1
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Owens MC, Yanas A, Liu KF. Sex chromosome-encoded protein homologs: current progress and open questions. Nat Struct Mol Biol 2024; 31:1156-1166. [PMID: 39123067 DOI: 10.1038/s41594-024-01362-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/28/2024] [Indexed: 08/12/2024]
Abstract
The complexity of biological sex differences is markedly evident in human physiology and pathology. Although many of these differences can be ascribed to the expression of sex hormones, another contributor to sex differences lies in the sex chromosomes beyond their role in sex determination. Although largely nonhomologous, the human sex chromosomes express seventeen pairs of homologous genes, referred to as the 'X-Y pairs.' The X chromosome-encoded homologs of these Y-encoded proteins are crucial players in several cellular processes, and their dysregulation frequently results in disease development. Many diseases related to these X-encoded homologs present with sex-biased incidence or severity. By contrast, comparatively little is known about the differential functions of the Y-linked homologs. Here, we summarize and discuss the current understanding of five of these X-Y paired proteins, with recent evidence of differential functions and of having a potential link to sex biases in disease, highlighting how amino acid-level sequence differences may differentiate their functions and contribute to sex biases in human disease.
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Affiliation(s)
- Michael C Owens
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Amber Yanas
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Wu J, Jiang Y, Zhang Q, Mao X, Wu T, Hao M, Zhang S, Meng Y, Wan X, Qiu L, Han J. KDM6A-SND1 interaction maintains genomic stability by protecting the nascent DNA and contributes to cancer chemoresistance. Nucleic Acids Res 2024; 52:7665-7686. [PMID: 38850159 PMCID: PMC11260493 DOI: 10.1093/nar/gkae487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 06/10/2024] Open
Abstract
Genomic instability is one of the hallmarks of cancer. While loss of histone demethylase KDM6A increases the risk of tumorigenesis, its specific role in maintaining genomic stability remains poorly understood. Here, we propose a mechanism in which KDM6A maintains genomic stability independently on its demethylase activity. This occurs through its interaction with SND1, resulting in the establishment of a protective chromatin state that prevents replication fork collapse by recruiting of RPA and Ku70 to nascent DNA strand. Notably, KDM6A-SND1 interaction is up-regulated by KDM6A SUMOylation, while KDM6AK90A mutation almost abolish the interaction. Loss of KDM6A or SND1 leads to increased enrichment of H3K9ac and H4K8ac but attenuates the enrichment of Ku70 and H3K4me3 at nascent DNA strand. This subsequently results in enhanced cellular sensitivity to genotoxins and genomic instability. Consistent with these findings, knockdown of KDM6A and SND1 in esophageal squamous cell carcinoma (ESCC) cells increases genotoxin sensitivity. Intriguingly, KDM6A H101D & P110S, N1156T and D1216N mutations identified in ESCC patients promote genotoxin resistance via increased SND1 association. Our finding provides novel insights into the pivotal role of KDM6A-SND1 in genomic stability and chemoresistance, implying that targeting KDM6A and/or its interaction with SND1 may be a promising strategy to overcome the chemoresistance.
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Affiliation(s)
- Jian Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yixin Jiang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qin Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaobing Mao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tong Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mengqiu Hao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Su Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Meng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaowen Wan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lei Qiu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Junhong Han
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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3
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Zhang W, Li Z, Wang X, Sun T. Phase separation is regulated by post-translational modifications and participates in the developments of human diseases. Heliyon 2024; 10:e34035. [PMID: 39071719 PMCID: PMC11279762 DOI: 10.1016/j.heliyon.2024.e34035] [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: 02/28/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) of intracellular proteins has emerged as a hot research topic in recent years. Membrane-less and liquid-like condensates provide dense spaces that ensure cells to high efficiently regulate genes transcription and rapidly respond to burst changes from the environment. The fomation and activity of LLPS are not only modulated by the cytosol conditions including but not limited to salt concentration and temperture. Interestingly, recent studies have shown that phase separation is also regulated by various post-translational modifications (PTMs) through modulating proteins multivalency, such as solubility and charge interactions. The regulation mechanism is crucial for normal functioning of cells, as aberrant protein aggregates are often closely related with the occurrence and development of human diseases including cancer and nurodegenerative diseases. Therefore, studying phase separation in the perspective of protein PTMs has long-term significance for human health. In this review, we summarized the properties and cellular physiological functions of LLPS, particularly its relationships with PTMs in human diseases according to recent researches.
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Affiliation(s)
- Weibo Zhang
- Faculty of Health Sciences Building University of Macau E12 Avenida da Universidade, Taipa, Macau, China
| | - Zhengfeng Li
- Faculty of Health Sciences Building University of Macau E12 Avenida da Universidade, Taipa, Macau, China
| | - Xianju Wang
- Faculty of Health Sciences Building University of Macau E12 Avenida da Universidade, Taipa, Macau, China
| | - Ting Sun
- Faculty of Health Sciences Building University of Macau E12 Avenida da Universidade, Taipa, Macau, China
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4
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Dakal TC, Dhabhai B, Pant A, Moar K, Chaudhary K, Yadav V, Ranga V, Sharma NK, Kumar A, Maurya PK, Maciaczyk J, Schmidt‐Wolf IGH, Sharma A. Oncogenes and tumor suppressor genes: functions and roles in cancers. MedComm (Beijing) 2024; 5:e582. [PMID: 38827026 PMCID: PMC11141506 DOI: 10.1002/mco2.582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/21/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Cancer, being the most formidable ailment, has had a profound impact on the human health. The disease is primarily associated with genetic mutations that impact oncogenes and tumor suppressor genes (TSGs). Recently, growing evidence have shown that X-linked TSGs have specific role in cancer progression and metastasis as well. Interestingly, our genome harbors around substantial portion of genes that function as tumor suppressors, and the X chromosome alone harbors a considerable number of TSGs. The scenario becomes even more compelling as X-linked TSGs are adaptive to key epigenetic processes such as X chromosome inactivation. Therefore, delineating the new paradigm related to X-linked TSGs, for instance, their crosstalk with autosome and involvement in cancer initiation, progression, and metastasis becomes utmost importance. Considering this, herein, we present a comprehensive discussion of X-linked TSG dysregulation in various cancers as a consequence of genetic variations and epigenetic alterations. In addition, the dynamic role of X-linked TSGs in sex chromosome-autosome crosstalk in cancer genome remodeling is being explored thoroughly. Besides, the functional roles of ncRNAs, role of X-linked TSG in immunomodulation and in gender-based cancer disparities has also been highlighted. Overall, the focal idea of the present article is to recapitulate the findings on X-linked TSG regulation in the cancer landscape and to redefine their role toward improving cancer treatment strategies.
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Affiliation(s)
- Tikam Chand Dakal
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Bhanupriya Dhabhai
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Anuja Pant
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kareena Moar
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kanika Chaudhary
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vikas Yadav
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vipin Ranga
- Dearptment of Agricultural BiotechnologyDBT‐NECAB, Assam Agricultural UniversityJorhatAssamIndia
| | | | - Abhishek Kumar
- Manipal Academy of Higher EducationManipalKarnatakaIndia
- Institute of Bioinformatics, International Technology ParkBangaloreIndia
| | - Pawan Kumar Maurya
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Jarek Maciaczyk
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
| | - Ingo G. H. Schmidt‐Wolf
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
| | - Amit Sharma
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
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5
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Jamali M, Barar E, Shi J. Unveiling the Molecular Landscape of Pancreatic Ductal Adenocarcinoma: Insights into the Role of the COMPASS-like Complex. Int J Mol Sci 2024; 25:5069. [PMID: 38791111 PMCID: PMC11121229 DOI: 10.3390/ijms25105069] [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: 04/03/2024] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is poised to become the second leading cause of cancer-related death by 2030, necessitating innovative therapeutic strategies. Genetic and epigenetic alterations, including those involving the COMPASS-like complex genes, have emerged as critical drivers of PDAC progression. This review explores the genetic and epigenetic landscape of PDAC, focusing on the role of the COMPASS-like complex in regulating chromatin accessibility and gene expression. Specifically, we delve into the functions of key components such as KDM6A, KMT2D, KMT2C, KMT2A, and KMT2B, highlighting their significance as potential therapeutic targets. Furthermore, we discuss the implications of these findings for developing novel treatment modalities for PDAC.
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Affiliation(s)
- Marzieh Jamali
- Department of Pathology & Clinical Labs, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erfaneh Barar
- Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 1416634793, Iran
| | - Jiaqi Shi
- Department of Pathology & Clinical Labs, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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6
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Dupéré-Richer D, Riva A, Maji S, Barwick BG, Román HC, Sobh A, Quickstad G, Li J, De U, Piper C, Kulis M, Ezponda T, Martin-Subero JI, Tonon G, Zhang W, Mitsiades CS, Boise LH, Bennett RL, Licht JD. KDM6A Regulates Immune Response Genes in Multiple Myeloma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579179. [PMID: 38405853 PMCID: PMC10888870 DOI: 10.1101/2024.02.12.579179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The histone H3K27 demethylase KDM6A is a tumor suppressor in multiple cancers, including multiple myeloma (MM). We created isogenic MM cells disrupted for KDM6A and tagged the endogenous protein to facilitate genome wide studies. KDM6A binds genes associated with immune recognition and cytokine signaling. Most importantly, KDM6A binds and activates NLRC5 and CIITA encoding regulators of Major Histocompatibility Complex (MHC) genes. Patient data indicate that NLRC5 and CIITA, are downregulated in MM with low KDM6A expression. Chromatin analysis shows that KDM6A binds poised and active enhancers and KDM6A loss led to decreased H3K27ac at enhancers, increased H3K27me3 levels in body of genes bound by KDM6A and decreased gene expression. Reestablishing histone acetylation with an HDAC3 inhibitor leads to upregulation of MHC expression, offering a strategy to restore immunogenicity of KDM6A deficient tumors. Loss of Kdm6a in murine RAS-transformed fibroblasts led to increased growth in vivo associated with decreased T cell infiltration. Statement of significance We show that KDM6A participates in immune recognition of myeloma tumor cells by directly regulating the expression of the master regulators of MHC-I and II, NLRC5 and CIITA. The expression of these regulators can by rescued by the HDAC3 inhibitors in KDM6A-null cell lines.
