1
|
O’Neil EV, Dupont SM, Capel B. The basic helix-loop-helix transcription factor TCF4 recruits the Mediator Complex to activate gonadal genes and drive ovarian development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.28.640455. [PMID: 40093061 PMCID: PMC11908221 DOI: 10.1101/2025.02.28.640455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
The bipotential gonad is the precursor organ to both the ovary and testis and develops as part of the embryonic urogenital system. In mice, gonadogenesis initiates around embryonic day 9.5 (E9.5), when coelomic epithelial (CE) cells overlaying the mesonephric ducts proliferate and acquire the competence to differentiate into the two main cell types of the embryonic gonad, the pre-supporting cells and interstitial cell lineages. While some transcription factors that drive gonadal cell fate are known, HLH factors have not been investigated in this capacity. In the present study, we found that HLH binding sites are highly represented upstream of gonadal genes. We investigated the HLH factor Transcription Factor 4 (TCF4) which is expressed in the CE and GATA4+ somatic cells in both sexes prior to sex determination. TCF4 is maintained in ovarian pre-supporting cells and interstitial cells of both sexes but is silenced specifically in male pre-supporting cells. To characterize TCF4's role in gonad differentiation in vivo, we acquired a mutant mouse model that lacks the TCF4 DNA-binding domain and assessed morphology of the gonads at E15.5. While mutants develop gonads, we observed sex-specific effects on the gonads. Relative to wildtype littermates, SOX9 expression was higher in the Sertoli cells of XY Tcf4 STOP/STOP mutant testes, while FOXL2 and NR2F2 were reduced in the supporting and interstitial cell lineages of XX Tcf4 STOP/STOP mutant ovaries, respectively. Furthermore, the supporting: interstitial cell ratio was altered in XX Tcf4 STOP/STOP ovaries. These effects may occur downstream of changes to epigenetic programming or gene expression in somatic gonadal cells in mutant mice, as TCF4 binds the Mediator complex, RNA polymerase holoenzyme, and chromatin remodelers in early somatic cells. We hypothesize that TCF4 drives a gonadal program that advances female fate but is specifically silenced in male supporting cells as these pathways diverge.
Collapse
Affiliation(s)
- EV O’Neil
- Department of Cell Biology, Duke University School of Medicine, Durham NC 27710
| | - SM Dupont
- Department of Cell Biology, Duke University School of Medicine, Durham NC 27710
| | - B Capel
- Department of Cell Biology, Duke University School of Medicine, Durham NC 27710
| |
Collapse
|
2
|
Mertens M, Khalife L, Ma X, Bodamer O. Animal models of Kabuki syndrome and their applicability to novel drug discovery. Expert Opin Drug Discov 2025; 20:253-265. [PMID: 39862154 DOI: 10.1080/17460441.2025.2457624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 11/27/2024] [Accepted: 01/20/2025] [Indexed: 01/27/2025]
Abstract
INTRODUCTION Kabuki Syndrome (KS) is a rare genetic disorder characterized by distinctive facial features, intellectual disability, and multiple congenital anomalies. It is caused by pathogenic variants in the KMT2D and KDM6A genes. Despite its significant disease burden, there are currently no approved therapies for KS, highlighting the need for advanced research and therapeutic development. AREAS COVERED This review examines the use of animal models in KS research, including mice, fish, frogs, and nematodes. These models replicate key mechanistic and clinical aspects of Kabuki Syndrome, facilitating preclinical studies to demonstrate therapeutic efficacy. The literature search focused on identifying studies that utilized these models to investigate the pathophysiology of Kabuki Syndrome and evaluate potential treatments. EXPERT OPINION Refining animal models is essential to enhance their relevance to human disease and accelerate the development of effective therapies for Kabuki Syndrome. Insights from these models are invaluable in understanding underlying molecular mechanisms and identifying therapeutic targets. Continued research and collaboration are crucial to translating these findings into clinical practice, offering hope for future treatments.
Collapse
Affiliation(s)
- Mareike Mertens
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Leen Khalife
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Xiaoting Ma
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Olaf Bodamer
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| |
Collapse
|
3
|
Lin J, Zhang J, Ma L, Fang H, Ma R, Groneck C, Filippova GN, Deng X, Kinoshita C, Young JE, Ma W, Disteche CM, Berletch JB. KDM6A facilitates Xist upregulation at the onset of X inactivation. Biol Sex Differ 2025; 16:1. [PMID: 39754175 PMCID: PMC11699772 DOI: 10.1186/s13293-024-00683-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 12/09/2024] [Indexed: 01/06/2025] Open
Abstract
BACKGROUND X chromosome inactivation (XCI) is a female-specific process in which one X chromosome is silenced to balance X-linked gene expression between the sexes. XCI is initiated in early development by upregulation of the lncRNA Xist on the future inactive X (Xi). A subset of X-linked genes escape silencing and thus have higher expression in females, suggesting female-specific functions. One of these genes is the highly conserved gene Kdm6a, which encodes a histone demethylase that removes methyl groups at H3K27 to facilitate gene expression. KDM6A mutations have been implicated in congenital disorders such as Kabuki Syndrome, as well as in sex differences in development and cancer. METHODS Kdm6a was knocked out (KO) using CRISPR/Cas9 gene editing in hybrid female mouse embryonic stem (ES) cells derived either from a 129 × Mus castaneus (cast) cross or a BL6 x cast cross. In one of the lines a transcriptional stop signal inserted in Tsix results in completely skewed X silencing upon differentiation. The effects of both homozygous and heterozygous Kdm6a KO on Xist expression during the onset of XCI were measured by RT-PCR and RNA-FISH. Changes in gene expression and in H3K27me3 enrichment were investigated using allele-specific RNA-seq and Cut&Run, respectively. KDM6A binding to the Xist gene was characterized by Cut&Run. RESULTS We observed impaired upregulation of Xist and reduced coating of the Xi during early stages of differentiation in Kdm6a KO cells, both homozygous and heterozygous, suggesting a threshold effect of KDM6A. This was associated with aberrant overexpression of genes from the Xi after differentiation, indicating loss of X inactivation potency. Consistent with KDM6A having a direct role in Xist regulation, we found that the histone demethylase binds to the Xist promoter and KO cells show an increase in H3K27me3 at Xist, consistent with reduced expression. CONCLUSIONS These results reveal a novel female-specific role for the X-linked histone demethylase, KDM6A in the initiation of XCI through histone demethylase-dependent activation of Xist during early differentiation. X chromosome inactivation is a female-specific mechanism that evolved to balance sex-linked gene dosage between females (XX) and males (XY) by silencing one X chromosome in females. X inactivation begins with the upregulation of the long noncoding RNA Xist on the future inactive X chromosome. While most genes become silenced on the inactive X chromosome some genes escape inactivation and thus have higher expression in females compared to males, suggesting that escape genes may have female-specific functions. One such gene encodes the histone demethylase KDM6A which function is to turn on gene expression by removing repressive histone modifications. In this study, we investigated the role of KDM6A in the regulation of Xist expression during the onset of X inactivation. We found that KDM6A binds to the Xist gene to remove repressive histone marks and facilitate its expression in early development. Indeed, depletion of KDM6A prevents upregulation of Xist due to abnormal persistence of repressive histone modifications. In turn, this results in aberrant overexpression of genes from the inactive X chromosome. Our findings point to a novel mechanism of Xist regulation during the initiation of X inactivation, which may lead to new avenues of treatment to alleviate congenital disorders such as Kabuki syndrome and sex-biased immune disorders where X-linked gene dosage is perturbed.
Collapse
Affiliation(s)
- Josephine Lin
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Jinli Zhang
- Department of Statistics, University of California Riverside, Riverside, CA, 92521, USA
| | - Li Ma
- Department of Microbiology, Immunology & Cell Biology, University of West Virginia, Morgantown, WV, 26506, USA
| | - He Fang
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Rui Ma
- Department of Statistics, University of California Riverside, Riverside, CA, 92521, USA
| | - Camille Groneck
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Galina N Filippova
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Xinxian Deng
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Chizuru Kinoshita
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Jessica E Young
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Wenxiu Ma
- Department of Statistics, University of California Riverside, Riverside, CA, 92521, USA.
| | - Christine M Disteche
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, 98195, USA.
- Department of Medicine, School of Medicine, University of Washington, Seattle, WA, 98195, USA.
| | - Joel B Berletch
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
4
|
Liao C, Walters BW, DiStasio M, Lesch BJ. Human-specific epigenomic states in spermatogenesis. Comput Struct Biotechnol J 2024; 23:577-588. [PMID: 38274996 PMCID: PMC10809009 DOI: 10.1016/j.csbj.2023.12.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024] Open
Abstract
Infertility is becoming increasingly common, affecting one in six people globally. Half of these cases can be attributed to male factors, many driven by abnormalities in the process of sperm development. Emerging evidence from genome-wide association studies, genetic screening of patient cohorts, and animal models highlights an important genetic contribution to spermatogenic defects, but comprehensive identification and characterization of the genes critical for male fertility remain lacking. High divergence of gene regulation in spermatogenic cells across species poses challenges for delineating the genetic pathways required for human spermatogenesis using common model organisms. In this study, we leveraged post-translational histone modification and gene transcription data for 15,491 genes in four mammalian species (human, rhesus macaque, mouse, and opossum), to identify human-specific patterns of gene regulation during spermatogenesis. We combined H3K27me3 ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data to define epigenetic states for each gene at two stages of spermatogenesis, pachytene spermatocytes and round spermatids, in each species. We identified 239 genes that are uniquely active, poised, or dynamically regulated in human spermatogenic cells distinct from the other three species. While some of these genes have been implicated in reproductive functions, many more have not yet been associated with human infertility and may be candidates for further molecular and epidemiologic studies. Our analysis offers an example of the opportunities provided by evolutionary and epigenomic data for broadly screening candidate genes implicated in reproduction, which might lead to discoveries of novel genetic targets for diagnosis and management of male infertility and male contraception.
Collapse
Affiliation(s)
- Caiyun Liao
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
| | | | - Marcello DiStasio
- Department of Pathology, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
- Department of Opthamology & Visual Sciences, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
| | - Bluma J. Lesch
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
- Department of Genetics, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
- Yale Cancer Center, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
| |
Collapse
|
5
|
Lee CL, Chuang CK, Chen MR, Lin JL, Chiu HC, Chang YH, Tu YR, Lo YT, Lin HY, Lin SP. Illuminating the Genetic Basis of Congenital Heart Disease in Patients with Kabuki Syndrome. Diagnostics (Basel) 2024; 14:846. [PMID: 38667491 PMCID: PMC11049448 DOI: 10.3390/diagnostics14080846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Congenital heart defects (CHDs) affect a substantial proportion of patients with Kabuki syndrome. However, the prevalence and type of CHD and the genotype-phenotype correlations in Asian populations are not fully elucidated. This study performed a retrospective analysis of 23 Taiwanese patients with molecularly confirmed Kabuki syndrome. Twenty-two patients presented with pathogenic variants in the KMT2D gene. Comprehensive clinical assessments were performed. A literature review was conducted to summarize the spectrum of CHDs in patients with Kabuki syndrome. In total, 16 (73.9%) of 22 patients with pathogenic KMT2D variants had CHDs. The most common types of CHD were atrial septal defects (37.5%), ventricular septal defects (18.8%), coarctation of the aorta (18.8%), bicuspid aortic valve (12.5%), persistent left superior vena cava (12.5%), mitral valve prolapse (12.5%), mitral regurgitation (12.5%), and patent ductus arteriosus (12.5%). Other cardiac abnormalities were less common. Further, there were no clear genotype-phenotype correlations found. A literature review revealed similar patterns of CHDs, with a predominance of left-sided obstructive lesions and septal defects. In conclusion, the most common types of CHDs in Taiwanese patients with Kabuki syndrome who presented with KMT2D mutations are left-sided obstructive lesions and septal defects.
