1
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Cao R, Thatavarty A, King KY. Forged in the fire: Lasting impacts of inflammation on hematopoietic progenitors. Exp Hematol 2024; 134:104215. [PMID: 38580008 DOI: 10.1016/j.exphem.2024.104215] [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: 01/11/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
Quiescence and differentiation of hematopoietic stem and progenitor cells (HSPC) can be modified by systemic inflammatory cues. Such cues can not only yield short-term changes in HSPCs such as in supporting emergency granulopoiesis but can also promote lasting influences on the HSPC compartment. First, inflammation can be a driver for clonal expansion, promoting clonal hematopoiesis for certain mutant clones, reducing overall clonal diversity, and reshaping the composition of the HSPC pool with significant health consequences. Second, inflammation can generate lasting cell-autonomous changes in HSPCs themselves, leading to changes in the epigenetic state, metabolism, and function of downstream innate immune cells. This concept, termed "trained immunity," suggests that inflammatory stimuli can alter subsequent immune responses leading to improved innate immunity or, conversely, autoimmunity. Both of these concepts have major implications in human health. Here we reviewed current literature about the lasting effects of inflammation on the HSPC compartment and opportunities for future advancement in this fast-developing field.
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Affiliation(s)
- Ruoqiong Cao
- Department of Pediatrics - Division of Infectious Disease, Texas Children's Hospital, Baylor College of Medicine, Houston, TX; Graduate Program in Immunology and Microbiology, Baylor College of Medicine, Houston, TX; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Apoorva Thatavarty
- Department of Pediatrics - Division of Infectious Disease, Texas Children's Hospital, Baylor College of Medicine, Houston, TX; Graduate Program in Genetics and Genomics, Baylor College of Medicine, Houston, Texas; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Katherine Y King
- Department of Pediatrics - Division of Infectious Disease, Texas Children's Hospital, Baylor College of Medicine, Houston, TX; Graduate Program in Immunology and Microbiology, Baylor College of Medicine, Houston, TX; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX.
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2
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Mas-Ponte D, Supek F. Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation. Nucleic Acids Res 2024; 52:4393-4408. [PMID: 38587182 PMCID: PMC11077091 DOI: 10.1093/nar/gkae252] [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: 09/18/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
Local mutation rates in human are highly heterogeneous, with known variability at the scale of megabase-sized chromosomal domains, and, on the other extreme, at the scale of oligonucleotides. The intermediate, kilobase-scale heterogeneity in mutation risk is less well characterized. Here, by analyzing thousands of somatic genomes, we studied mutation risk gradients along gene bodies, representing a genomic scale spanning roughly 1-10 kb, hypothesizing that different mutational mechanisms are differently distributed across gene segments. The main heterogeneity concerns several kilobases at the transcription start site and further downstream into 5' ends of gene bodies; these are commonly hypomutated with several mutational signatures, most prominently the ubiquitous C > T changes at CpG dinucleotides. The width and shape of this mutational coldspot at 5' gene ends is variable across genes, and corresponds to variable interval of lowered DNA methylation depending on gene activity level and regulation. Such hypomutated loci, at 5' gene ends or elsewhere, correspond to DNA hypomethylation that can associate with various landmarks, including intragenic enhancers, Polycomb-marked regions, or chromatin loop anchor points. Tissue-specific DNA hypomethylation begets tissue-specific local hypomutation. Of note, direction of mutation risk is inverted for AID/APOBEC3 cytosine deaminase activity, whose signatures are enriched in hypomethylated regions.
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Affiliation(s)
- David Mas-Ponte
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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3
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Kapadia CD, Goodell MA. Tissue mosaicism following stem cell aging: blood as an exemplar. NATURE AGING 2024; 4:295-308. [PMID: 38438628 DOI: 10.1038/s43587-024-00589-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024]
Abstract
Loss of stem cell regenerative potential underlies aging of all tissues. Somatic mosaicism, the emergence of cellular patchworks within tissues, increases with age and has been observed in every organ yet examined. In the hematopoietic system, as in most tissues, stem cell aging through a variety of mechanisms occurs in lockstep with the emergence of somatic mosaicism. Here, we draw on insights from aging hematopoiesis to illustrate fundamental principles of stem cell aging and somatic mosaicism. We describe the generalizable changes intrinsic to aged stem cells and their milieu that provide the backdrop for somatic mosaicism to emerge. We discuss genetic and nongenetic mechanisms that can result in tissue somatic mosaicism and existing methodologies to detect such clonal outgrowths. Finally, we propose potential avenues to modify mosaicism during aging, with the ultimate aim of increasing tissue resiliency.