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7
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Walters BW, Rainsford SR, Heuer RA, Dias N, Huang X, de Rooij D, Lesch BJ. KDM6A/UTX promotes spermatogenic gene expression across generations and is not required for male fertility†. Biol Reprod 2024; 110:391-407. [PMID: 37861693 DOI: 10.1093/biolre/ioad141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 10/21/2023] Open
Abstract
Paternal chromatin undergoes extensive structural and epigenetic changes during mammalian spermatogenesis, producing sperm with an epigenome optimized for the transition to embryogenesis. Lysine demethylase 6a (KDM6A, also called UTX) promotes gene activation in part via demethylation of H3K27me3, a developmentally important repressive modification abundant throughout the epigenome of spermatogenic cells and sperm. We previously demonstrated increased cancer risk in genetically wild-type mice derived from a paternal germ line lacking Kdm6a (Kdm6a cKO), indicating a role for KDM6A in regulating heritable epigenetic states. However, the regulatory function of KDM6A during spermatogenesis is not known. Here, we show that Kdm6a is transiently expressed in spermatogenesis, with RNA and protein expression largely limited to late spermatogonia and early meiotic prophase. Kdm6a cKO males do not have defects in fertility or the overall progression of spermatogenesis. However, hundreds of genes are deregulated upon loss of Kdm6a in spermatogenic cells, with a strong bias toward downregulation coinciding with the time when Kdm6a is expressed. Misregulated genes encode factors involved in chromatin organization and regulation of repetitive elements, and a subset of these genes was persistently deregulated in the male germ line across two generations of offspring of Kdm6a cKO males. Genome-wide epigenetic profiling revealed broadening of H3K27me3 peaks in differentiating spermatogonia of Kdm6a cKO mice, suggesting that KDM6A demarcates H3K27me3 domains in the male germ line. Our findings highlight KDM6A as a transcriptional activator in the mammalian male germ line that is dispensable for spermatogenesis but important for safeguarding gene regulatory state intergenerationally.
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Affiliation(s)
| | | | - Rachel A Heuer
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Nicolas Dias
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Xiaofang Huang
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Dirk de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bluma J Lesch
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
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8
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Isobe T, Kucinski I, Barile M, Wang X, Hannah R, Bastos HP, Chabra S, Vijayabaskar MS, Sturgess KHM, Williams MJ, Giotopoulos G, Marando L, Li J, Rak J, Gozdecka M, Prins D, Shepherd MS, Watcham S, Green AR, Kent DG, Vassiliou GS, Huntly BJP, Wilson NK, Göttgens B. Preleukemic single-cell landscapes reveal mutation-specific mechanisms and gene programs predictive of AML patient outcomes. CELL GENOMICS 2023; 3:100426. [PMID: 38116120 PMCID: PMC10726426 DOI: 10.1016/j.xgen.2023.100426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 12/21/2023]
Abstract
Acute myeloid leukemia (AML) and myeloid neoplasms develop through acquisition of somatic mutations that confer mutation-specific fitness advantages to hematopoietic stem and progenitor cells. However, our understanding of mutational effects remains limited to the resolution attainable within immunophenotypically and clinically accessible bulk cell populations. To decipher heterogeneous cellular fitness to preleukemic mutational perturbations, we performed single-cell RNA sequencing of eight different mouse models with driver mutations of myeloid malignancies, generating 269,048 single-cell profiles. Our analysis infers mutation-driven perturbations in cell abundance, cellular lineage fate, cellular metabolism, and gene expression at the continuous resolution, pinpointing cell populations with transcriptional alterations associated with differentiation bias. We further develop an 11-gene scoring system (Stem11) on the basis of preleukemic transcriptional signatures that predicts AML patient outcomes. Our results demonstrate that a single-cell-resolution deep characterization of preleukemic biology has the potential to enhance our understanding of AML heterogeneity and inform more effective risk stratification strategies.
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Affiliation(s)
- Tomoya Isobe
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Melania Barile
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Xiaonan Wang
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Rebecca Hannah
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Hugo P Bastos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Shirom Chabra
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - M S Vijayabaskar
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Katherine H M Sturgess
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Matthew J Williams
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Juan Li
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Justyna Rak
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK; Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Malgorzata Gozdecka
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK; Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Daniel Prins
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Mairi S Shepherd
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Sam Watcham
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Anthony R Green
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - David G Kent
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK; York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK; Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Brian J P Huntly
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK.
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK.
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9
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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10
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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.
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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
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11
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Li X, Jiang Y, Qian H. Lymphoma dissemination is a pathological hallmark for malignant progression of B-cell lymphoma. Front Immunol 2023; 14:1286411. [PMID: 38077394 PMCID: PMC10703179 DOI: 10.3389/fimmu.2023.1286411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Extranodal lymphoma occurs in one-third of lymphoma patients and is a key indicator of the international prognostic index, associated with unfavorable outcomes. Due to the lack of ideal models, the causes and characteristics of extranodal lymphoma are greatly underexplored. Recently, we observed a high incidence of extranodal lymphoma in two types of mouse models with tropism for the brain and kidneys. These findings prompt us to rethink the pathological progression of lymphoma colonization in lymph nodes and non-lymphoid organs. Nodal lymphoma, primary extranodal lymphoma and secondary extranodal lymphoma should be biologically and clinically distinctive scenarios. Based on the observations in mouse models with extranodal lymphoma, we propose that lymphoma dissemination can be seen as lymphoma losing the ability to home to lymph nodes. The pathological process of nodal lymphoma should be referred to as lymphoma homing to distinguish it from benign hyperplasia. Lymphoma dissemination, defined as a pathological process that lymphoma can occur in almost any part of the body, is a key pathological hallmark for malignant progression of B-cell lymphoma. Reshaping cellular plasticity is a promising strategy to allow transformed cells to homing back to lymph nodes and re-sensitize tumor cells to treatment. From this perspective, we provide new insights into the pathological progression of lymphoma dissemination and its inspiration on therapeutic interventions. We believe that establishing extranodal lymphoma mouse models, identifying molecular mechanism governing lymphoma dissemination, and developing therapies to prevent lymphoma dissemination will become emerging topics for fighting relapsed and refractory lymphoma.
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Affiliation(s)
- Xiaoxi Li
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | | | - Hui Qian
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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12
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Zhang Q, Li H, Chen X, Gu F, Zhang L, Zhang L, Chen T, Chen Q, Meng W, Wu Y, Chang H, Liu T, Chen C, Ma H, Liu Y. Identifying STRN3-RARA as a new fusion gene for acute promyelocytic leukemia. Blood 2023; 142:1494-1499. [PMID: 37624915 DOI: 10.1182/blood.2023020619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Here we report a new fusion gene, STRN3-RARA, in acute promyelocytic leukemia (APL). It cooperates with UTX deficiency to drive full-blown APL in mice. Although STRN3-RARA leukemia quickly relapses after all-trans retinoic acid treatment, it can be restrained by cepharanthine.
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Affiliation(s)
- Qi Zhang
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - He Li
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xuelan Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fan Gu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lanxin Zhang
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lu Zhang
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Tong Chen
- Sichuan Hua Xi Kindstar Medical Diagnostic Centre, Chengdu, Sichuan, China
| | - Qiang Chen
- Sichuan Neo-Life Stem Cell Biotech Inc, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Wentong Meng
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong Chang
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ting Liu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chong Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongbing Ma
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Liu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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13
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Fazazi MR, Ruda GF, Brennan PE, Rangachari M. The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system. Brain Res Bull 2023; 202:110748. [PMID: 37657612 DOI: 10.1016/j.brainresbull.2023.110748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
T cell-driven autoimmune responses are subject to striking sex-dependent effects. While the contributions of sex hormones are well-understood, those of sex chromosomes are meeting with increased appreciation. Here, we outline what is known about the contribution of sex chromosome-linked factors to experimental autoimmune encephalomyelitis (EAE), a mouse model that recapitulates many of the T cell-driven mechanisms of multiple sclerosis (MS) pathology. Particular attention is paid to the KDM family of histone demethylases, several of which - KDM5C, KDM5D and KDM6A - are sex chromosome encoded. Finally, we provide evidence that functional inhibition of KDM5 molecules can suppress interferon (IFN)γ production from murine male effector T cells, and that an increased ratio of inflammatory Kdm6a to immunomodulatory Kdm5c transcript is observed in T helper 17 (Th17) cells from women with the autoimmune disorder ankylosing spondylitis (AS). Histone lysine demethlyases thus represent intriguing targets for the treatment of T cell-driven autoimmune disorders.
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Affiliation(s)
- Mohamed Reda Fazazi
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Gian Filippo Ruda
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Alzheimer's Research UK, Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Manu Rangachari
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada; Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada.
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14
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Duplaquet L, Li Y, Booker MA, Xie Y, Olsen SN, Patel RA, Hong D, Hatton C, Denize T, Walton E, Laimon YN, Li R, Jiang Y, Bronson RT, Southard J, Li S, Signoretti S, Qiu X, Cejas P, Armstrong SA, Long HW, Tolstorukov MY, Haffner MC, Oser MG. KDM6A epigenetically regulates subtype plasticity in small cell lung cancer. Nat Cell Biol 2023; 25:1346-1358. [PMID: 37591951 PMCID: PMC10546329 DOI: 10.1038/s41556-023-01210-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Small cell lung cancer (SCLC) exists broadly in four molecular subtypes: ASCL1, NEUROD1, POU2F3 and Inflammatory. Initially, SCLC subtypes were thought to be mutually exclusive, but recent evidence shows intra-tumoural subtype heterogeneity and plasticity between subtypes. Here, using a CRISPR-based autochthonous SCLC genetically engineered mouse model to study the consequences of KDM6A/UTX inactivation, we show that KDM6A inactivation induced plasticity from ASCL1 to NEUROD1 resulting in SCLC tumours that express both ASCL1 and NEUROD1. Mechanistically, KDM6A normally maintains an active chromatin state that favours the ASCL1 subtype with its loss decreasing H3K4me1 and increasing H3K27me3 at enhancers of neuroendocrine genes leading to a cell state that is primed for ASCL1-to-NEUROD1 subtype switching. This work identifies KDM6A as an epigenetic regulator that controls ASCL1 to NEUROD1 subtype plasticity and provides an autochthonous SCLC genetically engineered mouse model to model ASCL1 and NEUROD1 subtype heterogeneity and plasticity, which is found in 35-40% of human SCLCs.