Collapse
Grants
- MMH-E-113-13, MMH-MM-112-14, MMH-E-112-13, and MMH-E-111-13 Mackay Memorial Hospital
- NSTC-112-2314-B-195-014-MY3, NSTC-112-2811-B-195-001, NSTC-112-2314-B-195-003, NSTC-111-2314-B-195-017, NSTC-111-2811-B-195-002, NSTC-111-2811-B-195-001, NSTC-110-2314-B-195-014, NSTC-110-2314-B-195-010-MY3, and NSTC-110-2314-B-195-029 Ministry of Science and Technology, Executive Yuan, Taiwan
Collapse
Affiliation(s)
- Chung-Lin Lee
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
- Institute of Clinical Medicine, National Yang-Ming Chiao-Tung University, Taipei 112304, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan;
- Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
- Department of Nursing, Mackay Junior College of Medicine, Nursing and Management, Taipei 112021, Taiwan
| | - Chih-Kuang Chuang
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-K.C.); (Y.-R.T.)
- College of Medicine, Fu-Jen Catholic University, Taipei 24205, Taiwan
| | - Ming-Ren Chen
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
| | - Ju-Li Lin
- Division of Endocrine & Medical Genetics, Department of Pediatrics, Chang Gung Children’s Medical Center, Chang Gung Memorial Hospital, Taoyuan 33378, Taiwan;
| | - Huei-Ching Chiu
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
| | - Ya-Hui Chang
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan;
| | - Yuan-Rong Tu
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-K.C.); (Y.-R.T.)
| | - Yun-Ting Lo
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan;
| | - Hsiang-Yu Lin
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan;
- Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
- Department of Nursing, Mackay Junior College of Medicine, Nursing and Management, Taipei 112021, Taiwan
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-K.C.); (Y.-R.T.)
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Shuan-Pei Lin
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan;
- Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-K.C.); (Y.-R.T.)
- Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei 11219, Taiwan
| |
Collapse
|
6
|
Hu K, Li W, Ma S, Fang D, Xu J. The identification and classification of candidate genes during the zygotic genome activation in the mammals. ZYGOTE 2024; 32:119-129. [PMID: 38248909 DOI: 10.1017/s0967199423000631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Zygotic genome activation (ZGA) is a critical event in early embryonic development, and thousands of genes are involved in this delicate and sophisticated biological process. To date, however, only a handful of these genes have revealed their core functions in this special process, and therefore the roles of other genes still remain unclear. In the present study, we used previously published transcriptome profiling to identify potential key genes (candidate genes) in minor ZGA and major ZGA in both human and mouse specimens, and further identified the conserved genes across species. Our results showed that 887 and 760 genes, respectively, were thought to be specific to human and mouse in major ZGA, and the other 135 genes were considered to be orthologous genes. Moreover, the conserved genes were most enriched in rRNA processing in the nucleus and cytosol, ribonucleoprotein complex biogenesis, ribonucleoprotein complex assembly and ribosome large subunit biogenesis. The findings of this first comprehensive identification and characterization of candidate genes in minor and major ZGA provide relevant insights for future studies on ZGA.
Collapse
Affiliation(s)
- Kaiyue Hu
- Luoyang maternal and Child Health Hospital, 206, Tongqu Road, Luoyang, Henan, 47100China
| | - Wenbo Li
- The First Affiliated Hospital of Zhengzhou University, 40, Daxue Road, Zhengzhou, Henan, 450052China
| | - Shuxia Ma
- Luoyang maternal and Child Health Hospital, 206, Tongqu Road, Luoyang, Henan, 47100China
| | - Dong Fang
- Luoyang maternal and Child Health Hospital, 206, Tongqu Road, Luoyang, Henan, 47100China
| | - Jiawei Xu
- The First Affiliated Hospital of Zhengzhou University, 40, Daxue Road, Zhengzhou, Henan, 450052China
| |
Collapse
|
7
|
Luchsinger-Morcelle SJ, Gribnau J, Mira-Bontenbal H. Orchestrating Asymmetric Expression: Mechanisms behind Xist Regulation. EPIGENOMES 2024; 8:6. [PMID: 38390897 PMCID: PMC10885031 DOI: 10.3390/epigenomes8010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Compensation for the gene dosage disequilibrium between sex chromosomes in mammals is achieved in female cells by repressing one of its X chromosomes through a process called X chromosome inactivation (XCI), exemplifying the control of gene expression by epigenetic mechanisms. A critical player in this mechanism is Xist, a long, non-coding RNA upregulated from a single X chromosome during early embryonic development in female cells. Over the past few decades, many factors involved at different levels in the regulation of Xist have been discovered. In this review, we hierarchically describe and analyze the different layers of Xist regulation operating concurrently and intricately interacting with each other to achieve asymmetric and monoallelic upregulation of Xist in murine female cells. We categorize these into five different classes: DNA elements, transcription factors, other regulatory proteins, long non-coding RNAs, and the chromatin and topological landscape surrounding Xist.
Collapse
Affiliation(s)
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Hegias Mira-Bontenbal
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
| |
Collapse
|
8
|
Cordeiro-Spinetti E, Rothbart SB. Lysine methylation signaling in skeletal muscle biology: from myogenesis to clinical insights. Biochem J 2023; 480:1969-1986. [PMID: 38054592 DOI: 10.1042/bcj20230223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Lysine methylation signaling is well studied for its key roles in the regulation of transcription states through modifications on histone proteins. While histone lysine methylation has been extensively studied, recent discoveries of lysine methylation on thousands of non-histone proteins has broadened our appreciation for this small chemical modification in the regulation of protein function. In this review, we highlight the significance of histone and non-histone lysine methylation signaling in skeletal muscle biology, spanning development, maintenance, regeneration, and disease progression. Furthermore, we discuss potential future implications for its roles in skeletal muscle biology as well as clinical applications for the treatment of skeletal muscle-related diseases.
Collapse
Affiliation(s)
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan 49503, U.S.A
| |
Collapse
|
9
|
Sun W, Lee KL, Poellinger L, Masai H, Kato H. Catalytic domain-dependent and -independent transcriptional activities of the tumour suppressor histone H3K27 demethylase UTX/KDM6A in specific cancer types. Epigenetics 2023; 18:2222245. [PMID: 37300822 DOI: 10.1080/15592294.2023.2222245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/10/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
The histone H3K27 demethylase, UTX/KDM6A, plays a critical role in the early development of vertebrates, and mutations are frequently found in various cancers. Several studies on developmental and cancer biology have focused on preferential transcriptional regulation by UTX independently of its H3K27 demethylase catalytic activity. Here, we analysed gene expression profiles of wild-type (WT) UTX and a catalytic activity-defective mutant in 786-O and HCT116 cells and confirmed that catalytic activity-dependent and -independent regulation contributes to the expression of most of the target genes. Indeed, the catalytic activity-defective mutant indeed suppressed colony formation similar to the WT in our assay system. However, the expression of several genes was significantly dependent on the catalytic activity of UTX in a cell type-specific manner, which could account for the inherent variation in the transcriptional landscape of various cancer types. The promoter/enhancer regions of the catalytic activity-dependent genes identified here were found to be preferentially modified with H3K4me1 and less with H3K27me3 than those of the independent genes. These findings, combined with previous reports, highlight not only the understanding of determinants for the catalytic activity dependency but also the development and application of pharmaceutical agents targeting the H3K27 or H3K4 modifications.
Collapse
Affiliation(s)
- Wendi Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapoe, Republic of Singapore
| | - Kian Leong Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapoe, Republic of Singapore
- Cancer & Stem Cell Biology Signature Research Programme, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Lorenz Poellinger
- Cancer Science Institute of Singapore, National University of Singapore, Singapoe, Republic of Singapore
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hisao Masai
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiroyuki Kato
- Cancer Science Institute of Singapore, National University of Singapore, Singapoe, Republic of Singapore
| |
Collapse
|
10
|
Bohuslavova R, Fabriciova V, Smolik O, Lebrón-Mora L, Abaffy P, Benesova S, Zucha D, Valihrach L, Berkova Z, Saudek F, Pavlinkova G. NEUROD1 reinforces endocrine cell fate acquisition in pancreatic development. Nat Commun 2023; 14:5554. [PMID: 37689751 PMCID: PMC10492842 DOI: 10.1038/s41467-023-41306-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023] Open
Abstract
NEUROD1 is a transcription factor that helps maintain a mature phenotype of pancreatic β cells. Disruption of Neurod1 during pancreatic development causes severe neonatal diabetes; however, the exact role of NEUROD1 in the differentiation programs of endocrine cells is unknown. Here, we report a crucial role of the NEUROD1 regulatory network in endocrine lineage commitment and differentiation. Mechanistically, transcriptome and chromatin landscape analyses demonstrate that Neurod1 inactivation triggers a downregulation of endocrine differentiation transcription factors and upregulation of non-endocrine genes within the Neurod1-deficient endocrine cell population, disturbing endocrine identity acquisition. Neurod1 deficiency altered the H3K27me3 histone modification pattern in promoter regions of differentially expressed genes, which resulted in gene regulatory network changes in the differentiation pathway of endocrine cells, compromising endocrine cell potential, differentiation, and functional properties.
Collapse
Affiliation(s)
- Romana Bohuslavova
- Laboratory of Molecular Pathogenetics, Institute of Biotechnology CAS, 25250, Vestec, Czechia
| | - Valeria Fabriciova
- Laboratory of Molecular Pathogenetics, Institute of Biotechnology CAS, 25250, Vestec, Czechia
| | - Ondrej Smolik
- Laboratory of Molecular Pathogenetics, Institute of Biotechnology CAS, 25250, Vestec, Czechia
| | - Laura Lebrón-Mora
- Laboratory of Molecular Pathogenetics, Institute of Biotechnology CAS, 25250, Vestec, Czechia
| | - Pavel Abaffy
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 25250, Vestec, Czechia
| | - Sarka Benesova
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 25250, Vestec, Czechia
| | - Daniel Zucha
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 25250, Vestec, Czechia
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 25250, Vestec, Czechia
| | - Zuzana Berkova
- Diabetes Centre, Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 14021, Prague, Czechia
| | - Frantisek Saudek
- Diabetes Centre, Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 14021, Prague, Czechia
| | - Gabriela Pavlinkova
- Laboratory of Molecular Pathogenetics, Institute of Biotechnology CAS, 25250, Vestec, Czechia.
| |
Collapse
|
11
|
Lin J, Zhang J, Ma L, Fang H, Ma R, Groneck C, Filippova GN, Deng X, Ma W, Disteche CM, Berletch JB. KDM6A facilitates Xist upregulation at the onset of X inactivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553617. [PMID: 37645756 PMCID: PMC10462084 DOI: 10.1101/2023.08.16.553617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
X chromosome inactivation (XCI) is a female-specific process in which one X chromosome is silenced to balance X-linked gene expression between the sexes. XCI is initiated in early development by upregulation of the lncRNA Xist on the future inactive X (Xi). A subset of X-linked genes escape silencing and thus have higher expression in females, suggesting female-specific functions. One of these genes is the highly conserved gene Kdm6a , which encodes a histone demethylase that removes methyl groups at H3K27 to facilitate gene expression. Here, we investigate the role of KDM6A in the regulation of Xist . We observed impaired upregulation of Xist during early stages of differentiation in hybrid mouse ES cells following CRISPR/Cas9 knockout of Kdm6a . This is associated with reduced Xist RNA coating of the Xi, suggesting diminished XCI potency. Indeed, Kdm6a knockout results in aberrant overexpression of genes from the Xi after differentiation. KDM6A binds to the Xist promoter and knockout cells show an increase in H3K27me3 at Xist . These results indicate that KDM6A plays a role in the initiation of XCI through histone demethylase-dependent activation of Xist during early differentiation.
