and partially reverse the CAG-induced perturbation in gut microbiota metabolism. These findings provided new insights into the biochemistry of CAG and mechanism of the therapeutic effect of electro-acupuncture stimulations.
Collapse
Affiliation(s)
- Jingjing Xu
- Department of Electronic Science, and Department of Traditional Chinese Medicine, Xiamen University, Xiamen 361005, China
| | - Xujuan Zheng
- Department of Electronic Science, and Department of Traditional Chinese Medicine, Xiamen University, Xiamen 361005, China
| | - Kian-Kai Cheng
- Department of Bioprocess &Polymer Engineering, Innovative Centre in Agritechnology, University Teknologi Malaysia, Johor 81310, Malaysia
| | - Xiaorong Chang
- College of Acupuncture and Moxibustion, Hunan University of Chinese Medicine, Changsha 410007, China
| | - Guiping Shen
- Department of Electronic Science, and Department of Traditional Chinese Medicine, Xiamen University, Xiamen 361005, China
| | - Mi Liu
- College of Acupuncture and Moxibustion, Hunan University of Chinese Medicine, Changsha 410007, China
| | - Yadong Wang
- Department of Electronic Science, and Department of Traditional Chinese Medicine, Xiamen University, Xiamen 361005, China
| | - Jiacheng Shen
- Department of Electronic Science, and Department of Traditional Chinese Medicine, Xiamen University, Xiamen 361005, China
| | - Yuan Zhang
- College of Acupuncture and Moxibustion, Hunan University of Chinese Medicine, Changsha 410007, China
| | - Qida He
- Department of Electronic Science, and Department of Traditional Chinese Medicine, Xiamen University, Xiamen 361005, China
| | - Jiyang Dong
- Department of Electronic Science, and Department of Traditional Chinese Medicine, Xiamen University, Xiamen 361005, China
| | - Zongbao Yang
- Department of Electronic Science, and Department of Traditional Chinese Medicine, Xiamen University, Xiamen 361005, China
| |
Collapse
|
36
|
Wu R, Wang Z, Zhang H, Gan H, Zhang Z. H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication. Nucleic Acids Res 2017; 45:169-180. [PMID: 27679476 PMCID: PMC5224507 DOI: 10.1093/nar/gkw848] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 11/30/2022] Open
Abstract
DNA replication is tightly regulated to occur once and only once per cell cycle. How chromatin, the physiological substrate of DNA replication machinery, regulates DNA replication remains largely unknown. Here we show that histone H3 lysine 9 demethylase Kdm4d regulates DNA replication in eukaryotic cells. Depletion of Kdm4d results in defects in DNA replication, which can be rescued by the expression of H3K9M, a histone H3 mutant transgene that reverses the effect of Kdm4d on H3K9 methylation. Kdm4d interacts with replication proteins, and its recruitment to DNA replication origins depends on the two pre-replicative complex components (origin recognition complex [ORC] and minichromosome maintenance [MCM] complex). Depletion of Kdm4d impairs the recruitment of Cdc45, proliferating cell nuclear antigen (PCNA), and polymerase δ, but not ORC and MCM proteins. These results demonstrate a novel mechanism by which Kdm4d regulates DNA replication by reducing the H3K9me3 level to facilitate formation of pre-initiative complex.
Collapse
Affiliation(s)
- Rentian Wu
- Department of Biochemistry and Molecular Biology, Mayo Clinic Cancer Center, Mayo Clinic, Rochester, MN 55902, USA
| | - Zhiquan Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic Cancer Center, Mayo Clinic, Rochester, MN 55902, USA
| | - Honglian Zhang
- Institute for Cancer Genetics, Department of Pediatric and Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Haiyun Gan
- Institute for Cancer Genetics, Department of Pediatric and Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatric and Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| |
Collapse
|
37
|
Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers. Proc Natl Acad Sci U S A 2016; 113:E4810-9. [PMID: 27436900 DOI: 10.1073/pnas.1609060113] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The origin recognition complex (ORC) binds sites from which DNA replication is initiated. We address ORC binding selectivity in vivo by mapping ∼52,000 ORC2 binding sites throughout the human genome. The ORC binding profile is broader than those of sequence-specific transcription factors, suggesting that ORC is not bound or recruited to specific DNA sequences. Instead, ORC binds nonspecifically to open (DNase I-hypersensitive) regions containing active chromatin marks such as H3 acetylation and H3K4 methylation. ORC sites in early and late replicating regions have similar properties, but there are far more ORC sites in early replicating regions. This suggests that replication timing is due primarily to ORC density and stochastic firing of origins. Computational simulation of stochastic firing from identified ORC sites is in accord with replication timing data. Large genomic regions with a paucity of ORC sites are strongly associated with common fragile sites and recurrent deletions in cancers. We suggest that replication origins, replication timing, and replication-dependent chromosome breaks are determined primarily by the genomic distribution of activator proteins at enhancers and promoters. These activators recruit nucleosome-modifying complexes to create the appropriate chromatin structure that allows ORC binding and subsequent origin firing.