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Affiliation(s)
- Leslie Duplaquet
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yixiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew A Booker
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Naomi Olsen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Radhika A Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Deli Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charlie Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Walton
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yasmin N Laimon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yijia Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Roderick T Bronson
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Jackson Southard
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuqiang Li
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, MA, USA.
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15
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Rizq O, Mimura N, Oshima M, Momose S, Takayama N, Itokawa N, Koide S, Shibamiya A, Miyamoto-Nagai Y, Rizk M, Nakajima-Takagi Y, Aoyama K, Wang C, Saraya A, Ito R, Seimiya M, Watanabe M, Yamasaki S, Shibata T, Yamaguchi K, Furukawa Y, Chiba T, Sakaida E, Nakaseko C, Tamaru JI, Tai YT, Anderson KC, Honda H, Iwama A. UTX inactivation in germinal center B cells promotes the development of multiple myeloma with extramedullary disease. Leukemia 2023; 37:1895-1907. [PMID: 37198323 PMCID: PMC10457198 DOI: 10.1038/s41375-023-01928-7] [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: 05/25/2022] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
Abstract
UTX/KDM6A, a histone H3K27 demethylase and a key component of the COMPASS complex, is frequently lost or mutated in cancer; however, its tumor suppressor function remains largely uncharacterized in multiple myeloma (MM). Here, we show that the conditional deletion of the X-linked Utx in germinal center (GC) derived cells collaborates with the activating BrafV600E mutation and promotes induction of lethal GC/post-GC B cell malignancies with MM-like plasma cell neoplasms being the most frequent. Mice that developed MM-like neoplasms showed expansion of clonal plasma cells in the bone marrow and extramedullary organs, serum M proteins, and anemia. Add-back of either wild-type UTX or a series of mutants revealed that cIDR domain, that forms phase-separated liquid condensates, is largely responsible for the catalytic activity-independent tumor suppressor function of UTX in MM cells. Utx loss in concert with BrafV600E only slightly induced MM-like profiles of transcriptome, chromatin accessibility, and H3K27 acetylation, however, it allowed plasma cells to gradually undergo full transformation through activation of transcriptional networks specific to MM that induce high levels of Myc expression. Our results reveal a tumor suppressor function of UTX in MM and implicate its insufficiency in the transcriptional reprogramming of plasma cells in the pathogenesis of MM.
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Affiliation(s)
- Ola Rizq
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Hematology, Chiba University Hospital, Chiba, Japan
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Naoya Mimura
- Department of Hematology, Chiba University Hospital, Chiba, Japan.
- Department of Transfusion Medicine and Cell Therapy, Chiba University Hospital, Chiba, Japan.
| | - Motohiko Oshima
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shuji Momose
- Department of Pathology, Saitama Medical Center, Saitama Medical University, Kawagoe, Japan
| | - Naoya Takayama
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naoki Itokawa
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shuhei Koide
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Asuka Shibamiya
- Department of Hematology, Chiba University Hospital, Chiba, Japan
| | | | - Mohamed Rizk
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yaeko Nakajima-Takagi
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazumasa Aoyama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Changshan Wang
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Atsunori Saraya
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ryoji Ito
- Central Institute for Experimental Animals, Kanagawa, Japan
| | - Masanori Seimiya
- Department of Medical Technology and Sciences, School of Health Sciences at Narita, International University of Health and Welfare, Narita, Japan
| | - Mariko Watanabe
- Department of Clinical Laboratory, Chiba University Hospital, Chiba, Japan
| | - Satoshi Yamasaki
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tetsuhiro Chiba
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Emiko Sakaida
- Department of Hematology, Chiba University Hospital, Chiba, Japan
- Department of Transfusion Medicine and Cell Therapy, Chiba University Hospital, Chiba, Japan
| | - Chiaki Nakaseko
- Department of Hematology, International University of Health and Welfare, Narita, Japan
| | - Jun-Ichi Tamaru
- Department of Pathology, Saitama Medical Center, Saitama Medical University, Kawagoe, Japan
| | - Yu-Tzu Tai
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kenneth C Anderson
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Hiroaki Honda
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Atsushi Iwama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
- Laboratoty of Cellular and Molecular Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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16
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Cheng MI, Hong L, Chen B, Chin S, Luthers CR, Bustillos C, Sheikh SZ, Su MA. Hypoxia-sensing by the Histone Demethylase UTX ( KDM6A ) Controls Colitogenic CD4 + T cell Fate and Mucosal Inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550746. [PMID: 37546969 PMCID: PMC10402149 DOI: 10.1101/2023.07.27.550746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Hypoxia is a feature of inflammatory conditions [e.g., inflammatory bowel disease (IBD)] and can exacerbate tissue damage in these diseases. To counteract hypoxia's deleterious effects, adaptive responses have evolved which protect against hypoxia-associated tissue injury. To date, much attention has focused on hypoxia-activated HIF (hypoxia-inducible factor) transcription factors in these responses. However, recent work has identified epigenetic regulators that are also oxygen-sensitive, but their role in adaptation to hypoxic inflammation is currently unclear. Here, we show that the oxygen-sensing epigenetic regulator UTX is a critical modulator of colitis severity. Unlike HIF transcription factors that act on gut epithelial cells, UTX functions in colitis through its effects on immune cells. Hypoxia results in decreased CD4 + T cell IFN-γ production and increased CD4 + regulatory T cells, and these findings are recapitulated by T cell-specific UTX deficiency. Hypoxia impairs the histone demethylase activity of UTX, and loss of UTX function leads to accumulation of repressive H3K27me3 epigenetic marks at IL12/STAT4 pathway genes ( Il12rb2, Tbx21, and Ifng ). In a colitis mouse model, T cell-specific UTX deletion ameliorates colonic inflammation, protects against weight loss, and increases survival. Together these findings implicate UTX's oxygen-sensitive histone demethylase activity in mediating protective, hypoxia-induced pathways in colitis.
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17
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Wei J, Alfajaro MM, Cai WL, Graziano VR, Strine MS, Filler RB, Biering SB, Sarnik SA, Patel S, Menasche BL, Compton SR, Konermann S, Hsu PD, Orchard RC, Yan Q, Wilen CB. The KDM6A-KMT2D-p300 axis regulates susceptibility to diverse coronaviruses by mediating viral receptor expression. PLoS Pathog 2023; 19:e1011351. [PMID: 37410700 PMCID: PMC10325096 DOI: 10.1371/journal.ppat.1011351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/10/2023] [Indexed: 07/08/2023] Open
Abstract
Identification of host determinants of coronavirus infection informs mechanisms of pathogenesis and may provide novel therapeutic targets. Here, we demonstrate that the histone demethylase KDM6A promotes infection of diverse coronaviruses, including SARS-CoV, SARS-CoV-2, MERS-CoV and mouse hepatitis virus (MHV) in a demethylase activity-independent manner. Mechanistic studies reveal that KDM6A promotes viral entry by regulating expression of multiple coronavirus receptors, including ACE2, DPP4 and Ceacam1. Importantly, the TPR domain of KDM6A is required for recruitment of the histone methyltransferase KMT2D and histone deacetylase p300. Together this KDM6A-KMT2D-p300 complex localizes to the proximal and distal enhancers of ACE2 and regulates receptor expression. Notably, small molecule inhibition of p300 catalytic activity abrogates ACE2 and DPP4 expression and confers resistance to all major SARS-CoV-2 variants and MERS-CoV in primary human airway and intestinal epithelial cells. These data highlight the role for KDM6A-KMT2D-p300 complex activities in conferring diverse coronaviruses susceptibility and reveal a potential pan-coronavirus therapeutic target to combat current and emerging coronaviruses. One Sentence Summary: The KDM6A/KMT2D/EP300 axis promotes expression of multiple viral receptors and represents a potential drug target for diverse coronaviruses.
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Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Wesley L. Cai
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Vincent R. Graziano
- Department of Immunology, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Madison S. Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Renata B. Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Sylvia A. Sarnik
- University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Sonam Patel
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Bridget L. Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Susan R. Compton
- Department of Comparative Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Silvana Konermann
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Arc Institute, Palo Alto, California, United States of America
| | - Patrick D. Hsu
- Arc Institute, Palo Alto, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, United States of America
- Center for Computational Biology, University of California, Berkeley, California, United States of America
| | - Robert C. Orchard
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
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18
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Morgan MA, Shilatifard A. Epigenetic moonlighting: Catalytic-independent functions of histone modifiers in regulating transcription. SCIENCE ADVANCES 2023; 9:eadg6593. [PMID: 37083523 PMCID: PMC10121172 DOI: 10.1126/sciadv.adg6593] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The past three decades have yielded a wealth of information regarding the chromatin regulatory mechanisms that control transcription. The "histone code" hypothesis-which posits that distinct combinations of posttranslational histone modifications are "read" by downstream effector proteins to regulate gene expression-has guided chromatin research to uncover fundamental mechanisms relevant to many aspects of biology. However, recent molecular and genetic studies revealed that the function of many histone-modifying enzymes extends independently and beyond their catalytic activities. In this review, we highlight original and recent advances in the understanding of noncatalytic functions of histone modifiers. Many of the histone modifications deposited by these enzymes-previously considered to be required for transcriptional activation-have been demonstrated to be dispensable for gene expression in living organisms. This perspective aims to prompt further examination of these enigmatic chromatin modifications by inspiring studies to define the noncatalytic "epigenetic moonlighting" functions of chromatin-modifying enzymes.