Collapse
|
12
|
Ramesh V, Liu F, Minto MS, Chan U, West AE. Bidirectional regulation of postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics. eLife 2023; 12:e86273. [PMID: 37092728 PMCID: PMC10181825 DOI: 10.7554/elife.86273] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/21/2023] [Indexed: 04/25/2023] Open
Abstract
The functional maturation of neurons is a prolonged process that extends past the mitotic exit and is mediated by the chromatin-dependent orchestration of gene transcription programs. We find that expression of this maturation gene program in mouse cerebellar granule neurons (CGNs) requires dynamic changes in the genomic distribution of histone H3 lysine 27 trimethylation (H3K27me3), demonstrating a function for this chromatin modification beyond its role in cell fate specification. The developmental loss of H3K27me3 at promoters of genes activated as CGNs mature is facilitated by the lysine demethylase and ASD-risk gene, Kdm6b. Interestingly, inhibition of the H3K27 methyltransferase EZH2 in newborn CGNs not only blocks the repression of progenitor genes but also impairs the induction of mature CGN genes, showing the importance of bidirectional H3K27me3 regulation across the genome. These data demonstrate that H3K27me3 turnover in developing postmitotic neurons regulates the temporal coordination of gene expression programs that underlie functional neuronal maturation.
Collapse
Affiliation(s)
- Vijyendra Ramesh
- Molecular Cancer Biology Program, Duke UniversityDurhamUnited States
| | - Fang Liu
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Melyssa S Minto
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Urann Chan
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Anne E West
- Molecular Cancer Biology Program, Duke UniversityDurhamUnited States
- Department of Neurobiology, Duke UniversityDurhamUnited States
| |
Collapse
|
13
|
Chen LJ, Xu XY, Zhong XD, Liu YJ, Zhu MH, Tao F, Li CY, She QS, Yang GJ, Chen J. The role of lysine-specific demethylase 6A (KDM6A) in tumorigenesis and its therapeutic potentials in cancer therapy. Bioorg Chem 2023; 133:106409. [PMID: 36753963 DOI: 10.1016/j.bioorg.2023.106409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Histone demethylation is a key post-translational modification of chromatin, and its dysregulation affects a wide array of nuclear activities including the maintenance of genome integrity, transcriptional regulation, and epigenetic inheritance. Lysine specific demethylase 6A (KDM6A, also known as UTX) is an Fe2+- and α-ketoglutarate- dependent oxidase which belongs to KDM6 Jumonji histone demethylase subfamily, and it can remove mono-, di- and tri-methyl groups from methylated lysine 27 of histone H3 (H3K27me1/2/3). Mounting studies indicate that KDM6A is responsible for driving multiple human diseases, particularly cancers and pharmacological inhibition of KDM6A is an effective strategy to treat varieties of KDM6A-amplified cancers in cellulo and in vivo. Although there are several reviews on the roles of KDM6 subfamily in cancer development and therapy, all of them only simply introduce the roles of KDM6A in cancer without systematically summarizing the specific mechanisms of KDM6A in tumorigenesis, which greatly limits the advances on the understanding of roles KDM6A in varieties of cancers, discovering targeting selective KDM6A inhibitors, and exploring the adaptive profiles of KDM6A antagonists. Herein, we present the structure and functions of KDM6A, simply outline the functions of KDM6A in homeostasis and non-cancer diseases, summarize the role of KDM6A and its distinct target genes/ligand proteins in development of varieties of cancers, systematically classify KDM6A inhibitors, sum up the difficulties encountered in the research of KDM6A and the discovery of related drugs, and provide the corresponding solutions, which will contribute to understanding the roles of KDM6A in carcinogenesis and advancing the progression of KDM6A as a drug target in cancer therapy.
Collapse
Affiliation(s)
- Li-Juan Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Xin-Yang Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Xiao-Dan Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Yan-Jun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, 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, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Fan Tao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Chang-Yun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Qiu-Sheng She
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan 467044, Henan, China.
| | - 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, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, 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, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
14
|
Tayari MM, Fang C, Ntziachristos P. Context-Dependent Functions of KDM6 Lysine Demethylases in Physiology and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:139-165. [PMID: 37751139 DOI: 10.1007/978-3-031-38176-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Histone lysine methylation is a major epigenetic modification that participates in several cellular processes including gene regulation and chromatin structure. This mark can go awry in disease contexts such as cancer. Two decades ago, the discovery of histone demethylase enzymes thirteen years ago sheds light on the complexity of the regulation of this mark. Here we address the roles of lysine demethylases JMJD3 and UTX in physiological and disease contexts. The two demethylases play pivotal roles in many developmental and disease contexts via regulation of di- and trimethylation of lysine 27 on histone H3 (H3K27me2/3) in repressing gene expression programs. JMJD3 and UTX participate in several biochemical settings including methyltransferase and chromatin remodeling complexes. They have histone demethylase-dependent and -independent activities and a variety of context-specific interacting factors. The structure, amounts, and function of the demethylases can be altered in disease due to genetic alterations or aberrant gene regulation. Therefore, academic and industrial initiatives have targeted these enzymes using a number of small molecule compounds in therapeutic approaches. In this chapter, we will touch upon inhibitor formulations, their properties, and current efforts to test them in preclinical contexts to optimize their therapeutic outcomes. Demethylase inhibitors are currently used in targeted therapeutic approaches that might be particularly effective when used in conjunction with systemic approaches such as chemotherapy.
Collapse
Affiliation(s)
- Mina Masoumeh Tayari
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Celestia Fang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Center for Medical Genetics, Ghent University, Medical Research Building 2 (MRB2), Entrance 38, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| |
Collapse
|
15
|
Ma W, Fang H, Pease N, Filippova GN, Disteche CM, Berletch JB. Sex-biased and parental allele-specific gene regulation by KDM6A. Biol Sex Differ 2022; 13:40. [PMID: 35871105 PMCID: PMC9308343 DOI: 10.1186/s13293-022-00452-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/09/2022] [Indexed: 12/22/2022] Open
Abstract
Abstract
Background
KDM6A is a demethylase encoded by a gene with female-biased expression due to escape from X inactivation. Its main role is to facilitate gene expression through removal of the repressive H3K27me3 mark, with evidence of some additional histone demethylase-independent functions. KDM6A mutations have been implicated in congenital disorders such as Kabuki Syndrome, as well as in sex differences in cancer.
Methods
Kdm6a was knocked out using CRISPR/Cas9 gene editing in F1 male and female mouse embryonic stem cells (ES) derived from reciprocal crosses between C57BL6 x Mus castaneus. Diploid and allelic RNA-seq analyses were done to compare gene expression between wild-type and Kdm6a knockout (KO) clones. The effects of Kdm6a KO on sex-biased gene expression were investigated by comparing gene expression between male and female ES cells. Changes in H3K27me3 enrichment and chromatin accessibility at promoter regions of genes with expression changes were characterized by ChIP-seq and ATAC-seq followed by diploid and allelic analyses.
Results
We report that Kdm6a KO in male and female embryonic stem (ES) cells derived from F1 hybrid mice cause extensive gene dysregulation, disruption of sex biases, and specific parental allele effects. Among the dysregulated genes are candidate genes that may explain abnormal developmental features of Kabuki syndrome caused by KDM6A mutations in human. Strikingly, Kdm6a knockouts result in a decrease in sex-biased expression and in preferential downregulation of the maternal alleles of a number of genes. Most promoters of dysregulated genes show concordant epigenetic changes including gain of H3K27me3 and loss of chromatin accessibility, but there was less concordance when considering allelic changes.
Conclusions
Our study reveals new sex-related roles of KDM6A in the regulation of developmental genes, the maintenance of sex-biased gene expression, and the differential expression of parental alleles.
Collapse
|
16
|
H3K27me3 at pericentromeric heterochromatin is a defining feature of the early mouse blastocyst. Sci Rep 2022; 12:13908. [PMID: 35974030 PMCID: PMC9381757 DOI: 10.1038/s41598-022-17730-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/29/2022] [Indexed: 11/09/2022] Open
Abstract
Early mouse development is characterized by structural and epigenetic changes while cells progress towards differentiation. At blastocyst stage, the segregation of the three primordial lineages is accompanied by establishment of differential patterns of DNA methylation and post-translational modifications of histones, such as H3K27me3. Here, we analysed the dynamics of H3K27me3 at pericentromeric heterochromatin (PCH) during early development. We also followed the localization of EZH2 and BEND3, previously shown in ESCs to drive PRC2 to hypomethylated PCH. We show that the location of H3K27me3 at PCH, in addition to H3K9me3, is a defining feature of embryonic cells in vivo. Moreover, it may play an important role in structuring PCH and preserving genomic integrity at a time of globally relaxed chromatin. At peri-implantation stages, while DNA methylation is still low, EZH2 and then H3K27me3, leave PCH in epiblast progenitors at the time of their spatial segregation from primitive endoderm cells, while BEND3 remains there up to implantation. The comparison with stem cells (ESCs and TSCs) reveals that the epigenetic marks (i.e. H3K9me3 and H3K27me3) of PCH are reset during in vitro derivation and only partially restored thereafter. This highlights possible divergences between in vitro and "in embryo" epigenetic regulation regarding constitutive heterochromatin.
Collapse
|
17
|
Nakka K, Hachmer S, Mokhtari Z, Kovac R, Bandukwala H, Bernard C, Li Y, Xie G, Liu C, Fallahi M, Megeney LA, Gondin J, Chazaud B, Brand M, Zha X, Ge K, Dilworth FJ. JMJD3 activated hyaluronan synthesis drives muscle regeneration in an inflammatory environment. Science 2022; 377:666-669. [PMID: 35926054 DOI: 10.1126/science.abm9735] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Muscle stem cells (MuSCs) reside in a specialized niche that ensures their regenerative capacity. Although we know that innate immune cells infiltrate the niche in response to injury, it remains unclear how MuSCs adapt to this altered environment for initiating repair. Here, we demonstrate that inflammatory cytokine signaling from the regenerative niche impairs the ability of quiescent MuSCs to reenter the cell cycle. The histone H3 lysine 27 (H3K27) demethylase JMJD3, but not UTX, allowed MuSCs to overcome inhibitory inflammation signaling by removing trimethylated H3K27 (H3K27me3) marks at the Has2 locus to initiate production of hyaluronic acid, which in turn established an extracellular matrix competent for integrating signals that direct MuSCs to exit quiescence. Thus, JMJD3-driven hyaluronic acid synthesis plays a proregenerative role that allows MuSC adaptation to inflammation and the initiation of muscle repair.