Collapse
|
38
|
Affiliation(s)
- Emily Brookes
- MRC Laboratory of Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom.
| |
Collapse
|
39
|
Li T, Zheng Q, An J, Wu M, Li H, Gui X, Pu H, Lu D. RETRACTED: SET1A Cooperates With CUDR to Promote Liver Cancer Growth and Hepatocyte-like Stem Cell Malignant Transformation Epigenetically. Mol Ther 2016; 24:261-275. [PMID: 26581161 PMCID: PMC4817816 DOI: 10.1038/mt.2015.208] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 11/08/2015] [Indexed: 12/16/2022] Open
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the editor-in-chief. Similarities were found between images in this article and an article in Oncotarget (Pu et al., 2015, Oncotarget 6, 40775-40798, https://doi.org/10.18632/oncotarget.5905) previously published by the same authors. Similarities were also found between images within this article. Image analysis performed by the editorial office confirmed findings of image reuse in Figures 2E and 6E of the Molecular Therapy article. Some of the original data provided by the authors do not match the published article. This reuse (and in part misrepresentation) of data without appropriate attribution represents a severe abuse of the scientific publishing system. No authors responded to the notice of retraction. The original email was undeliverable to 6 authors (not including the corresponding author; T.L., Q.Z., J.A., M.W., H.L., X.G.).
Collapse
Affiliation(s)
- Tianming Li
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Qidi Zheng
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Jiahui An
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Mengying Wu
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Haiyan Li
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xin Gui
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Hu Pu
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Dongdong Lu
- School of Life Science and Technology, Tongji University, Shanghai, China.
| |
Collapse
|
40
|
Dimitrova E, Turberfield AH, Klose RJ. Histone demethylases in chromatin biology and beyond. EMBO Rep 2015; 16:1620-39. [PMID: 26564907 PMCID: PMC4687429 DOI: 10.15252/embr.201541113] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/06/2015] [Indexed: 01/05/2023] Open
Abstract
Histone methylation plays fundamental roles in regulating chromatin‐based processes. With the discovery of histone demethylases over a decade ago, it is now clear that histone methylation is dynamically regulated to shape the epigenome and regulate important nuclear processes including transcription, cell cycle control and DNA repair. In addition, recent observations suggest that these enzymes could also have functions beyond their originally proposed role as histone demethylases. In this review, we focus on recent advances in our understanding of the molecular mechanisms that underpin the role of histone demethylases in a wide variety of normal cellular processes.
Collapse
Affiliation(s)
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
| |
Collapse
|
41
|
Rondinelli B, Rosano D, Antonini E, Frenquelli M, Montanini L, Huang D, Segalla S, Yoshihara K, Amin SB, Lazarevic D, The BT, Verhaak RGW, Futreal PA, Di Croce L, Chin L, Cittaro D, Tonon G. Histone demethylase JARID1C inactivation triggers genomic instability in sporadic renal cancer. J Clin Invest 2015; 125:4625-37. [PMID: 26551685 DOI: 10.1172/jci81040] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 10/08/2015] [Indexed: 12/16/2022] Open
Abstract
Mutations in genes encoding chromatin-remodeling proteins are often identified in a variety of cancers. For example, the histone demethylase JARID1C is frequently inactivated in patients with clear cell renal cell carcinoma (ccRCC); however, it is largely unknown how JARID1C dysfunction promotes cancer. Here, we determined that JARID1C binds broadly to chromatin domains characterized by the trimethylation of lysine 9 (H3K9me3), which is a histone mark enriched in heterochromatin. Moreover, we found that JARID1C localizes on heterochromatin, is required for heterochromatin replication, and forms a complex with established players of heterochromatin assembly, including SUV39H1 and HP1α, as well as with proteins not previously associated with heterochromatin assembly, such as the cullin 4 (CUL4) complex adaptor protein DDB1. Transcription on heterochromatin is tightly suppressed to safeguard the genome, and in ccRCC cells, JARID1C inactivation led to the unrestrained expression of heterochromatic noncoding RNAs (ncRNAs) that in turn triggered genomic instability. Moreover, ccRCC patients harboring JARID1C mutations exhibited aberrant ncRNA expression and increased genomic rearrangements compared with ccRCC patients with tumors endowed with other genetic lesions. Together, these data suggest that inactivation of JARID1C in renal cancer leads to heterochromatin disruption, genomic rearrangement, and aggressive ccRCCs. Moreover, our results shed light on a mechanism that underlies genomic instability in sporadic cancers.