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19
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The X-linked epigenetic regulator UTX controls NK cell-intrinsic sex differences. Nat Immunol 2023; 24:780-791. [PMID: 36928413 DOI: 10.1038/s41590-023-01463-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Viral infection outcomes are sex biased, with males generally more susceptible than females. Paradoxically, the numbers of antiviral natural killer (NK) cells are increased in males. We demonstrate that while numbers of NK cells are increased in male mice, they display decreased effector function compared to females in mice and humans. These differences were not solely dependent on gonadal hormones, because they persisted in gonadectomized mice. Kdm6a (which encodes the protein UTX), an epigenetic regulator that escapes X inactivation, was lower in male NK cells, while NK cell-intrinsic UTX deficiency in female mice increased NK cell numbers and reduced effector responses. Furthermore, mice with NK cell-intrinsic UTX deficiency showed increased lethality to mouse cytomegalovirus. Integrative multi-omics analysis revealed a critical role for UTX in regulating chromatin accessibility and gene expression critical for NK cell homeostasis and effector function. Collectively, these data implicate UTX as a critical molecular determinant of sex differences in NK cells.
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20
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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21
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Zhang L, Chen Y, Li Z, Lin C, Zhang T, Wang G. Development of JmjC-domain-containing histone demethylase (KDM2-7) inhibitors for cancer therapy. Drug Discov Today 2023; 28:103519. [PMID: 36754142 DOI: 10.1016/j.drudis.2023.103519] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/06/2022] [Accepted: 02/01/2023] [Indexed: 02/08/2023]
Abstract
Histone methylation is the most common histone modification and a highly dynamic regulator of gene transcription. Methylation of lysine residues can alter the structure of chromatin, helping to regulate DNA-based nuclear activities. Lysine demethylases control and maintain epigenetic factors that affect chromatin structure and cell characteristics. A variety of diseases, including malignant tumors, are connected to their dysregulation. Advances in biochemistry and pathogenesis have prompted the discovery of small molecule inhibitors and tool compounds that disrupt lysine demethylation. In this review, we focus on JmjC-domain-containing histone lysine demethylases (KDM2-7), discussing their structures and biological roles, representative inhibitors, and therapeutic potential in cancer therapy, and aiming to provide unique insights into the development of JmjC-KDM inhibitors.
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Affiliation(s)
- Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Yao Chen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Zhijia Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Congcong Lin
- The Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu 610031, China; Medical Research Center, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu 610031, China
| | - Tongtong Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China; Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China.
| | - Guan Wang
- The Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu 610031, China.
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22
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Boila LD, Ghosh S, Bandyopadhyay SK, Jin L, Murison A, Zeng AGX, Shaikh W, Bhowmik S, Muddineni SSNA, Biswas M, Sinha S, Chatterjee SS, Mbong N, Gan OI, Bose A, Chakraborty S, Arruda A, Kennedy JA, Mitchell A, Lechman ER, Banerjee D, Milyavsky M, Minden MD, Dick JE, Sengupta A. KDM6 demethylases integrate DNA repair gene regulation and loss of KDM6A sensitizes human acute myeloid leukemia to PARP and BCL2 inhibition. Leukemia 2023; 37:751-764. [PMID: 36720973 DOI: 10.1038/s41375-023-01833-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/01/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous, aggressive malignancy with dismal prognosis and with limited availability of targeted therapies. Epigenetic deregulation contributes to AML pathogenesis. KDM6 proteins are histone-3-lysine-27-demethylases that play context-dependent roles in AML. We inform that KDM6-demethylase function critically regulates DNA-damage-repair-(DDR) gene expression in AML. Mechanistically, KDM6 expression is regulated by genotoxic stress, with deficiency of KDM6A-(UTX) and KDM6B-(JMJD3) impairing DDR transcriptional activation and compromising repair potential. Acquired KDM6A loss-of-function mutations are implicated in chemoresistance, although a significant percentage of relapsed-AML has upregulated KDM6A. Olaparib treatment reduced engraftment of KDM6A-mutant-AML-patient-derived xenografts, highlighting synthetic lethality using Poly-(ADP-ribose)-polymerase-(PARP)-inhibition. Crucially, a higher KDM6A expression is correlated with venetoclax tolerance. Loss of KDM6A increased mitochondrial activity, BCL2 expression, and sensitized AML cells to venetoclax. Additionally, BCL2A1 associates with venetoclax resistance, and KDM6A loss was accompanied with a downregulated BCL2A1. Corroborating these results, dual targeting of PARP and BCL2 was superior to PARP or BCL2 inhibitor monotherapy in inducing AML apoptosis, and primary AML cells carrying KDM6A-domain mutations were even more sensitive to the combination. Together, our study illustrates a mechanistic rationale in support of a novel combination therapy for AML based on subtype-heterogeneity, and establishes KDM6A as a molecular regulator for determining therapeutic efficacy.
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Affiliation(s)
- Liberalis Debraj Boila
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Subhadeep Ghosh
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Subham K Bandyopadhyay
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Wasim Shaikh
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Satyaki Bhowmik
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | | | - Mayukh Biswas
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Irving Cancer Research Center, Columbia University Medical Center, New York, NY, 10032, USA
| | - Sayantani Sinha
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shankha Subhra Chatterjee
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Anwesha Bose
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Sayan Chakraborty
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, M5G 2C4, Canada.,Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Debasis Banerjee
- Park Clinic, Gorky Terrace and Ramakrishna Mission Seva Pratisthan, Kolkata, 700017, West Bengal, India
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, M5G 2C4, Canada.,Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Amitava Sengupta
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India. .,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India. .,CSIR-IICB-Cancer Biology & Inflammatory Disorder Division, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India.
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23
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Zhou X, Zhang P, Aryal S, Zhang L, Lu R. UTX loss alters therapeutic responses in KMT2A-rearranged acute myeloid leukemia. Leukemia 2023; 37:226-230. [PMID: 36309561 DOI: 10.1038/s41375-022-01741-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 02/01/2023]
Affiliation(s)
- Xinyue Zhou
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
| | - Pengcheng Zhang
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
| | - Sajesan Aryal
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
| | - Lixia Zhang
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
| | - Rui Lu
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA.
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24
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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.
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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.
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25
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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: 1] [Impact Index Per Article: 0.5] [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.
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26
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Koizumi M, Eto H, Saeki M, Seki M, Fukushima T, Mukai S, Ide H, Sera Y, Iwasaki M, Suzuki Y, Tohei A, Kishi Y, Honda H. UTX deficiency in neural stem/progenitor cells results in impaired neural development, fetal ventriculomegaly, and postnatal death. FASEB J 2022; 36:e22662. [PMID: 36412518 DOI: 10.1096/fj.202201002rr] [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: 07/02/2022] [Revised: 10/19/2022] [Accepted: 11/07/2022] [Indexed: 11/23/2022]
Abstract
Recent studies have demonstrated that epigenetic modifications are deeply involved in neurogenesis; however, the precise mechanisms remain largely unknown. To determine the role of UTX (also known as KDM6A), a demethylase of histone H3K27, in neural development, we generated Utx-deficient mice in neural stem/progenitor cells (NSPCs). Since Utx is an X chromosome-specific gene, the genotypes are sex-dependent; female mice lose both Utx alleles (UtxΔ/Δ ), and male mice lose one Utx allele yet retain one Uty allele, the counterpart of Utx on the Y chromosome (UtxΔ/Uty ). We found that UtxΔ/Δ mice exhibited fetal ventriculomegaly and died soon after birth. Immunofluorescence staining and EdU labeling revealed a significant increase in NSPCs and a significant decrease in intermediate-progenitor and differentiated neural cells. Molecular analyses revealed the downregulation of pathways related to DNA replication and increased H3K27me3 levels around the transcription start sites in UtxΔ/Δ NSPCs. These results indicate that UTX globally regulates the expression of genes required for proper neural development in NSPCs, and UTX deficiency leads to impaired cell cycle exit, reduced differentiation, and neonatal death. Interestingly, although UtxΔ/Uty mice survived the postnatal period, most died of hydrocephalus, a clinical feature of Kabuki syndrome, a congenital anomaly involving UTX mutations. Our findings provide novel insights into the role of histone modifiers in neural development and suggest that UtxΔ/Uty mice are a potential disease model for Kabuki syndrome.