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Affiliation(s)
- Chiraag D Kapadia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
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4
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Verdikt R, Thienpont B. Epigenetic remodelling under hypoxia. Semin Cancer Biol 2024; 98:1-10. [PMID: 38029868 DOI: 10.1016/j.semcancer.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Hypoxia is intrinsic to tumours and contributes to malignancy and metastasis while hindering the efficiency of existing treatments. Epigenetic mechanisms play a crucial role in the regulation of hypoxic cancer cell programs, both in the initial phases of sensing the decrease in oxygen levels and during adaptation to chronic lack of oxygen. During the latter, the epigenetic regulation of tumour biology intersects with hypoxia-sensitive transcription factors in a complex network of gene regulation that also involves metabolic reprogramming. Here, we review the current literature on the epigenetic control of gene programs in hypoxic cancer cells. We highlight common themes and features of such epigenetic remodelling and discuss their relevance for the development of therapeutic strategies.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium; KU Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
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5
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Feng Y, Zhang Z, Hong Y, Ding Y, Liu L, Gao S, Fang H, Shi J. A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns. Genome Res 2023; 33:gr.278146.123. [PMID: 37940553 PMCID: PMC10760529 DOI: 10.1101/gr.278146.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
DNA methylation and associated regulatory elements play a crucial role in gene expression regulation. Previous studies have focused primarily on the distribution of mean methylation levels. Advances in whole-genome bisulfite sequencing (WGBS) have enabled the characterization of DNA methylation haplotypes (MHAPs), representing CpG sites from the same read fragment on a single chromosome, and the subsequent identification of methylation haplotype blocks (MHBs), in which adjacent CpGs on the same fragment are comethylated. Using our expert-curated WGBS data sets, we report comprehensive landscapes of MHBs in 17 representative normal somatic human tissues and during early human embryonic development. Integrative analysis reveals MHBs as a distinctive type of regulatory element characterized by comethylation patterns rather than mean methylation levels. We show the enrichment of MHBs in open chromatin regions, tissue-specific histone marks, and enhancers, including super-enhancers. Moreover, we find that MHBs tend to localize near tissue-specific genes and show an association with differential gene expression that is independent of mean methylation. Similar findings are observed in the context of human embryonic development, highlighting the dynamic nature of MHBs during early development. Collectively, our comprehensive MHB landscapes provide valuable insights into the tissue specificity and developmental dynamics of DNA methylation.
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Affiliation(s)
- Yan Feng
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yuyang Hong
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi Ding
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Leiqin Liu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Siqi Gao
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiantao Shi
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China;
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6
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Gao X, Yi Y, Lv J, Li Y, Arulsamy K, Babu S, Bruno I, Zhang L, Cao Q, Chen K. Low RNA stability signifies strong expression regulatability of tumor suppressors. Nucleic Acids Res 2023; 51:11534-11548. [PMID: 37831104 PMCID: PMC10681714 DOI: 10.1093/nar/gkad838] [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: 04/25/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
RNA expression of a gene is determined by not only transcriptional regulation, but also post-transcriptional regulation of RNA decay. The precise regulation of RNA stability in the cell plays an important role in normal development. Dysregulation of RNA stability can lead to diseases such as cancer. Here we found tumor suppressor RNAs tended to decay fast in normal cell types when compared with other RNAs. Consistent with a negative effect of m6A modification on RNA stability, we observed preferential deposition of m6A on tumor suppressor RNAs. Moreover, abundant m6A and fast decay of tumor suppressor RNAs both tended to be further enhanced in prostate cancer cells relative to normal prostate epithelial cells. Further, knockdown of m6A methyltransferase METTL3 and reader YTHDF2 in prostate cancer cells both posed stronger effect on tumor suppressor RNAs than on other RNAs. These results indicated a strong post transcriptional expression regulatability mediated by abundant m6A modification on tumor suppressor RNAs.