Collapse
|
42
|
Ji X, Jin S, Qu X, Li K, Wang H, He H, Guo F, Dong L. Lysine-specific demethylase 5C promotes hepatocellular carcinoma cell invasion through inhibition BMP7 expression. BMC Cancer 2015; 15:801. [PMID: 26503415 PMCID: PMC4624178 DOI: 10.1186/s12885-015-1798-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/16/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common type of tumor and is associated with high morbidity and mortality rates. Patients with HCC routinely undergo surgery followed by adjuvant radiation therapy and chemotherapy. Despite such aggressive treatment approaches, median survival times remain under 1 year in most cases. KDM5C is a member of the family of JmjC domain-containing proteins that removes methyl residues from methylated lysine 4 on histone H3 lysine 4 (H3K4). KDM5C has been proposed as an oncogene in many types of tumors; however, its role and underlying mechanisms in HCC remain unclear. METHODS Expression level of KDM5C was examined by RT-PCR, and IHC. Forced expression of KDM5C was mediated by retroviruses, and KDM5C was downregulated by shRNAs expressing lentiviruses. Migration and invasion of HCC cells was measured by wound healing, Transwell and Matrigel assays respectively. RESULTS In this study, we report that KDM5C is abundantly expressed in invasive human HCC cells. Cellular depletion of KDM5C by shRNA inhibited HCC cell migration, invasion and epithelial-mesenchymal transition in vitro, and markedly decreased the metastasis capacity of invasive HCC cells in the liver and lung. Furthermore, ectopic expression of KDM5C in HCC cells promoted cell migration, invasion and epithelial-mesenchymal transition via the inactivation of BMP7. Knockdown of BMP7 significantly promotes shKDM5C-induced cell migration inhibition. CONCLUSIONS Taken together, these data suggest that KDM5C-mediated BMP7 inactivation is essential for HCC cell invasion.
Collapse
Affiliation(s)
- Xuening Ji
- Department of Oncology, Zhongshan Hospital of Dalian University, No. 6 Jiefang Street, Zhongshan District, Dalian, 116001, China.
| | - Shi Jin
- Department of Laparoscopic Surgery, First Affiliated Hospital of Dalian Medical University, No.193, Lianhe Street, Shahekou District, Dalian, 116001, China.
| | - Xiaotong Qu
- Department of Second Neurology, The Frist Affiliated Hospital of Dalian Medical University, No.222, Zhongshan Street, Xigang District, Dalian, 116000, China.
| | - Kejun Li
- Department of Laparoscopic Surgery, First Affiliated Hospital of Dalian Medical University, No.193, Lianhe Street, Shahekou District, Dalian, 116001, China.
| | - Hongjiang Wang
- Department of Breast Surgery, First Affiliated Hospital of Dalian Medical University, No.193, Lianhe Street, Shahekou District, Dalian, 116001, China.
| | - Hui He
- Department of Laparoscopic Surgery, First Affiliated Hospital of Dalian Medical University, No.193, Lianhe Street, Shahekou District, Dalian, 116001, China.
| | - Fuchao Guo
- Department of general surgery, The first people's Hospital of jinzhou District in Dalian City, No.683, Stalin Road, Jinzhou District, Dalian, 116100, China.
| | - Lei Dong
- Department of Laparoscopic Surgery, First Affiliated Hospital of Dalian Medical University, No.193, Lianhe Street, Shahekou District, Dalian, 116001, China.
| |
Collapse
|
43
|
Liu LJ, Lu L, Zhong HJ, He B, Kwong DWJ, Ma DL, Leung CH. An Iridium(III) Complex Inhibits JMJD2 Activities and Acts as a Potential Epigenetic Modulator. J Med Chem 2015. [DOI: 10.1021/acs.jmedchem.5b00375] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Li-Juan Liu
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Taipa, Macao P. R. China
| | - Lihua Lu
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Hai-Jing Zhong
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Taipa, Macao P. R. China
| | - Bingyong He
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Daniel W. J. Kwong
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Dik-Lung Ma
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Chung-Hang Leung
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Taipa, Macao P. R. China
| |
Collapse
|