Collapse
Affiliation(s)
- Kiran Nakka
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Sarah Hachmer
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Zeinab Mokhtari
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Radmila Kovac
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hina Bandukwala
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Clara Bernard
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS 5261, INSERM U1315, Université de Lyon, Lyon, France
| | - Yuefeng Li
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Guojia Xie
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Liu
- Transgenic Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Magid Fallahi
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Lynn A Megeney
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Julien Gondin
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS 5261, INSERM U1315, Université de Lyon, Lyon, France
| | - Bénédicte Chazaud
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS 5261, INSERM U1315, Université de Lyon, Lyon, France
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,LIFE Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Xiaohui Zha
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,LIFE Research Institute, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
18
|
Cicciarello D, Schaeffer L, Scionti I. Epigenetic Control of Muscle Stem Cells: Focus on Histone Lysine Demethylases. Front Cell Dev Biol 2022; 10:917771. [PMID: 35669509 PMCID: PMC9166302 DOI: 10.3389/fcell.2022.917771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/02/2022] [Indexed: 01/02/2023] Open
Abstract
Adult skeletal muscle is mainly composed of post-mitotic, multinucleated muscle fibers. Upon injury, it has the unique ability to regenerate thanks to the activation of a subset of quiescent muscle stem cells (MuSCs). Activated MuSCs either differentiate to repair muscle, or self-renew to maintain the pool of MuSC. MuSC fate determination is regulated by an intricate network of intrinsic and extrinsic factors that control the expression of specific subsets of genes. Among these, the myogenic regulatory factors (MRFs) are key for muscle development, cell identity and regeneration. More globally, cell fate determination involves important changes in the epigenetic landscape of the genome. Such epigenetic changes, which include DNA methylation and post-translational modifications of histone proteins, are able to alter chromatin organization by controlling the accessibility of specific gene loci for the transcriptional machinery. Among the numerous epigenetic modifications of chromatin, extensive studies have pointed out the key role of histone methylation in cell fate control. Particularly, since the discovery of the first histone demethylase in 2004, the role of histone demethylation in the regulation of skeletal muscle differentiation and muscle stem cell fate has emerged to be essential. In this review, we highlight the current knowledge regarding the role of histone demethylases in the regulation of muscle stem cell fate choice.
Collapse
Affiliation(s)
- Delia Cicciarello
- Pathophysiologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon I, Villeurbanne, France
| | - Laurent Schaeffer
- Pathophysiologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon I, Villeurbanne, France
| | - Isabella Scionti
- Pathophysiologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon I, Villeurbanne, France
| |
Collapse
|
19
|
Gao Y, Aljazi MB, He J. Kdm6b Haploinsufficiency Causes ASD/ADHD-Like Behavioral Deficits in Mice. Front Behav Neurosci 2022; 16:905783. [PMID: 35711692 PMCID: PMC9194811 DOI: 10.3389/fnbeh.2022.905783] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disease that has intellectual disability (ID) and attention-deficit/hyperactivity disorder (ADHD) as its common comorbidities. Recent genetic and clinical studies report that KDM6B, a gene encoding a histone H3 lysine 27-specific demethylase, is one of the highest ASD risk genes. However, the relationship between KDM6B mutations and neurodevelopmental diseases remains unclear. Here we use an animal model to show that genetic deletion of one Kdm6b allele in mice leads to autistic-like impaired sociability and object recognition memory. In addition, the mutant mice display markedly increased locomotor activity and impulsivity, two ADHD-like behavioral traits that are ameliorated by methylphenidate treatment. Thus, our study not only uncovers a potential causal link between disruptive KDM6B mutations and ASD/ADHD-like behavioral deficits but also provides a new mouse model for studying the cellular and molecular mechanisms underlying the Kdm6b-mutation-related neurodevelopmental diseases.
Collapse
|
20
|
Mbadhi MN, Tang JM, Zhang JX. Histone Lysine Methylation and Long Non-Coding RNA: The New Target Players in Skeletal Muscle Cell Regeneration. Front Cell Dev Biol 2021; 9:759237. [PMID: 34926450 PMCID: PMC8678087 DOI: 10.3389/fcell.2021.759237] [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: 08/16/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Satellite stem cell availability and high regenerative capacity have made them an ideal therapeutic approach for muscular dystrophies and neuromuscular diseases. Adult satellite stem cells remain in a quiescent state and become activated upon muscular injury. A series of molecular mechanisms succeed under the control of epigenetic regulation and various myogenic regulatory transcription factors myogenic regulatory factors, leading to their differentiation into skeletal muscles. The regulation of MRFs via various epigenetic factors, including DNA methylation, histone modification, and non-coding RNA, determine the fate of myogenesis. Furthermore, the development of histone deacetylation inhibitors (HDACi) has shown promising benefits in their use in clinical trials of muscular diseases. However, the complete application of using satellite stem cells in the clinic is still not achieved. While therapeutic advancements in the use of HDACi in clinical trials have emerged, histone methylation modulations and the long non-coding RNA (lncRNA) are still under study. A comprehensive understanding of these other significant epigenetic modulations is still incomplete. This review aims to discuss some of the current studies on these two significant epigenetic modulations, histone methylation and lncRNA, as potential epigenetic targets in skeletal muscle regeneration. Understanding the mechanisms that initiate myoblast differentiation from its proliferative state to generate new muscle fibres will provide valuable information to advance the field of regenerative medicine and stem cell transplant.
Collapse
Affiliation(s)
- Magdaleena Naemi Mbadhi
- Hubei Key Laboratory of Embryonic Stem Cell Research, Department of Physiology, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Jun-Ming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Department of Physiology, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Jing-Xuan Zhang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Department of Physiology, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| |
Collapse
|
21
|
Shao J, Shi T, Yu H, Ding Y, Li L, Wang X, Wang X. Cytosolic GDH1 degradation restricts protein synthesis to sustain tumor cell survival following amino acid deprivation. EMBO J 2021; 40:e107480. [PMID: 34269483 PMCID: PMC8521317 DOI: 10.15252/embj.2020107480] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/04/2021] [Accepted: 06/13/2021] [Indexed: 01/18/2023] Open
Abstract
The mTORC1 pathway plays key roles in regulating various biological processes, including sensing amino acid deprivation and driving expression of ribosomal protein (RP)-coding genes. In this study, we observed that depletion of glutamate dehydrogenase 1 (GDH1), an enzyme that converts glutamate to α-ketoglutarate (αKG), confers resistance to amino acid deprivation on kidney renal clear cell carcinoma (KIRC) cells. Mechanistically, under conditions of adequate nutrition, GDH1 maintains RP gene expression in a manner dependent on its enzymatic activity. Following amino acid deprivation or mTORC1 inhibition, GDH1 translocates from mitochondria to the cytoplasm, where it becomes ubiquitinated and degraded via the E3 ligase RNF213. GDH1 degradation reduces intracellular αKG levels by more than half and decreases the activity of αKG-dependent lysine demethylases (KDMs). Reduced KDM activity in turn leads to increased histone H3 lysine 9 and 27 methylation, further suppressing RP gene expression and preserving nutrition to support cell survival. In summary, our study exemplifies an economical and efficient strategy of solid tumor cells for coping with amino acid deficiency, which might in the future be targeted to block renal carcinoma progression.
Collapse
Affiliation(s)
- Jialiang Shao
- Department of UrologyShanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Tiezhu Shi
- Department of UrologyShanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Hua Yu
- CAS Key Laboratory of Tissue Microenvironment and TumorInstitute of Nutrition and Health SciencesChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Yufeng Ding
- Department of UrologyShanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Liping Li
- School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Xiang Wang
- Department of UrologyShanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Xiongjun Wang
- CAS Key Laboratory of Tissue Microenvironment and TumorInstitute of Nutrition and Health SciencesChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
| |
Collapse
|
22
|
Zhang F, Zhao X, Jiang R, Wang Y, Wang X, Gu Y, Xu L, Ye J, Chen CD, Guo S, Zhang D, Zhao D. Identification of Jmjd3 as an Essential Epigenetic Regulator of Hox Gene Temporal Collinear Activation for Body Axial Patterning in Mice. Front Cell Dev Biol 2021; 9:642931. [PMID: 34368113 PMCID: PMC8333871 DOI: 10.3389/fcell.2021.642931] [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: 12/17/2020] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Body axial patterning develops via a rostral-to-caudal sequence and relies on the temporal colinear activation of Hox genes. However, the underlying mechanism of Hox gene temporal colinear activation remains largely elusive. Here, with small-molecule inhibitors and conditional gene knockout mice, we identified Jmjd3, a subunit of TrxG, as an essential regulator of temporal colinear activation of Hox genes with its H3K27me3 demethylase activity. We demonstrated that Jmjd3 not only initiates but also maintains the temporal collinear expression of Hox genes. However, we detected no antagonistic roles between Jmjd3 and Ezh2, a core subunit of PcG repressive complex 2, during the processes of axial skeletal patterning. Our findings provide new insights into the regulation of Hox gene temporal collinear activation for body axial patterning in mice.
Collapse
Affiliation(s)
- Feng Zhang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pathology, Air Force Medical Center (Air Force General Hospital), Chinese People's Liberation Army, Beijing, China
| | - Xiong Zhao
- Department of Orthopedics, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Runmin Jiang
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Yuying Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xinli Wang
- Department of Orthopedics, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yu Gu
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Longyong Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing Ye
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuangping Guo
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Dawei Zhang
- Department of Orthopedics, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Daqing Zhao
- Department of Otolaryngology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| |
Collapse
|
23
|
UTX maintains the functional integrity of the murine hematopoietic system by globally regulating aging-associated genes. Blood 2021; 137:908-922. [PMID: 33174606 DOI: 10.1182/blood.2019001044] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
Epigenetic regulation is essential for the maintenance of the hematopoietic system, and its deregulation is implicated in hematopoietic disorders. In this study, UTX, a demethylase for lysine 27 on histone H3 (H3K27) and a component of COMPASS-like and SWI/SNF complexes, played an essential role in the hematopoietic system by globally regulating aging-associated genes. Utx-deficient (UtxΔ/Δ) mice exhibited myeloid skewing with dysplasia, extramedullary hematopoiesis, impaired hematopoietic reconstituting ability, and increased susceptibility to leukemia, which are the hallmarks of hematopoietic aging. RNA-sequencing (RNA-seq) analysis revealed that Utx deficiency converted the gene expression profiles of young hematopoietic stem-progenitor cells (HSPCs) to those of aged HSPCs. Utx expression in hematopoietic stem cells declined with age, and UtxΔ/Δ HSPCs exhibited increased expression of an aging-associated marker, accumulation of reactive oxygen species, and impaired repair of DNA double-strand breaks. Pathway and chromatin immunoprecipitation analyses coupled with RNA-seq data indicated that UTX contributed to hematopoietic homeostasis mainly by maintaining the expression of genes downregulated with aging via demethylase-dependent and -independent epigenetic programming. Of note, comparison of pathway changes in UtxΔ/Δ HSPCs, aged muscle stem cells, aged fibroblasts, and aged induced neurons showed substantial overlap, strongly suggesting common aging mechanisms among different tissue stem cells.
Collapse
|
24
|
Duong P, Ma KH, Ramesh R, Moran JJ, Won S, Svaren J. H3K27 demethylases are dispensable for activation of Polycomb-regulated injury response genes in peripheral nerve. J Biol Chem 2021; 297:100852. [PMID: 34090875 PMCID: PMC8258988 DOI: 10.1016/j.jbc.2021.100852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022] Open
Abstract
The induction of nerve injury response genes in Schwann cells depends on both transcriptional and epigenomic reprogramming. The nerve injury response program is regulated by the repressive histone mark H3K27 trimethylation (H3K27me3), deposited by Polycomb repressive complex 2 (PRC2). Loss of PRC2 function leads to early and augmented induction of the injury response gene network in peripheral nerves, suggesting H3K27 demethylases are required for derepression of Polycomb-regulated nerve injury genes. To determine the function of H3K27 demethylases in nerve injury, we generated Schwann cell-specific knockouts of H3K27 demethylase Kdm6b and double knockouts of Kdm6b/Kdm6a (encoding JMJD3 and UTX). We found that H3K27 demethylases are largely dispensable for Schwann cell development and myelination. In testing the function of H3K27 demethylases after injury, we found early induction of some nerve injury genes was diminished compared with control, but most injury genes were largely unaffected at 1 and 7 days post injury. Although it was proposed that H3K27 demethylases are required to activate expression of the cyclin-dependent kinase inhibitor Cdkn2a in response to injury, Schwann cell-specific deletion of H3K27 demethylases affected neither the expression of this gene nor Schwann cell proliferation after nerve injury. To further characterize the regulation of nerve injury response genes, we found that injury genes are associated with repressive histone H2AK119 ubiquitination catalyzed by PRC1, which declines after injury. Overall, our results indicate H3K27 demethylation is not required for induction of injury response genes and that other mechanisms likely are involved in activating Polycomb-repressed injury genes in peripheral nerve.