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Affiliation(s)
- Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yi
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jie Lv
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Kulandaisamy Arulsamy
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sahana Suresh Babu
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Ivone Bruno
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
- Prostate Cancer Program, Dana-Farber Harvard cancer Center, Boston, MA 02115, USA
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7
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Zhang W, Wang H, Ma Y, Gao B, Guan P, Huang X, Ouyang W, Guo M, Chen G, Li G, Li X. Domains Rearranged Methylase 2 maintains DNA methylation at large DNA hypomethylated shores and long-range chromatin interactions in rice. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2333-2347. [PMID: 37539491 PMCID: PMC10579712 DOI: 10.1111/pbi.14134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/25/2023] [Accepted: 07/08/2023] [Indexed: 08/05/2023]
Abstract
DNA methylation plays an important role in gene regulation and genomic stability. However, large DNA hypomethylated regions known as DNA methylation valleys (DMVs) or canyons have also been suggested to serve unique regulatory functions, largely unknown in rice (Oryza sativa). Here, we describe the DMVs in rice seedlings, which were highly enriched with developmental and transcription regulatory genes. Further detailed analysis indicated that grand DMVs (gDMVs) might be derived from nuclear integrants of organelle DNA (NORGs). Furthermore, Domains Rearranged Methylase 2 (OsDRM2) maintained DNA methylation at short DMV (sDMV) shores. Epigenetic maps indicated that sDMVs were marked with H3K4me3 and/or H3K27me3, although the loss of DNA methylation had a negligible effect on histone modification within these regions. In addition, we constructed H3K27me3-associated interaction maps for homozygous T-DNA insertion mutant of the gene (osdrm2) and wild type (WT). From a global perspective, most (90%) compartments were stable between osdrm2 and WT plants. At a high resolution, we observed a dramatic loss of long-range chromatin loops in osdrm2, which suffered an extensive loss of non-CG (CHG and CHH, H = A, T, or C) methylation. From another viewpoint, the loss of non-CG methylation at sDMV shores in osdrm2 could disrupt H3K27me3-mediated chromatin interaction networks. Overall, our results demonstrated that DMVs are a key genomic feature in rice and are precisely regulated by epigenetic modifications, including DNA methylation and histone modifications. OsDRM2 maintained DNA methylation at sDMV shores, while OsDRM2 deficiency strongly affected three-dimensional (3D) genome architectures.
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Affiliation(s)
- Wei Zhang
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Huanhuan Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yuning Ma
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Baibai Gao
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Pengpeng Guan
- Hubei Key Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Xingyu Huang
- Hubei Key Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Minrong Guo
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Guoting Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Guoliang Li
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of InformaticsHuazhong Agricultural UniversityWuhanChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhanChina
| | - Xingwang Li
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhanChina
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8
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Irie N, Lee SM, Lorenzi V, Xu H, Chen J, Inoue M, Kobayashi T, Sancho-Serra C, Drousioti E, Dietmann S, Vento-Tormo R, Song CX, Surani MA. DMRT1 regulates human germline commitment. Nat Cell Biol 2023; 25:1439-1452. [PMID: 37709822 PMCID: PMC10567552 DOI: 10.1038/s41556-023-01224-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/07/2023] [Indexed: 09/16/2023]
Abstract
Germline commitment following primordial germ cell (PGC) specification during early human development establishes an epigenetic programme and competence for gametogenesis. Here we follow the progression of nascent PGC-like cells derived from human embryonic stem cells in vitro. We show that switching from BMP signalling for PGC specification to Activin A and retinoic acid resulted in DMRT1 and CDH5 expression, the indicators of migratory PGCs in vivo. Moreover, the induction of DMRT1 and SOX17 in PGC-like cells promoted epigenetic resetting with striking global enrichment of 5-hydroxymethylcytosine and locus-specific loss of 5-methylcytosine at DMRT1 binding sites and the expression of DAZL representing DNA methylation-sensitive genes, a hallmark of the germline commitment programme. We provide insight into the unique role of DMRT1 in germline development for advances in human germ cell biology and in vitro gametogenesis.