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Affiliation(s)
- Miho Koizumi
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Hikaru Eto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Mai Saeki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,Laboratory of Molecular Neurobiology, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tsuyoshi Fukushima
- Section of Oncopathology and Regenerative Biology, Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Shoichiro Mukai
- Department of Urology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Hisamitsu Ide
- Department of Urology, Dokkyo Medical University, Saitama Medical Center, Saitama, Japan
| | - Yasuyuki Sera
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Masayuki Iwasaki
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Atsushi Tohei
- Laboratory of Experimental Animal Science, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Yusuke Kishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,Laboratory of Molecular Neurobiology, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Honda
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
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27
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Pingul BY, Huang H, Chen Q, Alikarami F, Zhang Z, Qi J, Bernt KM, Berger SL, Cao Z, Shi J. Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia. iScience 2022; 25:105139. [PMID: 36193052 PMCID: PMC9526175 DOI: 10.1016/j.isci.2022.105139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 08/05/2022] [Accepted: 09/10/2022] [Indexed: 11/26/2022] Open
Abstract
Transcriptional dysregulation is a prominent feature in leukemia. Here, we systematically surveyed transcription factor (TF) vulnerabilities in leukemia and uncovered TF clusters that exhibit context-specific vulnerabilities within and between different subtypes of leukemia. Among these TF clusters, we demonstrated that acute myeloid leukemia (AML) with high IRF8 expression was addicted to MEF2D. MEF2D and IRF8 form an autoregulatory loop via direct binding to mutual enhancer elements. One important function of this circuit in AML is to sustain PU.1/MEIS1 co-regulated transcriptional outputs via stabilizing PU.1’s chromatin occupancy. We illustrated that AML could acquire dependency on this circuit through various oncogenic mechanisms that results in the activation of their enhancers. In addition to forming a circuit, MEF2D and IRF8 can also separately regulate gene expression, and dual perturbation of these two TFs leads to a more robust inhibition of AML proliferation. Collectively, our results revealed a TF circuit essential for AML survival. MEF2D is a context-specific vulnerability in IRF8hi AML MEF2D and IRF8 form a transcriptional circuit via binding to each other’s enhancers MEF2D-IRF8 circuit supports PU.1’s chromatin occupancy and transcriptional output MEF2D and IRF8 can regulate separate gene expression programs alongside the circuit
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28
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Preto AJ, Matos-Filipe P, Mourão J, Moreira IS. SYNPRED: prediction of drug combination effects in cancer using different synergy metrics and ensemble learning. Gigascience 2022; 11:6717722. [PMID: 36155782 PMCID: PMC9511701 DOI: 10.1093/gigascience/giac087] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 06/14/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022] Open
Abstract
Background In cancer research, high-throughput screening technologies produce large amounts of multiomics data from different populations and cell types. However, analysis of such data encounters difficulties due to disease heterogeneity, further exacerbated by human biological complexity and genomic variability. The specific profile of cancer as a disease (or, more realistically, a set of diseases) urges the development of approaches that maximize the effect while minimizing the dosage of drugs. Now is the time to redefine the approach to drug discovery, bringing an artificial intelligence (AI)–powered informational view that integrates the relevant scientific fields and explores new territories. Results Here, we show SYNPRED, an interdisciplinary approach that leverages specifically designed ensembles of AI algorithms, as well as links omics and biophysical traits to predict anticancer drug synergy. It uses 5 reference models (Bliss, Highest Single Agent, Loewe, Zero Interaction Potency, and Combination Sensitivity Score), which, coupled with AI algorithms, allowed us to attain the ones with the best predictive performance and pinpoint the most appropriate reference model for synergy prediction, often overlooked in similar studies. By using an independent test set, SYNPRED exhibits state-of-the-art performance metrics either in the classification (accuracy, 0.85; precision, 0.91; recall, 0.90; area under the receiver operating characteristic, 0.80; and F1-score, 0.91) or in the regression models, mainly when using the Combination Sensitivity Score synergy reference model (root mean square error, 11.07; mean squared error, 122.61; Pearson, 0.86; mean absolute error, 7.43; Spearman, 0.87). Moreover, data interpretability was achieved by deploying the most current and robust feature importance approaches. A simple web-based application was constructed, allowing easy access by nonexpert researchers. Conclusions The performance of SYNPRED rivals that of the existing methods that tackle the same problem, yielding unbiased results trained with one of the most comprehensive datasets available (NCI ALMANAC). The leveraging of different reference models allowed deeper insights into which of them can be more appropriately used for synergy prediction. The Combination Sensitivity Score clearly stood out with improved performance among the full scope of surveyed approaches and synergy reference models. Furthermore, SYNPRED takes a particular focus on data interpretability, which has been in the spotlight lately when using the most advanced AI techniques.
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Affiliation(s)
- António J Preto
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal.,PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal
| | - Pedro Matos-Filipe
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Joana Mourão
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal
| | - Irina S Moreira
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal.,CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal
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Lam CM, Li Z, Theodorescu D, Li X. Mechanism of Sex Differences in Bladder Cancer: Evident and Elusive Sex-biasing Factors. Bladder Cancer 2022; 8:241-254. [PMID: 36277328 PMCID: PMC9536425 DOI: 10.3233/blc-211658] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/14/2022] [Indexed: 11/26/2022]
Abstract
Bladder cancer incidence is drastically higher in males than females across geographical, racial, and socioeconomic strata. Despite potential differences in tumor biology, however, male and female bladder cancer patients are still clinically managed in highly similar ways. While sex hormones and sex chromosomes have been shown to promote observed sex differences, a more complex story lies beneath these evident sex-biasing factors than previously appreciated. Advances in genomic technology have spurred numerous preclinical studies characterizing elusive sex-biasing factors such as epigenetics, X chromosome inactivation escape genes, single nucleotide polymorphism, transcription regulation, metabolism, immunity, and many more. Sex-biasing effects, if properly understood, can be leveraged by future efforts in precision medicine based on a patient's biological sex. In this review, we will highlight key findings from the last half century that demystify the intricate ways in which sex-specific biology contribute to differences in pathogenesis as well as discuss future research directions.
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Affiliation(s)
- Christa M. Lam
- Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center – The James, Columbus, OH, USA
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xue Li
- Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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30
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JMJD family proteins in cancer and inflammation. Signal Transduct Target Ther 2022; 7:304. [PMID: 36050314 PMCID: PMC9434538 DOI: 10.1038/s41392-022-01145-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/22/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
The occurrence of cancer entails a series of genetic mutations that favor uncontrollable tumor growth. It is believed that various factors collectively contribute to cancer, and there is no one single explanation for tumorigenesis. Epigenetic changes such as the dysregulation of enzymes modifying DNA or histones are actively involved in oncogenesis and inflammatory response. The methylation of lysine residues on histone proteins represents a class of post-translational modifications. The human Jumonji C domain-containing (JMJD) protein family consists of more than 30 members. The JMJD proteins have long been identified with histone lysine demethylases (KDM) and histone arginine demethylases activities and thus could function as epigenetic modulators in physiological processes and diseases. Importantly, growing evidence has demonstrated the aberrant expression of JMJD proteins in cancer and inflammatory diseases, which might serve as an underlying mechanism for the initiation and progression of such diseases. Here, we discuss the role of key JMJD proteins in cancer and inflammation, including the intensively studied histone lysine demethylases, as well as the understudied group of JMJD members. In particular, we focused on epigenetic changes induced by each JMJD member and summarized recent research progress evaluating their therapeutic potential for the treatment of cancer and inflammatory diseases.
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31
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Sex differences in normal and malignant hematopoiesis. BLOOD SCIENCE 2022; 4:185-191. [PMID: 36311819 PMCID: PMC9592170 DOI: 10.1097/bs9.0000000000000133] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/10/2022] [Indexed: 12/09/2022] Open
Abstract
Hematopoiesis is a continuous and well-regulated process requiring both the capacity for self-renewal and the potential for differentiation of hematopoietic stem cells. Multiple studies indicate that sex hormones exert significant effects on not only hematopoietic stem and progenitor cells, but also the development of hematopoietic lineages, resulting in sexual dimorphisms in normal hematopoiesis. Hematologic malignancies comprise a wide variety of cancers affecting the blood, bone marrow, and lymphatic system, such as leukemia, lymphoma, myeloma, myelodysplastic syndrome, and myeloproliferative diseases. Overall, males are at greater risk and have worse prognosis for most of these malignancies compared with females. A better understanding of the differences between male and female could be of substantial value in research as well as clinical management.
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Shen H, Yanas A, Owens MC, Zhang C, Fritsch C, Fare CM, Copley KE, Shorter J, Goldman YE, Liu KF. Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separation. Mol Cell 2022; 82:2588-2603.e9. [PMID: 35588748 PMCID: PMC9308757 DOI: 10.1016/j.molcel.2022.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 04/09/2022] [Accepted: 04/19/2022] [Indexed: 02/05/2023]
Abstract
Sex differences are pervasive in human health and disease. One major key to sex-biased differences lies in the sex chromosomes. Although the functions of the X chromosome proteins are well appreciated, how they compare with their Y chromosome homologs remains elusive. Herein, using ensemble and single-molecule techniques, we report that the sex chromosome-encoded RNA helicases DDX3X and DDX3Y are distinct in their propensities for liquid-liquid phase separation (LLPS), dissolution, and translation repression. We demonstrate that the N-terminal intrinsically disordered region of DDX3Y more strongly promotes LLPS than the corresponding region of DDX3X and that the weaker ATPase activity of DDX3Y, compared with DDX3X, contributes to the slower disassembly dynamics of DDX3Y-positive condensates. Interestingly, DDX3Y-dependent LLPS represses mRNA translation and enhances aggregation of FUS more strongly than DDX3X-dependent LLPS. Our study provides a platform for future comparisons of sex chromosome-encoded protein homologs, providing insights into sex differences in RNA metabolism and human disease.
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Affiliation(s)
- Hui Shen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amber Yanas
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael C Owens
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Celia Zhang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clark Fritsch
- Graduate Group in Cellular and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katie E Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Cellular and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yale E Goldman
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Cīrulis A, Hansson B, Abbott JK. Sex-limited chromosomes and non-reproductive traits. BMC Biol 2022; 20:156. [PMID: 35794589 PMCID: PMC9261002 DOI: 10.1186/s12915-022-01357-5] [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: 11/07/2021] [Accepted: 06/22/2022] [Indexed: 12/03/2022] Open
Abstract
Sex chromosomes are typically viewed as having originated from a pair of autosomes, and differentiated as the sex-limited chromosome (e.g. Y) has degenerated by losing most genes through cessation of recombination. While often thought that degenerated sex-limited chromosomes primarily affect traits involved in sex determination and sex cell production, accumulating evidence suggests they also influence traits not sex-limited or directly involved in reproduction. Here, we provide an overview of the effects of sex-limited chromosomes on non-reproductive traits in XY, ZW or UV sex determination systems, and discuss evolutionary processes maintaining variation at sex-limited chromosomes and molecular mechanisms affecting non-reproductive traits.