Collapse
Affiliation(s)
- Phu Duong
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ki H Ma
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Raghu Ramesh
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John J Moran
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Seongsik Won
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John Svaren
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, USA.
| |
Collapse
|
25
|
Alarcón T, Sardanyés J, Guillamon A, Menendez JA. Bivalent chromatin as a therapeutic target in cancer: An in silico predictive approach for combining epigenetic drugs. PLoS Comput Biol 2021; 17:e1008408. [PMID: 34153035 PMCID: PMC8248646 DOI: 10.1371/journal.pcbi.1008408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 07/01/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022] Open
Abstract
Tumour cell heterogeneity is a major barrier for efficient design of targeted anti-cancer therapies. A diverse distribution of phenotypically distinct tumour-cell subpopulations prior to drug treatment predisposes to non-uniform responses, leading to the elimination of sensitive cancer cells whilst leaving resistant subpopulations unharmed. Few strategies have been proposed for quantifying the variability associated to individual cancer-cell heterogeneity and minimizing its undesirable impact on clinical outcomes. Here, we report a computational approach that allows the rational design of combinatorial therapies involving epigenetic drugs against chromatin modifiers. We have formulated a stochastic model of a bivalent transcription factor that allows us to characterise three different qualitative behaviours, namely: bistable, high- and low-gene expression. Comparison between analytical results and experimental data determined that the so-called bistable and high-gene expression behaviours can be identified with undifferentiated and differentiated cell types, respectively. Since undifferentiated cells with an aberrant self-renewing potential might exhibit a cancer/metastasis-initiating phenotype, we analysed the efficiency of combining epigenetic drugs against the background of heterogeneity within the bistable sub-ensemble. Whereas single-targeted approaches mostly failed to circumvent the therapeutic problems represented by tumour heterogeneity, combinatorial strategies fared much better. Specifically, the more successful combinations were predicted to involve modulators of the histone H3K4 and H3K27 demethylases KDM5 and KDM6A/UTX. Those strategies involving the H3K4 and H3K27 methyltransferases MLL2 and EZH2, however, were predicted to be less effective. Our theoretical framework provides a coherent basis for the development of an in silico platform capable of identifying the epigenetic drugs combinations best-suited to therapeutically manage non-uniform responses of heterogenous cancer cell populations.
Collapse
Affiliation(s)
- Tomás Alarcón
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre de Recerca Matemàtica, Cerdanyola del Vallès, Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | - Antoni Guillamon
- Centre de Recerca Matemàtica, Cerdanyola del Vallès, Spain
- Departament de Matemàtiques, EPSEB, Universitat Politècnica de Catalunya, Barcelona, Spain
- Institut de Matemàtiques de la UPC-BarcelonaTech (IMTech), Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Javier A. Menendez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain
- Girona Biomedical Research Institute, Salt, Girona, Spain
| |
Collapse
|
26
|
Hogg SJ, Motorna O, Cluse LA, Johanson TM, Coughlan HD, Raviram R, Myers RM, Costacurta M, Todorovski I, Pijpers L, Bjelosevic S, Williams T, Huskins SN, Kearney CJ, Devlin JR, Fan Z, Jabbari JS, Martin BP, Fareh M, Kelly MJ, Dupéré-Richer D, Sandow JJ, Feran B, Knight D, Khong T, Spencer A, Harrison SJ, Gregory G, Wickramasinghe VO, Webb AI, Taberlay PC, Bromberg KD, Lai A, Papenfuss AT, Smyth GK, Allan RS, Licht JD, Landau DA, Abdel-Wahab O, Shortt J, Vervoort SJ, Johnstone RW. Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition. Mol Cell 2021; 81:2183-2200.e13. [PMID: 34019788 PMCID: PMC8183601 DOI: 10.1016/j.molcel.2021.04.015] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 01/19/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
To separate causal effects of histone acetylation on chromatin accessibility and transcriptional output, we used integrated epigenomic and transcriptomic analyses following acute inhibition of major cellular lysine acetyltransferases P300 and CBP in hematological malignancies. We found that catalytic P300/CBP inhibition dynamically perturbs steady-state acetylation kinetics and suppresses oncogenic transcriptional networks in the absence of changes to chromatin accessibility. CRISPR-Cas9 screening identified NCOR1 and HDAC3 transcriptional co-repressors as the principal antagonists of P300/CBP by counteracting acetylation turnover kinetics. Finally, deacetylation of H3K27 provides nucleation sites for reciprocal methylation switching, a feature that can be exploited therapeutically by concomitant KDM6A and P300/CBP inhibition. Overall, this study indicates that the steady-state histone acetylation-methylation equilibrium functions as a molecular rheostat governing cellular transcription that is amenable to therapeutic exploitation as an anti-cancer regimen.
Collapse
Affiliation(s)
- Simon J Hogg
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Olga Motorna
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Leonie A Cluse
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Hannah D Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | | | - Robert M Myers
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Matteo Costacurta
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Izabela Todorovski
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Lizzy Pijpers
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Stefan Bjelosevic
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Tobias Williams
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Shannon N Huskins
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, 7000, Australia
| | - Conor J Kearney
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Jennifer R Devlin
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Zheng Fan
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Jafar S Jabbari
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Australia
| | - Ben P Martin
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Mohamed Fareh
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Madison J Kelly
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Daphné Dupéré-Richer
- Division of Hematology/Oncology, The University of Florida Health Cancer Center, Gainesville, FL 32608, USA
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Breon Feran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Deborah Knight
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Tiffany Khong
- Australian Center for Blood Diseases, Monash University, Melbourne, 3004, Australia
| | - Andrew Spencer
- Australian Center for Blood Diseases, Monash University, Melbourne, 3004, Australia
| | - Simon J Harrison
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Clinical Hematology, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Royal Melbourne Hospital, Melbourne, 3000, Australia
| | - Gareth Gregory
- Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Vihandha O Wickramasinghe
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, 7000, Australia
| | - Kenneth D Bromberg
- Discovery, Global Pharmaceutical Research and Development, AbbVie, North Chicago, IL 60064, USA
| | - Albert Lai
- Discovery, Global Pharmaceutical Research and Development, AbbVie, North Chicago, IL 60064, USA
| | - Anthony T Papenfuss
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, 3010, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Jonathan D Licht
- Division of Hematology/Oncology, The University of Florida Health Cancer Center, Gainesville, FL 32608, USA
| | - Dan A Landau
- New York Genome Center, New York, NY 10013, USA; Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jake Shortt
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Stephin J Vervoort
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia.
| | - Ricky W Johnstone
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia.
| |
Collapse
|
27
|
|
28
|
Mehboob R, Kurdi M, Ahmad M, Gilani SA, Khalid S, Nasief H, Mirdad A, Malibary H, Hakamy S, Hassan A, Alaifan M, Bamaga A, Shahzad SA. Comprehensive Analysis of Genes Associated With Sudden Infant Death Syndrome. Front Pediatr 2021; 9:742225. [PMID: 34722422 PMCID: PMC8555024 DOI: 10.3389/fped.2021.742225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Sudden infant death syndrome (SIDS) is a tragic incident which remains a mystery even after post-mortem investigation and thorough researches. Methods: This comprehensive review is based on the genes reported in the molecular autopsy studies conducted on SIDS so far. A total of 20 original studies and 7 case reports were identified and included in this analysis. The genes identified in children or adults were not included. Most of the genes reported in these studies belonged to cardiac channel and cardiomyopathy. Cardiac channel genes in SIDS were scrutinized for further analysis. Results: After screening and removing the duplicates, 42 unique genes were extracted. When the location of these genes was assessed, it was observed that most of these belonged to Chromosomes 11, 1 and 3 in sequential manner. The pathway analysis shows that these genes are involved in the regulation of heart rate, action potential, cardiac muscle cell contraction and heart contraction. The protein-protein interaction network was also very big and highly interactive. SCN5A, CAV3, ALG10B, AKAP9 and many more were mainly found in these cases and were regulated by many transcription factors such as MYOG C2C1 and CBX3 HCT11. Micro RNA, "hsa-miR-133a-3p" was found to be prevalent in the targeted genes. Conclusions: Molecular and computational approaches are a step forward toward exploration of these sad demises. It is so far a new arena but seems promising to dig out the genetic cause of SIDS in the years to come.
Collapse
Affiliation(s)
- Riffat Mehboob
- Research Unit, Faculty of Allied Health Sciences, The University of Lahore, Lahore, Pakistan.,Lahore Medical Research Center, LLP, Lahore, Pakistan
| | - Maher Kurdi
- Department of Pathology, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mursleen Ahmad
- Department of Medicine, Sahiwal Medical College, Sahiwal, Pakistan
| | - Syed Amir Gilani
- Research Unit, Faculty of Allied Health Sciences, The University of Lahore, Lahore, Pakistan
| | - Sidra Khalid
- Lahore Medical Research Center, LLP, Lahore, Pakistan
| | - Hisham Nasief
- Department of Obstetric and Gynecology, Faculty of Medicine, King Abdulaziz University and Hospital, Jeddah, Saudi Arabia
| | - Abeer Mirdad
- Pediatric Department, East Jeddah Hospital, Jeddah, Saudi Arabia
| | - Husam Malibary
- Department of Internal Medicine, Faculty of Medicine, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Sahar Hakamy
- Center of Excellence in Genomic Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amber Hassan
- Research Unit, Faculty of Allied Health Sciences, The University of Lahore, Lahore, Pakistan
| | - Meshari Alaifan
- Department of Paediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bamaga
- Paediatric Department, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia.,Neurology and Pediatric Department, Faculty of Medicine, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Syed Adnan Shahzad
- Faculty of Medicine and University Hospital of Cologne, Institute of Virology, University of Cologne, Cologne, Germany
| |
Collapse
|
29
|
Loss of UTX/KDM6A and the activation of FGFR3 converge to regulate differentiation gene-expression programs in bladder cancer. Proc Natl Acad Sci U S A 2020; 117:25732-25741. [PMID: 32989154 DOI: 10.1073/pnas.2008017117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bladder cancer prognosis is closely linked to the underlying differentiation state of the tumor, ranging from the less aggressive and most-differentiated luminal tumors to the more aggressive and least-differentiated basal tumors. Sequencing of bladder cancer has revealed that loss-of-function mutations in chromatin regulators and mutations that activate receptor tyrosine kinase (RTK) signaling frequently occur in bladder cancer. However, little is known as to whether and how these two types of mutations functionally interact or cooperate to regulate tumor growth and differentiation state. Here, we focus on loss of the histone demethylase UTX (also known as KDM6A) and activation of the RTK FGFR3, two events that commonly cooccur in muscle invasive bladder tumors. We show that UTX loss and FGFR3 activation cooperate to disrupt the balance of luminal and basal gene expression in bladder cells. UTX localized to enhancers surrounding many genes that are important for luminal cell fate, and supported the transcription of these genes in a catalytic-independent manner. In contrast to UTX, FGFR3 activation was associated with lower expression of luminal genes in tumors and FGFR inhibition increased transcription of these same genes in cell culture models. This suggests an antagonistic relationship between UTX and FGFR3. In support of this model, UTX loss-of-function potentiated FGFR3-dependent transcriptional effects and the presence of UTX blocked an FGFR3-mediated increase in the colony formation of bladder cells. Taken together, our study reveals how mutations in UTX and FGFR3 converge to disrupt bladder differentiation programs that could serve as a therapeutic target.