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Affiliation(s)
- Naoko Irie
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, UK.
- Metabolic Systems Laboratory, Live Imaging Center, Central Institute for Experimental Animals, Kanagawa, Japan.
| | - Sun-Min Lee
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, UK
- Department of Physics, Konkuk University, Seoul, Republic of Korea
| | - Valentina Lorenzi
- Wellcome Sanger Institute, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Haiqi Xu
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jinfeng Chen
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Masato Inoue
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Toshihiro Kobayashi
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Aichi, Japan
| | | | - Elena Drousioti
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, UK
| | - Sabine Dietmann
- Department of Developmental Biology and Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Chun-Xiao Song
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, UK.
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, UK.
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9
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Barbosa K, Deshpande AJ. Therapeutic targeting of leukemia stem cells in acute myeloid leukemia. Front Oncol 2023; 13:1204895. [PMID: 37601659 PMCID: PMC10437214 DOI: 10.3389/fonc.2023.1204895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
One of the distinguishing properties of hematopoietic stem cells is their ability to self-renew. Since self-renewal is important for the continuous replenishment of the hematopoietic stem cell pool, this property is often hijacked in blood cancers. Acute myeloid leukemia (AML) is believed to be arranged in a hierarchy, with self-renewing leukemia stem cells (LSCs) giving rise to the bulk tumor. Some of the earliest characterizations of LSCs were made in seminal studies that assessed the ability of prospectively isolated candidate AML stem cells to repopulate the entire heterogeneity of the tumor in mice. Further studies indicated that LSCs may be responsible for chemotherapy resistance and therefore act as a reservoir for secondary disease and leukemia relapse. In recent years, a number of studies have helped illuminate the complexity of clonality in bone marrow pathologies, including leukemias. Many features distinguishing LSCs from normal hematopoietic stem cells have been identified, and these studies have opened up diverse avenues for targeting LSCs, with an impact on the clinical management of AML patients. This review will discuss the role of self-renewal in AML and its implications, distinguishing characteristics between normal and leukemia stem cells, and opportunities for therapeutic targeting of AML LSCs.
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Affiliation(s)
- Karina Barbosa
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Aniruddha J. Deshpande
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
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10
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Sikking MA, Stroeks SLVM, Waring OJ, Henkens MTHM, Riksen NP, Hoischen A, Heymans SRB, Verdonschot JAJ. Clonal Hematopoiesis of Indeterminate Potential From a Heart Failure Specialist's Point of View. J Am Heart Assoc 2023; 12:e030603. [PMID: 37489738 PMCID: PMC10492961 DOI: 10.1161/jaha.123.030603] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/06/2023] [Indexed: 07/26/2023]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a common bone marrow abnormality induced by age-related DNA mutations, which give rise to proinflammatory immune cells. These immune cells exacerbate atherosclerotic cardiovascular disease and may induce or accelerate heart failure. The mechanisms involved are complex but point toward a central role for proinflammatory macrophages and an inflammasome-dependent immune response (IL-1 [interleukin-1] and IL-6 [interleukin-6]) in the atherosclerotic plaque or directly in the myocardium. Intracardiac inflammation may decrease cardiac function and induce cardiac fibrosis, even in the absence of atherosclerotic cardiovascular disease. The pathophysiology and consequences of CHIP may differ among implicated genes as well as subgroups of patients with heart failure, based on cause (ischemic versus nonischemic) and ejection fraction (reduced ejection fraction versus preserved ejection fraction). Evidence is accumulating that CHIP is associated with cardiovascular mortality in ischemic and nonischemic heart failure with reduced ejection fraction and involved in the development of heart failure with preserved ejection fraction. CHIP and corresponding inflammatory pathways provide a highly potent therapeutic target. Randomized controlled trials in patients with well-phenotyped heart failure, where readily available anti-inflammatory therapies are used to intervene with clonal hematopoiesis, may pave the way for a new area of heart failure treatment. The first clinical trials that target CHIP are already registered.