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Affiliation(s)
- Aivars Cīrulis
- Department of Biology, Lund University, 223 62, Lund, Sweden.
| | - Bengt Hansson
- Department of Biology, Lund University, 223 62, Lund, Sweden
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Mitchell E, Spencer Chapman M, Williams N, Dawson KJ, Mende N, Calderbank EF, Jung H, Mitchell T, Coorens THH, Spencer DH, Machado H, Lee-Six H, Davies M, Hayler D, Fabre MA, Mahbubani K, Abascal F, Cagan A, Vassiliou GS, Baxter J, Martincorena I, Stratton MR, Kent DG, Chatterjee K, Parsy KS, Green AR, Nangalia J, Laurenti E, Campbell PJ. Clonal dynamics of haematopoiesis across the human lifespan. Nature 2022; 606:343-350. [PMID: 35650442 PMCID: PMC9177428 DOI: 10.1038/s41586-022-04786-y] [Citation(s) in RCA: 160] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Age-related change in human haematopoiesis causes reduced regenerative capacity1, cytopenias2, immune dysfunction3 and increased risk of blood cancer4-6, but the reason for such abrupt functional decline after 70 years of age remains unclear. Here we sequenced 3,579 genomes from single cell-derived colonies of haematopoietic cells across 10 human subjects from 0 to 81 years of age. Haematopoietic stem cells or multipotent progenitors (HSC/MPPs) accumulated a mean of 17 mutations per year after birth and lost 30 base pairs per year of telomere length. Haematopoiesis in adults less than 65 years of age was massively polyclonal, with high clonal diversity and a stable population of 20,000-200,000 HSC/MPPs contributing evenly to blood production. By contrast, haematopoiesis in individuals aged over 75 showed profoundly decreased clonal diversity. In each of the older subjects, 30-60% of haematopoiesis was accounted for by 12-18 independent clones, each contributing 1-34% of blood production. Most clones had begun their expansion before the subject was 40 years old, but only 22% had known driver mutations. Genome-wide selection analysis estimated that between 1 in 34 and 1 in 12 non-synonymous mutations were drivers, accruing at constant rates throughout life, affecting more genes than identified in blood cancers. Loss of the Y chromosome conferred selective benefits in males. Simulations of haematopoiesis, with constant stem cell population size and constant acquisition of driver mutations conferring moderate fitness benefits, entirely explained the abrupt change in clonal structure in the elderly. Rapidly decreasing clonal diversity is a universal feature of haematopoiesis in aged humans, underpinned by pervasive positive selection acting on many more genes than currently identified.
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Affiliation(s)
- Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | | | - Nicole Mende
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Emily F Calderbank
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | | | | | | | - David H Spencer
- Department of Medicine, McDonnell Genome Institute, Washington University, St Louis, MO, USA
| | | | | | - Megan Davies
- Cambridge Molecular Diagnostics, Milton Road, Cambridge, UK
| | - Daniel Hayler
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Margarete A Fabre
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Krishnaa Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | | | | | - George S Vassiliou
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Joanna Baxter
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | - David G Kent
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Krishna Chatterjee
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Anthony R Green
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Elisa Laurenti
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.
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35
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Kania AK, Price MJ, George-Alexander LE, Patterson DG, Hicks SL, Scharer CD, Boss JM. H3K27me3 Demethylase UTX Restrains Plasma Cell Formation. THE JOURNAL OF IMMUNOLOGY 2022; 208:1873-1885. [PMID: 35346967 PMCID: PMC9012698 DOI: 10.4049/jimmunol.2100948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/02/2022] [Indexed: 11/19/2022]
Abstract
B cell differentiation is associated with substantial transcriptional, metabolic, and epigenetic remodeling, including redistribution of histone 3 lysine 27 trimethylation (H3K27me3), which is associated with a repressive chromatin state and gene silencing. Although the role of the methyltransferase EZH2 (Enhancer of zeste homolog 2) in B cell fate decisions has been well established, it is not known whether H3K27me3 demethylation is equally important. In this study, we showed that simultaneous genetic deletion of the two H3K27 demethylases UTX and JMJD3 (double-knockout [Utx fl/fl Jmjd3 fl/fl Cd19 cre/+] [dKO]) led to a significant increase in plasma cell (PC) formation after stimulation with the T cell-independent Ags LPS and NP-Ficoll. This phenotype occurred in a UTX-dependent manner as UTX single-knockout mice, but not JMJD3 single-knockout mice, mimicked the dKO. Although UTX- and JMJD3-deficient marginal zone B cells showed increased proliferation, dKO follicular B cells also showed increased PC formation. PCs from dKO mice upregulated genes associated with oxidative phosphorylation and exhibited increased spare respiratory capacity. Mechanistically, deletion of Utx and Jmjd3 resulted in higher levels of H3K27me3 at proapoptotic genes and resulted in reduced apoptosis of dKO PCs in vivo. Furthermore, UTX regulated chromatin accessibility at regions containing ETS and IFN regulatory factor (IRF) transcription factor family motifs, including motifs of known repressors of PC fate. Taken together, these data demonstrate that the H3K27me3 demethylases restrain B cell differentiation.
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Affiliation(s)
- Anna K Kania
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Madeline J Price
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | | | - Dillon G Patterson
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:cells11071113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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Intravesical delivery of KDM6A-mRNA via mucoadhesive nanoparticles inhibits the metastasis of bladder cancer. Proc Natl Acad Sci U S A 2022; 119:2112696119. [PMID: 35131941 PMCID: PMC8851555 DOI: 10.1073/pnas.2112696119] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2021] [Indexed: 12/24/2022] Open
Abstract
This study provides proof-of-principle evidence for intravesical delivery of messenger RNA (mRNA) via a mucoadhesive nanoparticle (NP) strategy and reveals the therapeutic potential of KDM6A in treating bladder cancer metastasis, which remains difficult due to the physiological bladder barriers. The mucoadhesive NPs could protect loaded mRNA, prolong exposure of mRNA in disease sites, and benefit the penetration and effective expression, which all represent challenging hurdles for intravesical delivery of mRNA therapeutics. mRNA local delivery can also avoid potential toxicity issues via systemic delivery and unwanted protein expression throughout the body. We expect this mucoadhesive mRNA nanotechnology can be useful for the effective up-regulation of targeted proteins in bladder tissues in situ for both mechanistic understanding and translational study of bladder-related diseases. Lysine-specific demethylase 6A (KDM6A), also named UTX, is frequently mutated in bladder cancer (BCa). Although known as a tumor suppressor, KDM6A’s therapeutic potential in the metastasis of BCa remains elusive. It also remains difficult to fulfill the effective up-regulation of KDM6A levels in bladder tumor tissues in situ to verify its potential in treating BCa metastasis. Here, we report a mucoadhesive messenger RNA (mRNA) nanoparticle (NP) strategy for the intravesical delivery of KDM6A-mRNA in mice bearing orthotopic Kdm6a-null BCa and show evidence of KDM6A’s therapeutic potential in inhibiting the metastasis of BCa. Through this mucoadhesive mRNA NP strategy, the exposure of KDM6A-mRNA to the in situ BCa tumors can be greatly prolonged for effective expression, and the penetration can be also enhanced by adhering to the bladder for sustained delivery. This mRNA NP strategy is also demonstrated to be effective for combination cancer therapy with other clinically approved drugs (e.g., elemene), which could further enhance therapeutic outcomes. Our findings not only report intravesical delivery of mRNA via a mucoadhesive mRNA NP strategy but also provide the proof-of-concept for the usefulness of these mRNA NPs as tools in both mechanistic understanding and translational study of bladder-related diseases.
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Huang Y, Xie Y, Yang D, Xiong M, Chen X, Wu D, Wang Q, Chen H, Zheng L, Huang K. Histone demethylase UTX aggravates acetaminophen overdose induced hepatotoxicity through dual mechanisms. Pharmacol Res 2022; 175:106021. [PMID: 34883214 DOI: 10.1016/j.phrs.2021.106021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/21/2021] [Accepted: 12/03/2021] [Indexed: 11/25/2022]
Abstract
Acetaminophen (APAP) overdose is a major cause of acute liver failure, while the underlying mechanisms of APAP hepatotoxicity are not fully understood. Recently, emerging evidence suggests that epigenetic enzymes play roles in APAP-induced liver injury. Here, we found that Utx (ubiquitously transcribed tetratricopeptide repeat, X chromosome, also known as KDM6A), a X-linked histone demethylase which removes the di- and tri-methyl groups from histone H3K27, was markedly induced in the liver of APAP-overdosed female mice. Hepatic deletion of Utx suppressed APAP overdose-induced hepatotoxicity in female but not male mice. RNA-sequencing analysis suggested that Utx deficiency in female mice upregulated antitoxic phase II conjugating enzymes, including sulfotransferase family 2 A member 1 (Sult2a1), thus reduces the amount of toxic APAP metabolites in injured liver; while Utx deficiency also alleviated ER stress through downregulating transcription of ER stress genes including Atf4, Atf3, and Chop. Mechanistically, Utx promoted transcription of ER stress related genes in a demethylase activity-dependent manner, while repressed Sult2a1 expression through mediating H3K27ac levels independent of its demethylase activity. Moreover, overexpression of Sult2a1 in the liver of female mice rescued APAP-overdose induced liver injury. Together, our results indicated a novel UTX-Sult2a1 axis for the prevention or treatment of APAP-induced liver injury.
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Affiliation(s)
- Yixue Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yunhao Xie
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dong Yang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mingrui Xiong
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xingrui Chen
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Di Wu
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qing Wang
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hong Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ling Zheng
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Hua C, Chen J, Li S, Zhou J, Fu J, Sun W, Wang W. KDM6 Demethylases and Their Roles in Human Cancers. Front Oncol 2021; 11:779918. [PMID: 34950587 PMCID: PMC8688854 DOI: 10.3389/fonc.2021.779918] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/17/2021] [Indexed: 12/31/2022] Open
Abstract
Cancer therapy is moving beyond traditional chemotherapy to include epigenetic approaches. KDM6 demethylases are dynamic regulation of gene expression by histone demethylation in response to diverse stimuli, and thus their dysregulation has been observed in various cancers. In this review, we first briefly introduce structural features of KDM6 subfamily, and then discuss the regulation of KDM6, which involves the coordinated control between cellular metabolism (intrinsic regulators) and tumor microenvironment (extrinsic stimuli). We further describe the aberrant functions of KDM6 in human cancers, acting as either a tumor suppressor or an oncoprotein in a context-dependent manner. Finally, we propose potential therapy of KDM6 enzymes based on their structural features, epigenetics, and immunomodulatory mechanisms, providing novel insights for prevention and treatment of cancers.