Collapse
|
30
|
The role of histone methylation in the development of digestive cancers: a potential direction for cancer management. Signal Transduct Target Ther 2020; 5:143. [PMID: 32747629 PMCID: PMC7398912 DOI: 10.1038/s41392-020-00252-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/22/2020] [Accepted: 07/15/2020] [Indexed: 02/08/2023] Open
Abstract
Digestive cancers are the leading cause of cancer-related death worldwide and have high risks of morbidity and mortality. Histone methylation, which is mediated mainly by lysine methyltransferases, lysine demethylases, and protein arginine methyltransferases, has emerged as an essential mechanism regulating pathological processes in digestive cancers. Under certain conditions, aberrant expression of these modifiers leads to abnormal histone methylation or demethylation in the corresponding cancer-related genes, which contributes to different processes and phenotypes, such as carcinogenesis, proliferation, metabolic reprogramming, epithelial–mesenchymal transition, invasion, and migration, during digestive cancer development. In this review, we focus on the association between histone methylation regulation and the development of digestive cancers, including gastric cancer, liver cancer, pancreatic cancer, and colorectal cancer, as well as on its clinical application prospects, aiming to provide a new perspective on the management of digestive cancers.
Collapse
|
31
|
Shpargel KB, Mangini CL, Xie G, Ge K, Magnuson T. The KMT2D Kabuki syndrome histone methylase controls neural crest cell differentiation and facial morphology. Development 2020; 147:dev.187997. [PMID: 32541010 DOI: 10.1242/dev.187997] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/02/2020] [Indexed: 12/13/2022]
Abstract
Kabuki syndrome (KS) is a congenital craniofacial disorder resulting from mutations in the KMT2D histone methylase (KS1) or the UTX histone demethylase (KS2). With small cohorts of KS2 patients, it is not clear whether differences exist in clinical manifestations relative to KS1. We mutated KMT2D in neural crest cells (NCCs) to study cellular and molecular functions in craniofacial development with respect to UTX. Similar to UTX, KMT2D NCC knockout mice demonstrate hypoplasia with reductions in frontonasal bone lengths. We have traced the onset of KMT2D and UTX mutant NCC frontal dysfunction to a stage of altered osteochondral progenitor differentiation. KMT2D NCC loss-of-function does exhibit unique phenotypes distinct from UTX mutation, including fully penetrant cleft palate, mandible hypoplasia and deficits in cranial base ossification. KMT2D mutant NCCs lead to defective secondary palatal shelf elevation with reduced expression of extracellular matrix components. KMT2D mutant chondrocytes in the cranial base fail to properly differentiate, leading to defective endochondral ossification. We conclude that KMT2D is required for appropriate cranial NCC differentiation and KMT2D-specific phenotypes may underlie differences between Kabuki syndrome subtypes.
Collapse
Affiliation(s)
- Karl B Shpargel
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Cassidy L Mangini
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Guojia Xie
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Terry Magnuson
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| |
Collapse
|
32
|
Kralemann LEM, Liu S, Trejo-Arellano MS, Muñoz-Viana R, Köhler C, Hennig L. Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis. Genome Biol 2020; 21:144. [PMID: 32546254 PMCID: PMC7296913 DOI: 10.1186/s13059-020-02062-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Stable gene repression is essential for normal growth and development. Polycomb repressive complexes 1 and 2 (PRC1&2) are involved in this process by establishing monoubiquitination of histone 2A (H2Aub1) and subsequent trimethylation of lysine 27 of histone 3 (H3K27me3). Previous work proposed that H2Aub1 removal by the ubiquitin-specific proteases 12 and 13 (UBP12 and UBP13) is part of the repressive PRC1&2 system, but its functional role remains elusive. RESULTS We show that UBP12 and UBP13 work together with PRC1, PRC2, and EMF1 to repress genes involved in stimulus response. We find that PRC1-mediated H2Aub1 is associated with gene responsiveness, and its repressive function requires PRC2 recruitment. We further show that the requirement of PRC1 for PRC2 recruitment depends on the initial expression status of genes. Lastly, we demonstrate that removal of H2Aub1 by UBP12/13 prevents loss of H3K27me3, consistent with our finding that the H3K27me3 demethylase REF6 is positively associated with H2Aub1. CONCLUSIONS Our data allow us to propose a model in which deposition of H2Aub1 permits genes to switch between repression and activation by H3K27me3 deposition and removal. Removal of H2Aub1 by UBP12/13 is required to achieve stable PRC2-mediated repression.
Collapse
Affiliation(s)
- Lejon E. M. Kralemann
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden
| | - Shujing Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden
| | - Minerva S. Trejo-Arellano
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden
| | - Rafael Muñoz-Viana
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, 03550 Sant Joan d’Alacant, Spain
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden
| |
Collapse
|
33
|
|
34
|
Histone H3K27me3 demethylases regulate human Th17 cell development and effector functions by impacting on metabolism. Proc Natl Acad Sci U S A 2020; 117:6056-6066. [PMID: 32123118 PMCID: PMC7084125 DOI: 10.1073/pnas.1919893117] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
T cells control many immune functions, with Th17 cells critical in regulating inflammation. Following activation, T cells undergo metabolic reprogramming and utilize glycolysis to increase the ATP availability. Epigenetic mechanisms controlling metabolic functions in T cells are currently not well-defined. Here, we establish an epigenetic link between the histone H3K27me3 demethylases KDM6A/B and the coordination of a metabolic response. Inhibition of KDM6A/B leads to global increases in the repressive H3K27me3 histone mark, resulting in down-regulation of key transcription factors, followed by metabolic reprogramming and anergy. This work suggests a critical role of H3K27 demethylase enzymes in maintaining Th17 functions by controlling metabolic switches. Short-term treatment with KDM6 enzyme inhibitors may be useful in the therapy of chronic inflammatory diseases. T helper (Th) cells are CD4+ effector T cells that play a critical role in immunity by shaping the inflammatory cytokine environment in a variety of physiological and pathological situations. Using a combined chemico-genetic approach, we identify histone H3K27 demethylases KDM6A and KDM6B as central regulators of human Th subsets. The prototypic KDM6 inhibitor GSK-J4 increases genome-wide levels of the repressive H3K27me3 chromatin mark and leads to suppression of the key transcription factor RORγt during Th17 differentiation. In mature Th17 cells, GSK-J4 induces an altered transcriptional program with a profound metabolic reprogramming and concomitant suppression of IL-17 cytokine levels and reduced proliferation. Single-cell analysis reveals a specific shift from highly inflammatory cell subsets toward a resting state upon demethylase inhibition. The root cause of the observed antiinflammatory phenotype in stimulated Th17 cells is reduced expression of key metabolic transcription factors, such as PPRC1. Overall, this leads to reduced mitochondrial biogenesis, resulting in a metabolic switch with concomitant antiinflammatory effects. These data are consistent with an effect of GSK-J4 on Th17 T cell differentiation pathways directly related to proliferation and include regulation of effector cytokine profiles. This suggests that inhibiting KDM6 demethylases may be an effective, even in the short term, therapeutic target for autoimmune diseases, including ankylosing spondylitis.
Collapse
|
35
|
Shan Y, Zhang Y, Zhao Y, Wang T, Zhang J, Yao J, Ma N, Liang Z, Huang W, Huang K, Zhang T, Su Z, Chen Q, Zhu Y, Wu C, Zhou T, Sun W, Wei Y, Zhang C, Li C, Su S, Liao B, Zhong M, Zhong X, Nie J, Pei D, Pan G. JMJD3 and UTX determine fidelity and lineage specification of human neural progenitor cells. Nat Commun 2020; 11:382. [PMID: 31959746 PMCID: PMC6971254 DOI: 10.1038/s41467-019-14028-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/13/2019] [Indexed: 02/08/2023] Open
Abstract
Neurogenesis, a highly orchestrated process, entails the transition from a pluripotent to neural state and involves neural progenitor cells (NPCs) and neuronal/glial subtypes. However, the precise epigenetic mechanisms underlying fate decision remain poorly understood. Here, we delete KDM6s (JMJD3 and/or UTX), the H3K27me3 demethylases, in human embryonic stem cells (hESCs) and show that their deletion does not impede NPC generation from hESCs. However, KDM6-deficient NPCs exhibit poor proliferation and a failure to differentiate into neurons and glia. Mechanistically, both JMJD3 and UTX are found to be enriched in gene loci essential for neural development in hNPCs, and KDM6 impairment leads to H3K27me3 accumulation and blockade of DNA accessibility at these genes. Interestingly, forced expression of neuron-specific chromatin remodelling BAF (nBAF) rescues the neuron/glia defect in KDM6-deficient NPCs despite H3K27me3 accumulation. Our findings uncover the differential requirement of KDM6s in specifying NPCs and neurons/glia and highlight the contribution of individual epigenetic regulators in fate decisions in a human development model. Neurogenesis is an ordered transition from pluriptotent cells to neural precursor cells (NPCs) to neurons. Here the authors show that loss of the lysine demethylases JMJD3 and UTX leads reduced DNA accessibility at neurogenesis loci in human NPCs, and that the chromatin remodeller BAF can rescue differentiation defects.
Collapse
Affiliation(s)
- Yongli Shan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanqi Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yuan Zhao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tianyu Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jingyuan Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jiao Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Ning Ma
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Zechuan Liang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Wenhao Huang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Ke Huang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tian Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Zhenghui Su
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Qianyu Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanling Zhu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Chuman Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tiancheng Zhou
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Wei Sun
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanxing Wei
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Cong Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Chenxu Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Shuquan Su
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Baojian Liao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Mei Zhong
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaofen Zhong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jinfu Nie
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China. .,Shandong Medicinal Biotechnology Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250012, China. .,Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong, China.
| |
Collapse
|
36
|
Yin X, Yang S, Zhang M, Yue Y. The role and prospect of JMJD3 in stem cells and cancer. Biomed Pharmacother 2019; 118:109384. [PMID: 31545292 DOI: 10.1016/j.biopha.2019.109384] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/12/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Currently, stem cells are reported to be involved in tumor formation, drug resistance and recurrence. Inhibiting the proliferation of tumor cells, promoting their senescence and apoptosis has been the most important anti-tumor therapy. Epigenetics is involved in the regulation of gene expression and is closely related to cancer and stem cells. It mainly includes DNA methylation, histone modification, and chromatin remodeling. Histone methylation and demethylation play an important role in histone modification. Histone 3 lysine 27 trimethylation (H3K27me3) induces transcriptional inhibition and plays an important role in gene expression. Jumonji domain-containing protein-3 (JMJD3), one of the demethyases of histone H3K27me3, has been reported to be associated with the prognosis of many cancers and stem cells differentiation. Inhibition of JMJD3 can reduce proliferation and promote apoptosis in tumor cells, as well as suppress differentiation in stem cells. GSK-J4 is an inhibitor of demethylase JMJD3 and UTX, which has been shown to possess anti-cancer and inhibition of embryonic stem cells differentiation effects. In this review, we examine how JMJD3 regulates cellular fates of stem cells and cancer cells and references were identified through searches of PubMed, Medline, Web of Science.