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Affiliation(s)
- Chunyan Hua
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | | | - Shuting Li
- Wenzhou Medical University, Wenzhou, China
| | | | - Jiahong Fu
- Wenzhou Medical University, Wenzhou, China
| | - Weijian Sun
- Department of Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenqian Wang
- Department of Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
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Staehle HF, Pahl HL, Jutzi JS. The Cross Marks the Spot: The Emerging Role of JmjC Domain-Containing Proteins in Myeloid Malignancies. Biomolecules 2021; 11:biom11121911. [PMID: 34944554 PMCID: PMC8699298 DOI: 10.3390/biom11121911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
Histone methylation tightly regulates chromatin accessibility, transcription, proliferation, and cell differentiation, and its perturbation contributes to oncogenic reprogramming of cells. In particular, many myeloid malignancies show evidence of epigenetic dysregulation. Jumonji C (JmjC) domain-containing proteins comprise a large and diverse group of histone demethylases (KDMs), which remove methyl groups from lysines in histone tails and other proteins. Cumulating evidence suggests an emerging role for these demethylases in myeloid malignancies, rendering them attractive targets for drug interventions. In this review, we summarize the known functions of Jumonji C (JmjC) domain-containing proteins in myeloid malignancies. We highlight challenges in understanding the context-dependent mechanisms of these proteins and explore potential future pharmacological targeting.
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Affiliation(s)
- Hans Felix Staehle
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
| | - Heike Luise Pahl
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
| | - Jonas Samuel Jutzi
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02115, MA, USA
- Correspondence:
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Shi B, Li W, Jiang H. Epigenetic condensates regulate chromatin activity and tumorigenesis. Mol Cell Oncol 2021; 8:1997040. [PMID: 34859151 PMCID: PMC8632315 DOI: 10.1080/23723556.2021.1997040] [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] [Indexed: 11/10/2022]
Abstract
Alterations of epigenetic modulators are extensively associated with cancer, but their key molecular activities in cancer regulation are often unclear. We discovered that lysine demethylase 6A (KDM6A, also known as UTX) suppresses cancer by forming liquid-like condensates with lysine methyltransferase 2D (KMT2D, also known as MLL4) and regulating chromatin activity at multiple levels.
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Affiliation(s)
- Bi Shi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Uva Cancer Center, Charlottesville, VA, USA
| | - Wei Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Uva Cancer Center, Charlottesville, VA, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Uva Cancer Center, Charlottesville, VA, USA
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Kdm6a deficiency restricted to mouse hematopoietic cells causes an age- and sex-dependent myelodysplastic syndrome-like phenotype. PLoS One 2021; 16:e0255706. [PMID: 34780480 PMCID: PMC8592440 DOI: 10.1371/journal.pone.0255706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/19/2021] [Indexed: 12/18/2022] Open
Abstract
Kdm6a/Utx, a gene on the X chromosome, encodes a histone H3K27me3 demethylase that has an orthologue on the Y chromosome (Uty) (Zheng et al. 2018). We previously identified inactivating mutations of Kdm6a in approximately 50% of mouse acute promyelocytic leukemia samples; however, somatic mutations of KDM6A are more rare in human AML samples, ranging in frequency from 2–15% in different series of patients, where their role in pathogenesis is not yet clear. In this study, we show that female Kdm6aflox/flox mice (with allele inactivation initiated by Vav1-Cre in hematopoietic stem and progenitor cells (HSPCs) have a sex-specific phenotype that emerges with aging, with features resembling a myelodysplastic syndrome (MDS). Female Kdm6a-knockout (KO) mice have an age-dependent expansion of their HSPCs with aberrant self-renewal, but they did not differentiate normally into downstream progeny. These mice became mildly anemic and thrombocytopenic, but did not develop overt leukemia, or die from these cytopenias. ChIP-seq and ATAC-seq studies showed only minor changes in H3K27me3, H3K27ac, H3K4me, H3K4me3 and chromatin accessibility between Kdm6a-WT and Kdm6a-KO mice. Utilizing scRNA-seq, Kdm6a loss was linked to the transcriptional repression of genes that mediate hematopoietic cell fate determination. These data demonstrate that Kdm6a plays an important role in normal hematopoiesis, and that its inactivation may contribute to AML pathogenesis.
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Zhou L, Wang X, Lu J, Fu X, Li Y. EGFR transcriptionally upregulates UTX via STAT3 in non-small cell lung cancer. J Cancer Res Clin Oncol 2021; 148:309-319. [PMID: 34661759 PMCID: PMC8800904 DOI: 10.1007/s00432-021-03800-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/10/2021] [Indexed: 12/25/2022]
Abstract
Background Histone demethylase UTX has been reported to participate in the occurrence and development of many cancers in tissue-specific manners. However, the role of UTX in non-small cell lung cancer (NSCLC) and exactly what regulates the expression of UTX remains unclear. Here, we analyzed the role of UTX in NSCLC in association with the widely recognized tumor driver epidermal growth factor receptor (EGFR). Methods UTX levels in clinical samples were detected by immunohistochemistry staining, western blotting and real-time quantitative PCR. The expression of UTX in tumor tissue was correlated with the phosphorylation of EGFR. Cell proliferation and migration were evaluated by MTT and wound-healing assays. The impact of EGFR and its downstream pathways on UTX was explored with corresponding inhibitors, and examined by western blotting and real-time quantitative PCR. Results In this study, we found that the expression of UTX in cancer tissues of patients with NSCLC was significantly higher than that in paracancerous tissues, and positively associated with EGFR phosphorylation levels. In addition, in NSCLC cell lines, UTX can promote proliferation and migration, while inhibition of its enzyme activity suppressed cell growth. Moreover, UTX expression was significantly upregulated when EGFR signaling pathway was activated, and vice versa when EGFR pathway was inhibited by tyrosine kinase inhibitor. Further mechanistic studies suggested that the activation of EGFR activated its downstream JAK/STAT3 signaling pathway and promoted STAT3 phosphorylation; the phosphorylated STAT3 transcriptionally promoted the levels of UTX. Conclusions These results suggest an “EGFR-STAT3-UTX” axis that plays an oncogenic role in NSCLC. Supplementary Information The online version contains supplementary material available at 10.1007/s00432-021-03800-6.
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Affiliation(s)
- Lin Zhou
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaomu Wang
- Department of Clinical Pharmacy, Guangzhou First People's Hospital, Guangzhou, 510180, China
| | - Jingya Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiangning Fu
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yangkai Li
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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44
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Kalushkova A, Nylund P, Párraga AA, Lennartsson A, Jernberg-Wiklund H. One Omics Approach Does Not Rule Them All: The Metabolome and the Epigenome Join Forces in Haematological Malignancies. EPIGENOMES 2021; 5:epigenomes5040022. [PMID: 34968247 PMCID: PMC8715477 DOI: 10.3390/epigenomes5040022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/17/2021] [Accepted: 09/26/2021] [Indexed: 02/01/2023] Open
Abstract
Aberrant DNA methylation, dysregulation of chromatin-modifying enzymes, and microRNAs (miRNAs) play a crucial role in haematological malignancies. These epimutations, with an impact on chromatin accessibility and transcriptional output, are often associated with genomic instability and the emergence of drug resistance, disease progression, and poor survival. In order to exert their functions, epigenetic enzymes utilize cellular metabolites as co-factors and are highly dependent on their availability. By affecting the expression of metabolic enzymes, epigenetic modifiers may aid the generation of metabolite signatures that could be utilized as targets and biomarkers in cancer. This interdependency remains often neglected and poorly represented in studies, despite well-established methods to study the cellular metabolome. This review critically summarizes the current knowledge in the field to provide an integral picture of the interplay between epigenomic alterations and the cellular metabolome in haematological malignancies. Our recent findings defining a distinct metabolic signature upon response to enhancer of zeste homolog 2 (EZH2) inhibition in multiple myeloma (MM) highlight how a shift of preferred metabolic pathways may potentiate novel treatments. The suggested link between the epigenome and the metabolome in haematopoietic tumours holds promise for the use of metabolic signatures as possible biomarkers of response to treatment.
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Affiliation(s)
- Antonia Kalushkova
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (P.N.); (A.A.P.); (H.J.-W.)
- Correspondence:
| | - Patrick Nylund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (P.N.); (A.A.P.); (H.J.-W.)
| | - Alba Atienza Párraga
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (P.N.); (A.A.P.); (H.J.-W.)
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NEO, Karolinska Institutet, 14157 Huddinge, Sweden;
| | - Helena Jernberg-Wiklund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (P.N.); (A.A.P.); (H.J.-W.)
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45
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Yun H, Narayan N, Vohra S, Giotopoulos G, Mupo A, Madrigal P, Sasca D, Lara-Astiaso D, Horton SJ, Agrawal-Singh S, Meduri E, Basheer F, Marando L, Gozdecka M, Dovey OM, Castillo-Venzor A, Wang X, Gallipoli P, Müller-Tidow C, Osborne CS, Vassiliou GS, Huntly BJP. Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression. Nat Genet 2021; 53:1443-1455. [PMID: 34556857 PMCID: PMC7611829 DOI: 10.1038/s41588-021-00925-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Altered transcription is a cardinal feature of acute myeloid leukemia (AML); however, exactly how mutations synergize to remodel the epigenetic landscape and rewire three-dimensional DNA topology is unknown. Here, we apply an integrated genomic approach to a murine allelic series that models the two most common mutations in AML: Flt3-ITD and Npm1c. We then deconvolute the contribution of each mutation to alterations of the epigenetic landscape and genome organization, and infer how mutations synergize in the induction of AML. Our studies demonstrate that Flt3-ITD signals to chromatin to alter the epigenetic environment and synergizes with mutations in Npm1c to alter gene expression and drive leukemia induction. These analyses also allow the identification of long-range cis-regulatory circuits, including a previously unknown superenhancer of Hoxa locus, as well as larger and more detailed gene-regulatory networks, driven by transcription factors including PU.1 and IRF8, whose importance we demonstrate through perturbation of network members.
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MESH Headings
- Animals
- Base Sequence
- Chromatin Assembly and Disassembly/genetics
- DNA, Neoplasm/chemistry
- Disease Models, Animal
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Genetic Loci
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Mice, Inbred C57BL
- Mutation/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Principal Component Analysis
- Protein Processing, Post-Translational
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic
- fms-Like Tyrosine Kinase 3/metabolism
- Mice
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Affiliation(s)
- Haiyang Yun
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nisha Narayan
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shabana Vohra
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Annalisa Mupo
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Pedro Madrigal
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Daniel Sasca
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - David Lara-Astiaso
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah J Horton
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shuchi Agrawal-Singh
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eshwar Meduri
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Faisal Basheer
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Oliver M Dovey
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | | | - Xiaonan Wang
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gallipoli
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Cameron S Osborne
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - George S Vassiliou
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Brian J P Huntly
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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46
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Lara-Astiaso D, Huntly BJP. Protein condensates provide a platform for controlling chromatin. Nature 2021. [DOI: 10.1038/d41586-021-02365-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Shi B, Li W, Song Y, Wang Z, Ju R, Ulman A, Hu J, Palomba F, Zhao Y, Le JP, Jarrard W, Dimoff D, Digman MA, Gratton E, Zang C, Jiang H. UTX condensation underlies its tumour-suppressive activity. Nature 2021; 597:726-731. [PMID: 34526716 PMCID: PMC9008583 DOI: 10.1038/s41586-021-03903-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
UTX (also known as KDM6A) encodes a histone H3K27 demethylase and is an important tumour suppressor that is frequently mutated in human cancers1. However, as the demethylase activity of UTX is often dispensable for mediating tumour suppression and developmental regulation2-8, the underlying molecular activity of UTX remains unknown. Here we show that phase separation of UTX underlies its chromatin-regulatory activity in tumour suppression. A core intrinsically disordered region (cIDR) of UTX forms phase-separated liquid condensates, and cIDR loss caused by the most frequent cancer mutation of UTX is mainly responsible for abolishing tumour suppression. Deletion, mutagenesis and replacement assays of the intrinsically disordered region demonstrate a critical role of UTX condensation in tumour suppression and embryonic stem cell differentiation. As shown by reconstitution in vitro and engineered systems in cells, UTX recruits the histone methyltransferase MLL4 (also known as KMT2D) to the same condensates and enriches the H3K4 methylation activity of MLL4. Moreover, UTX regulates genome-wide histone modifications and high-order chromatin interactions in a condensation-dependent manner. We also found that UTY, the Y chromosome homologue of UTX with weaker tumour-suppressive activity, forms condensates with reduced molecular dynamics. These studies demonstrate a crucial biological function of liquid condensates with proper material states in enabling the tumour-suppressive activity of a chromatin regulator.
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Affiliation(s)
- Bi Shi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Wei Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Yansu Song
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Rui Ju
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Aleksandra Ulman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jing Hu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Francesco Palomba
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Yanfang Zhao
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - John Philip Le
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - William Jarrard
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - David Dimoff
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Michelle A. Digman
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Enrico Gratton
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Chongzhi Zang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA,Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA,Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA,UVA Cancer Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA,UVA Cancer Center, University of Virginia School of Medicine, Charlottesville, VA, USA
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48
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Zeisig BB, So CWE. Therapeutic Opportunities of Targeting Canonical and Noncanonical PcG/TrxG Functions in Acute Myeloid Leukemia. Annu Rev Genomics Hum Genet 2021; 22:103-125. [PMID: 33929894 DOI: 10.1146/annurev-genom-111120-102443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcriptional deregulation is a key driver of acute myeloid leukemia (AML), a heterogeneous blood cancer with poor survival rates. Polycomb group (PcG) and Trithorax group (TrxG) genes, originally identified in Drosophila melanogaster several decades ago as master regulators of cellular identity and epigenetic memory, not only are important in mammalian development but also play a key role in AML disease biology. In addition to their classical canonical antagonistic transcriptional functions, noncanonical synergistic and nontranscriptional functions of PcG and TrxG are emerging. Here, we review the biochemical properties of major mammalian PcG and TrxG complexes and their roles in AML disease biology, including disease maintenance as well as drug resistance. We summarize current efforts on targeting PcG and TrxG for treatment of AML and propose rational synthetic lethality and drug-induced antagonistic pleiotropy options involving PcG and TrxG as potential new therapeutic avenues for treatment of AML.
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Affiliation(s)
- Bernd B Zeisig
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London SE5 9NU, United Kingdom;
- Department of Haematological Medicine, King's College Hospital, London SE5 9RS, United Kingdom
| | - Chi Wai Eric So
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London SE5 9NU, United Kingdom;
- Department of Haematological Medicine, King's College Hospital, London SE5 9RS, United Kingdom
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49
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Ciptasari U, van Bokhoven H. The phenomenal epigenome in neurodevelopmental disorders. Hum Mol Genet 2021; 29:R42-R50. [PMID: 32766754 PMCID: PMC7530535 DOI: 10.1093/hmg/ddaa175] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Disruption of chromatin structure due to epimutations is a leading genetic etiology of neurodevelopmental disorders, collectively known as chromatinopathies. We show that there is an increasing level of convergence from the high diversity of genes that are affected by mutations to the molecular networks and pathways involving the respective proteins, the disrupted cellular and subcellular processes, and their consequence for higher order cellular network function. This convergence is ultimately reflected by specific phenotypic features shared across the various chromatinopathies. Based on these observations, we propose that the commonly disrupted molecular and cellular anomalies might provide a rational target for the development of symptomatic interventions for defined groups of genetically distinct neurodevelopmental disorders.
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Affiliation(s)
- Ummi Ciptasari
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
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50
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Aiderus A, Newberg JY, Guzman-Rojas L, Contreras-Sandoval AM, Meshey AL, Jones DJ, Amaya-Manzanares F, Rangel R, Ward JM, Lee SC, Ban KHK, Rogers K, Rogers SM, Selvanesan L, McNoe LA, Copeland NG, Jenkins NA, Tsai KY, Black MA, Mann KM, Mann MB. Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression. PLoS Genet 2021; 17:e1009094. [PMID: 34398873 PMCID: PMC8389471 DOI: 10.1371/journal.pgen.1009094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 08/26/2021] [Accepted: 07/14/2021] [Indexed: 12/01/2022] Open
Abstract
The systematic identification of genetic events driving cellular transformation and tumor progression in the absence of a highly recurrent oncogenic driver mutation is a challenge in cutaneous oncology. In cutaneous squamous cell carcinoma (cuSCC), the high UV-induced mutational burden poses a hurdle to achieve a complete molecular landscape of this disease. Here, we utilized the Sleeping Beauty transposon mutagenesis system to statistically define drivers of keratinocyte transformation and cuSCC progression in vivo in the absence of UV-IR, and identified both known tumor suppressor genes and novel oncogenic drivers of cuSCC. Functional analysis confirms an oncogenic role for the ZMIZ genes, and tumor suppressive roles for KMT2C, CREBBP and NCOA2, in the initiation or progression of human cuSCC. Taken together, our in vivo screen demonstrates an extremely heterogeneous genetic landscape of cuSCC initiation and progression, which can be harnessed to better understand skin oncogenic etiology and prioritize therapeutic candidates. Non-melanoma skin cancers, the most common cancers in the US, are caused by UV skin exposure. Nearly 1 million cases of cutaneous squamous cell carcinoma (cuSCC) are diagnosed in the US each year. While most cuSCCs are highly treatable, more than twice as many individuals die from this disease as from melanoma. The high burden of UV-induced DNA damage in human skin poses a challenge for identifying initiating and cooperating mutations that promote cuSCC development and for defining potential therapeutic targets. Here, we describe a genetic screen in mice using a DNA transposon system to mutagenize the genome of keratinocytes and drive squamous cell carcinoma in the absence of UV. By sequencing where the transposons selectively integrated in the genomes of normal skin, skin with pre-cancerous lesions and skin with fully developed cuSCCs from our mouse model, we were able to identify frequently mutated genes likely important for this disease. Our analysis also defined cooperation between sets of genes not previously appreciated in cuSCC. Our mouse model and ensuing data provide a framework for understanding the genetics of cuSCC and for defining the molecular changes that may lead to the future therapies for patients.
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Affiliation(s)
- Aziz Aiderus
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Justin Y. Newberg
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Liliana Guzman-Rojas
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Ana M. Contreras-Sandoval
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Amanda L. Meshey
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Devin J. Jones
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Felipe Amaya-Manzanares
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Roberto Rangel
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Jerrold M. Ward
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Republic of Singapore
| | - Song-Choon Lee
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Republic of Singapore
| | - Kenneth Hon-Kim Ban
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Republic of Singapore
| | - Keith Rogers
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Republic of Singapore
| | - Susan M. Rogers
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Republic of Singapore
| | - Luxmanan Selvanesan
- Centre for Translational Cancer Research, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Leslie A. McNoe
- Centre for Translational Cancer Research, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Neal G. Copeland
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, United States of America
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Republic of Singapore
| | - Nancy A. Jenkins
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, United States of America
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Republic of Singapore
| | - Kenneth Y. Tsai
- Departments of Anatomic Pathology & Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Donald A. Adam Melanoma and Skin Cancer Research Center of Excellence, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Michael A. Black
- Centre for Translational Cancer Research, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Karen M. Mann
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, United States of America
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Republic of Singapore
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Departments of Gastrointestinal Oncology & Malignant Hematology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Cancer Biology and Evolution Program, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Michael B. Mann
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, United States of America
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Republic of Singapore
- Donald A. Adam Melanoma and Skin Cancer Research Center of Excellence, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Cancer Biology and Evolution Program, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- * E-mail:
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