Collapse
Affiliation(s)
- Xiaojiao Yin
- Department of Gynecological Oncology, The First Hospital of Jilin University, Changchun 130000, China
| | - Siyu Yang
- Department of Gynecological Oncology, The First Hospital of Jilin University, Changchun 130000, China
| | - Mingyue Zhang
- Department of Gynecological Oncology, The First Hospital of Jilin University, Changchun 130000, China
| | - Ying Yue
- Department of Gynecological Oncology, The First Hospital of Jilin University, Changchun 130000, China.
| |
Collapse
|
37
|
Itoh Y, Golden LC, Itoh N, Matsukawa MA, Ren E, Tse V, Arnold AP, Voskuhl RR. The X-linked histone demethylase Kdm6a in CD4+ T lymphocytes modulates autoimmunity. J Clin Invest 2019; 129:3852-3863. [PMID: 31403472 DOI: 10.1172/jci126250] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/11/2019] [Indexed: 01/05/2023] Open
Abstract
Multiple sclerosis (MS) is a putative T cell-mediated autoimmune disease. As with many autoimmune diseases, females are more susceptible than males. Sexual dimorphisms may be due to differences in sex hormones, sex chromosomes, or both. Regarding sex chromosome genes, a small percentage of X chromosome genes escape X inactivation and have higher expression in females (XX) compared with males (XY). Here, high-throughput gene expression analysis in CD4+ T cells showed that the top sexually dimorphic gene was Kdm6a, a histone demethylase on the X chromosome. There was higher expression of Kdm6a in females compared with males in humans and mice, and the four core genotypes (FCG) mouse model showed higher expression in XX compared with XY. Deletion of Kdm6a in CD4+ T cells ameliorated clinical disease and reduced neuropathology in the classic CD4+ T cell-mediated autoimmune disease experimental autoimmune encephalomyelitis (EAE). Global transcriptome analysis in CD4+ T cells from EAE mice with a specific deletion of Kdm6a showed upregulation of Th2 and Th1 activation pathways and downregulation of neuroinflammation signaling pathways. Together, these data demonstrate that the X escapee Kdm6a regulates multiple immune response genes, providing a mechanism for sex differences in autoimmune disease susceptibility.
Collapse
Affiliation(s)
- Yuichiro Itoh
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Lisa C Golden
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Noriko Itoh
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Macy Akiyo Matsukawa
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Emily Ren
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Vincent Tse
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Arthur P Arnold
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, California, USA
| | - Rhonda R Voskuhl
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| |
Collapse
|
38
|
Stolerman ES, Francisco E, Stallworth JL, Jones JR, Monaghan KG, Keller-Ramey J, Person R, Wentzensen IM, McWalter K, Keren B, Heron B, Nava C, Heron D, Kim K, Burton B, Al-Musafri F, O'Grady L, Sahai I, Escobar LF, Meuwissen M, Reyniers E, Kooy F, Lacassie Y, Gunay-Aygun M, Schatz KS, Hochstenbach R, Zwijnenburg PJG, Waisfisz Q, van Slegtenhorst M, Mancini GMS, Louie RJ. Genetic variants in the KDM6B gene are associated with neurodevelopmental delays and dysmorphic features. Am J Med Genet A 2019; 179:1276-1286. [PMID: 31124279 DOI: 10.1002/ajmg.a.61173] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/29/2022]
Abstract
Lysine-specific demethylase 6B (KDM6B) demethylates trimethylated lysine-27 on histone H3. The methylation and demethylation of histone proteins affects gene expression during development. Pathogenic alterations in histone lysine methylation and demethylation genes have been associated with multiple neurodevelopmental disorders. We have identified a number of de novo alterations in the KDM6B gene via whole exome sequencing (WES) in a cohort of 12 unrelated patients with developmental delay, intellectual disability, dysmorphic facial features, and other clinical findings. Our findings will allow for further investigation in to the role of the KDM6B gene in human neurodevelopmental disorders.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Boris Keren
- APHP, Hôpital Armand Trousseau, Paris, France
| | | | | | | | - Katherine Kim
- Division of Genetics, Birth Defects and Metabolism, Ann and Robert H. Lurie Children's Hospital, Chicago, Illinois.,Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Barbara Burton
- Division of Genetics, Birth Defects and Metabolism, Ann and Robert H. Lurie Children's Hospital, Chicago, Illinois.,Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | | | | | - Luis F Escobar
- Medical Genetics and Neurodevelopmental Center, Peyton Manning Children's, Hospital at St. Vincent, Indianapolis, Indiana
| | | | - Edwin Reyniers
- Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Frank Kooy
- Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Yves Lacassie
- Children's Hospital New Orleans, New Orleans, Louisiana.,Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Meral Gunay-Aygun
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | - Ron Hochstenbach
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | | |
Collapse
|
39
|
Wu B, Pan X, Chen X, Chen M, Shi K, Xu J, Zheng J, Niu T, Chen C, Shuai X, Liu Y. Epigenetic drug library screening identified an LSD1 inhibitor to target UTX-deficient cells for differentiation therapy. Signal Transduct Target Ther 2019; 4:11. [PMID: 31044091 PMCID: PMC6483994 DOI: 10.1038/s41392-019-0040-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 02/22/2019] [Accepted: 02/24/2019] [Indexed: 02/05/2023] Open
Abstract
UTX (also known as KDM6A), a histone 3 lysine 27 demethylase, is among the most frequently mutated epigenetic regulators in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Recent studies have suggested that UTX mutations promote MDS and AML by blocking the differentiation of hematopoietic stem and progenitor cells (HSPCs). Here, we performed an epigenetic drug library screening for small molecules able to release the differentiation block on HSPCs induced by UTX deficiency. We found that SP2509, a selective inhibitor of LSD1, specifically promoted the differentiation of Utx-null HSPCs while sparing wild-type HSPCs. Transcriptome profiling showed that Utx loss reduced the expression of differentiation-related and tumor suppressor genes, correlating with their potential roles in HSPC self-renewal and leukemogenesis. In contrast, SP2509 treatment reversed these changes in gene expression in Utx-null HSPCs. Accordingly, Utx loss decreased H3K4 methylation level probably through the COMPASS-like complex, while LSD1 inhibition by SP2509 partially reversed the reduction of H3K4 methylation in Utx-deficient HSPCs. Further, SP2509 promoted the differentiation of Utx-null AML cells in vitro and in vivo and, therefore, extended the survival of these leukemic mice. Thus, our study identified a novel strategy to specifically target both premalignant and malignant cells with Utx deficiency for differentiation therapy and provided insights into the molecular mechanisms underlying the role of Utx in regulating HSPCs and related diseases.
Collapse
Affiliation(s)
- Baohong Wu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xiangyu Pan
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xuelan Chen
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Mei Chen
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Kaidou Shi
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Jing Xu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Jianan Zheng
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Ting Niu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Chong Chen
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xiao Shuai
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Yu Liu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| |
Collapse
|
40
|
Laugesen A, Højfeldt JW, Helin K. Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation. Mol Cell 2019; 74:8-18. [PMID: 30951652 PMCID: PMC6452890 DOI: 10.1016/j.molcel.2019.03.011] [Citation(s) in RCA: 390] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/12/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
The polycomb repressive complex 2 (PRC2) is a chromatin-associated methyltransferase catalyzing mono-, di-, and trimethylation of lysine 27 on histone H3 (H3K27). This activity is required for normal organismal development and maintenance of gene expression patterns to uphold cell identity. PRC2 function is often deregulated in disease and is a promising candidate for therapeutic targeting in cancer. In this review, we discuss the molecular mechanisms proposed to take part in modulating PRC2 recruitment and shaping H3K27 methylation patterns across the genome. This includes consideration of factors influencing PRC2 residence time on chromatin and PRC2 catalytic activity with a focus on the mechanisms giving rise to regional preferences and differential deposition of H3K27 methylation. We further discuss existing evidence for functional diversity between distinct subsets of PRC2 complexes with the aim of extracting key concepts and highlighting major open questions toward a more complete understanding of PRC2 function.
Collapse
Affiliation(s)
- Anne Laugesen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Jonas Westergaard Højfeldt
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
41
|
Bosselut R. Control of Intra-Thymic αβ T Cell Selection and Maturation by H3K27 Methylation and Demethylation. Front Immunol 2019; 10:688. [PMID: 31001282 PMCID: PMC6456692 DOI: 10.3389/fimmu.2019.00688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/13/2019] [Indexed: 12/25/2022] Open
Abstract
In addition to transcription factor binding, the dynamics of DNA modifications (methylation) and chromatin structure are essential contributors to the control of transcription in eukaryotes. Research in the past few years has emphasized the importance of histone H3 methylation at lysine 27 for lineage specific gene repression, demonstrated that deposition of this mark at specific genes is subject to differentiation-induced changes during development, and identified enzymatic activities, methyl transferases and demethylases, that control these changes. The present review discusses the importance of these mechanisms during intrathymic αβ T cell selection and late differentiation.
Collapse
Affiliation(s)
- Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
42
|
Swahari V, West AE. Histone demethylases in neuronal differentiation, plasticity, and disease. Curr Opin Neurobiol 2019; 59:9-15. [PMID: 30878844 DOI: 10.1016/j.conb.2019.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/14/2019] [Indexed: 12/29/2022]
Abstract
For more than 40 years after its discovery, histone methylation was thought to be largely irreversible. However, the first histone demethylase (HDM) was identified in 2004, challenging this notion. Since that time, more than 20 HDMs have been identified and characterized, and many have been shown to have critical roles in organismal development, cell fate, and disease. Here, we highlight some of the recent advances in our understanding of the function of HDMs in the context of neuronal development, plasticity, and disease. We focus, in particular, on molecular genetic studies of LSD1, Kdm6b, and Kdm5c that have elucidated both enzymatic and non-enzymatic gene regulatory functions of these HDMs in neurons.
Collapse
Affiliation(s)
- Vijay Swahari
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anne E West
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
| |
Collapse
|
43
|
Comprehensive profiling of JMJD3 in gastric cancer and its influence on patient survival. Sci Rep 2019; 9:868. [PMID: 30696880 PMCID: PMC6351656 DOI: 10.1038/s41598-018-37340-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/04/2018] [Indexed: 01/19/2023] Open
Abstract
Histone methylation is thought to control the regulation of genetic program and the dysregulation of it has been found to be closely associated with cancer. JMJD3 has been identified as an H3K27 demethylase and its role in cancer development is context specific. The role of JMJD3 in gastric cancer (GC) has not been examined. In this study, JMJD3 expression was determined. The prognostic significance of JMJD3 and its association with clinical parameters were evaluated. JMJD3 dysregulation mechanism and targets were analyzed. The effect of JMJD3 mutation was determined by functional study. Results showed that JMJD3 was overexpressed in different patient cohorts and also by bioinformatics analysis. High JMJD3 expression was correlated with shortened overall survival in patients with GC and was an independent prognosis predictor. Genetic aberration and DNA methylation might be involved in the deregulation of JMJD3 in GC. Downstream network of JMJD3 was analyzed and several novel potential targets were identified. Furthermore, functional study discovered that both demethylase-dependent and demethylase-independent mechanisms were involved in the oncogenic role of JMJD3 in GC. Importantly, histone demethylase inhibitor GSK-J4 could reverse the oncogenic effect of JMJD3 overexpression. In conclusion, our study report the oncogenic role of JMJD3 in GC for the first time. JMJD3 might serve as an important epigenetic therapeutic target and/or prognostic predictor in GC.
Collapse
|
44
|
Zhou C, Wang Y, Zhang J, Su J, An Q, Liu X, Zhang M, Wang Y, Liu J, Zhang Y. H3K27me3 is an epigenetic barrier while KDM6A overexpression improves nuclear reprogramming efficiency. FASEB J 2019; 33:4638-4652. [PMID: 30673507 DOI: 10.1096/fj.201801887r] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aberrant epigenetic reprogramming is a major factor of developmental failure of cloned embryos. Histone H3 lysine 27 trimethylation (H3K27me3), a histone mark for transcriptional repression, plays important roles in mammalian embryonic development and induced pluripotent stem cell (iPSC) generation. The global loss of H3K27me3 marks may facilitate iPSC generation in mice and humans. However, the H3K27me3 level and its role in bovine somatic cell nuclear transfer (SCNT) reprogramming remain poorly understood. Here, we show that SCNT embryos exhibit global H3K27me3 hypermethylation from the 2- to 8-cell stage and that its removal by ectopically expressed H3K27me3 lysine demethylase (KDM)6A greatly improves nuclear reprogramming efficiency. In contrast, H3K27me3 reduction by H3K27me3 methylase enhancer of zeste 2 polycomb repressive complex knockdown or donor cell treatment with the enhancer of zeste 2 polycomb repressive complex-selective inhibitor GSK343 suppressed blastocyst formation by SCNT embryos. KDM6A overexpression enhanced the transcription of genes involved in cell adhesion and cellular metabolism and X-linked genes. Furthermore, we identified methyl-CpG-binding domain protein 3-like 2, which was reactivated by KDM6A, as a factor that is required for effective reprogramming in bovines. These results show that H3K27me3 functions as an epigenetic barrier and that KDM6A overexpression improves SCNT efficiency by facilitating transcriptional reprogramming.-Zhou, C., Wang, Y., Zhang, J., Su, J., An, Q., Liu, X., Zhang, M., Wang, Y., Liu, J., Zhang, Y. H3K27me3 is an epigenetic barrier while KDM6A overexpression improves nuclear reprogramming efficiency.
Collapse
Affiliation(s)
- Chuan Zhou
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yizhi Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jianmin Su
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Quanli An
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xin Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Min Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yongsheng Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| |
Collapse
|
45
|
Lee HK, Ismail T, Kim C, Kim Y, Park JW, Kwon OS, Kang BS, Lee DS, Kwon T, Park TJ, Lee HS. Lysine demethylase 3a in craniofacial and neural development during Xenopus embryogenesis. Int J Mol Med 2018; 43:1105-1113. [PMID: 30569092 DOI: 10.3892/ijmm.2018.4024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/05/2018] [Indexed: 11/05/2022] Open
Abstract
Epigenetic modifier lysine demethylase 3a (Kdm3a) specifically demethylates mono‑ and di‑methylated ninth lysine of histone 3 and belongs to the Jumonji domain‑containing group of demethylases. Kdm3a serves roles during various biological and pathophysiological processes, including spermatogenesis and metabolism, determination of sex, androgen receptor‑mediated transcription and embryonic carcinoma cell differentiation. In the present study, physiological functions of Kdm3a were evaluated during embryogenesis of Xenopus laevis. Spatiotemporal expression pattern indicated that kdm3a exhibited its expression from early embryonic stages until tadpole stage, however considerable increase of kdm3a expression was observed during the neurula stage of Xenopus development. Depleting kdm3a using kdm3a antisense morpholino oligonucleotides induced anomalies, including head deformities, small‑sized eyes and abnormal pigmentation. Whole‑mount in situ hybridization results demonstrated that kdm3a knockdown was associated with defects in neural crest migration. Further, quantitative polymerase chain reaction revealed abnormal expression of neural markers in kdm3a morphants. RNA sequencing of kdm3a morphants indicated that kdm3a was implicated in mesoderm formation, cell adhesion and metabolic processes of embryonic development. In conclusion, the results of the present study indicated that Kdm3a may serve a role in neural development during Xenopus embryogenesis and may be targeted for treatment of developmental disorders. Further investigation is required to elucidate the molecular mechanism underlying the regulation of neural development by Kdm3a.
Collapse
Affiliation(s)
- Hyun-Kyung Lee
- Cell and Matrix Research Institute, Kyungpook National University‑Center for Nonlinear Dynamics, School of Life Sciences, Brain Korea 21 Plus Kyungpook National University Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Tayaba Ismail
- Cell and Matrix Research Institute, Kyungpook National University‑Center for Nonlinear Dynamics, School of Life Sciences, Brain Korea 21 Plus Kyungpook National University Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Chowon Kim
- Cell and Matrix Research Institute, Kyungpook National University‑Center for Nonlinear Dynamics, School of Life Sciences, Brain Korea 21 Plus Kyungpook National University Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Youni Kim
- Cell and Matrix Research Institute, Kyungpook National University‑Center for Nonlinear Dynamics, School of Life Sciences, Brain Korea 21 Plus Kyungpook National University Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeen-Woo Park
- Cell and Matrix Research Institute, Kyungpook National University‑Center for Nonlinear Dynamics, School of Life Sciences, Brain Korea 21 Plus Kyungpook National University Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Oh-Shin Kwon
- Cell and Matrix Research Institute, Kyungpook National University‑Center for Nonlinear Dynamics, School of Life Sciences, Brain Korea 21 Plus Kyungpook National University Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Beom-Sik Kang
- Cell and Matrix Research Institute, Kyungpook National University‑Center for Nonlinear Dynamics, School of Life Sciences, Brain Korea 21 Plus Kyungpook National University Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Dong-Seok Lee
- Cell and Matrix Research Institute, Kyungpook National University‑Center for Nonlinear Dynamics, School of Life Sciences, Brain Korea 21 Plus Kyungpook National University Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Taejoon Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Tae Joo Park
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyun-Shik Lee
- Cell and Matrix Research Institute, Kyungpook National University‑Center for Nonlinear Dynamics, School of Life Sciences, Brain Korea 21 Plus Kyungpook National University Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| |
Collapse
|
46
|
Jones SE, Olsen L, Dorosz J, Seger ST, Andersson JL, Kristensen LH, Gajhede M. Peptides Derived from Histone 3 and Modified at Position 18 Inhibit Histone Demethylase KDM6 Enzymes. Chembiochem 2018; 19:1817-1822. [PMID: 29878441 DOI: 10.1002/cbic.201800185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Indexed: 11/12/2022]
Abstract
The KDM6 subfamily of histone lysine demethylases has recently been implicated as a putative target in the treatment of a number of diseases; this makes the availability of potent and selective inhibitors important. Due to high sequence similarity of the catalytic domain of Jumonji C histone demethylases, the development of small-molecule, family-specific inhibitors has, however, proven challenging. One approach to achieve the selective inhibition of these enzymes is the use of peptides derived from the substrate, the histone 3 C terminus. Here we used computational methods to optimize such inhibitors of the KDM6 family. Through natural amino acid substitution, it is shown that a K18I variant of a histone H3 derived peptide significantly increases affinity towards the KDM6 enzymes. The crystal structure of KDM6B in complex with a histone 3 derived K18I peptide reveals a tighter fit of the isoleucine side chain, compared with that of the arginine. As a consequence, the peptide R17 residue also has increased hydrophilic interactions. These interactions of the optimized peptide are likely to be responsible for the increased affinity to the KDM6 enzymes.
Collapse
Affiliation(s)
- Sarah E Jones
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Lars Olsen
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Jerzy Dorosz
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Signe T Seger
- Novo Nordisk Pharmatech, Københavnsvej 216, 4600, Køge, Denmark
| | - Jan L Andersson
- Nuevolution AB (publ.), Rønnegade 8, 2100, Copenhagen, Denmark
| | | | - Michael Gajhede
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| |
Collapse
|
47
|
Tran KA, Dillingham CM, Sridharan R. The role of α-ketoglutarate-dependent proteins in pluripotency acquisition and maintenance. J Biol Chem 2018; 294:5408-5419. [PMID: 30181211 DOI: 10.1074/jbc.tm118.000831] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
α-Ketoglutarate is an important metabolic intermediate that acts as a cofactor for several chromatin-modifying enzymes, including histone demethylases and the Tet family of enzymes that are involved in DNA demethylation. In this review, we focus on the function and genomic localization of these α-ketoglutarate-dependent enzymes in the maintenance of pluripotency during cellular reprogramming to induced pluripotent stem cells and in disruption of pluripotency during in vitro differentiation. The enzymatic function of many of these α-ketoglutarate-dependent proteins is required for pluripotency acquisition and maintenance. A better understanding of their specific function will be essential in furthering our knowledge of pluripotency.
Collapse
Affiliation(s)
- Khoa A Tran
- From the Wisconsin Institute for Discovery.,Molecular and Cellular Pharmacology Program, and
| | - Caleb M Dillingham
- From the Wisconsin Institute for Discovery.,Cellular and Molecular Pathology Program, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - Rupa Sridharan
- From the Wisconsin Institute for Discovery, .,Department of Cell and Regenerative Biology
| |
Collapse
|
48
|
Filipp FV. Crosstalk between epigenetics and metabolism-Yin and Yang of histone demethylases and methyltransferases in cancer. Brief Funct Genomics 2018; 16:320-325. [PMID: 28369194 PMCID: PMC5860014 DOI: 10.1093/bfgp/elx001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Histone methylation is an epigenetic modification of chromatin undergoing dynamic changes and balancing tissue-specific demands of proliferation and differentiation. In cancer, aberrant histone methylation can facilitate oncogenic and tumor suppression programs by modulating gene expression. Histone remodelers such as lysine methyltransferases and lysine demethylases are seemingly opposite or contrary forces but may be part of an interconnected network complementing each other. We identify several layers of molecular communication where epigenetic master regulators engage in crosstalk between tumor metabolism and histone remodeling. Epigenetic master regulators have the ability to cooperate with members of the transcriptional machinery, DNA methyltransferases, as well as other histone modifiers. High-throughput sequencing and omics data in combination with cancer systems biology analysis have the power to prioritize regulatory events epigenome-wide.
Collapse
|
49
|
|
50
|
Gozdecka M, Meduri E, Mazan M, Tzelepis K, Dudek M, Knights AJ, Pardo M, Yu L, Choudhary JS, Metzakopian E, Iyer V, Yun H, Park N, Varela I, Bautista R, Collord G, Dovey O, Garyfallos DA, De Braekeleer E, Kondo S, Cooper J, Göttgens B, Bullinger L, Northcott PA, Adams D, Vassiliou GS, Huntly BJP. UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs. Nat Genet 2018; 50:883-894. [PMID: 29736013 PMCID: PMC6029661 DOI: 10.1038/s41588-018-0114-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/19/2018] [Indexed: 01/22/2023]
Abstract
The histone H3 Lys27-specific demethylase UTX (or KDM6A) is targeted by loss-of-function mutations in multiple cancers. Here, we demonstrate that UTX suppresses myeloid leukemogenesis through noncatalytic functions, a property shared with its catalytically inactive Y-chromosome paralog, UTY (or KDM6C). In keeping with this, we demonstrate concomitant loss/mutation of KDM6A (UTX) and UTY in multiple human cancers. Mechanistically, global genomic profiling showed only minor changes in H3K27me3 but significant and bidirectional alterations in H3K27ac and chromatin accessibility; a predominant loss of H3K4me1 modifications; alterations in ETS and GATA-factor binding; and altered gene expression after Utx loss. By integrating proteomic and genomic analyses, we link these changes to UTX regulation of ATP-dependent chromatin remodeling, coordination of the COMPASS complex and enhanced pioneering activity of ETS factors during evolution to AML. Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs.
Collapse
Affiliation(s)
- Malgorzata Gozdecka
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Eshwar Meduri
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Milena Mazan
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | | | - Monika Dudek
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew J Knights
- Genomics of Gene Regulation, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Mercedes Pardo
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Lu Yu
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jyoti S Choudhary
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Vivek Iyer
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Haiyang Yun
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Naomi Park
- Sequencing Research Group, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Ruben Bautista
- New Pipeline Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Grace Collord
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Oliver Dovey
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | - Saki Kondo
- Laboratory of Molecular Genetics, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Jonathan Cooper
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Berthold Göttgens
- Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council, Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Lars Bullinger
- Department of Internal Medicine III, Ulm University Medical Centre, Ulm, Germany
- Medical Department, Division of Hematology, Oncology and Tumour Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - David Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK.
| | - Brian J P Huntly
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
- Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council, Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK.
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK.
| |
Collapse
|