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Affiliation(s)
- Maurits A. Sikking
- Department of CardiologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
| | - Sophie L. V. M. Stroeks
- Department of CardiologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
| | - Olivia J. Waring
- Department of PathologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
| | - Michiel T. H. M. Henkens
- Department of PathologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
- Netherlands Heart Institute (NLHI)Utrechtthe Netherlands
| | - Niels P. Riksen
- Department of Internal MedicineRadboud University Medical CenterNijmegenthe Netherlands
| | - Alexander Hoischen
- Department of Human GeneticsRadboud University Medical CenterNijmegenthe Netherlands
| | - Stephane R. B. Heymans
- Department of CardiologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
- Department of Cardiovascular ResearchUniversity of LeuvenBelgium
| | - Job A. J. Verdonschot
- Department of CardiologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
- Department of Clinical GeneticsMaastricht University Medical Center (MUMC)Maastrichtthe Netherlands
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11
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Li Y, Yi Y, Lv J, Gao X, Yu Y, Babu S, Bruno I, Zhao D, Xia B, Peng W, Zhu J, Chen H, Zhang L, Cao Q, Chen K. Low RNA stability signifies increased post-transcriptional regulation of cell identity genes. Nucleic Acids Res 2023; 51:6020-6038. [PMID: 37125636 PMCID: PMC10325912 DOI: 10.1093/nar/gkad300] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023] Open
Abstract
Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g. by super-enhancers and broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m6A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains and their associated genes. METTL3 binding intensity is positively correlated with RNA m6A methylation and negatively correlated with RNA stability of cell identity genes, probably due to co-transcriptional m6A modifications promoting RNA decay. Nanopore direct RNA-sequencing showed that METTL3 knockdown has a stronger effect on RNA m6A and mRNA stability for cell identity genes. Our data suggest a run-and-brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression.
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Affiliation(s)
- Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yi
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jie Lv
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yu
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sahana Suresh Babu
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Ivone Bruno
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Dongyu Zhao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Bo Xia
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC 20052, USA
| | - Jun Zhu
- Systems Biology Center, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Hong Chen
- Vascular Biology Program, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
- Broad Institute of MIT and Harvard, Boston, MA 02115, USA
- Dana-Farber/Harvard Cancer Center, Boston, MA 02115, USA
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12
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van der Veer BK, Chen L, Custers C, Athanasouli P, Schroiff M, Cornelis R, Chui JSH, Finnell R, Lluis F, Koh K. Dual functions of TET1 in germ layer lineage bifurcation distinguished by genomic context and dependence on 5-methylcytosine oxidation. Nucleic Acids Res 2023; 51:5469-5498. [PMID: 37021585 PMCID: PMC10287924 DOI: 10.1093/nar/gkad231] [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: 10/07/2022] [Revised: 03/12/2023] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
Gastrulation begins when the epiblast forms the primitive streak or becomes definitive ectoderm. During this lineage bifurcation, the DNA dioxygenase TET1 has bipartite functions in transcriptional activation and repression, but the mechanisms remain unclear. By converting mouse embryonic stem cells (ESCs) into neuroprogenitors, we defined how Tet1-/- cells switch from neuroectoderm fate to form mesoderm and endoderm. We identified the Wnt repressor Tcf7l1 as a TET1 target that suppresses Wnt/β-catenin and Nodal signalling. ESCs expressing catalytic dead TET1 retain neural potential but activate Nodal and subsequently Wnt/β-catenin pathways to generate also mesoderm and endoderm. At CpG-poor distal enhancers, TET1 maintains accessible chromatin at neuroectodermal loci independently of DNA demethylation. At CpG-rich promoters, DNA demethylation by TET1 affects the expression of bivalent genes. In ESCs, a non-catalytic TET1 cooperation with Polycomb represses primitive streak genes; post-lineage priming, the interaction becomes antagonistic at neuronal genes, when TET1's catalytic activity is further involved by repressing Wnt signalling. The convergence of repressive DNA and histone methylation does not inhibit neural induction in Tet1-deficient cells, but some DNA hypermethylated loci persist at genes with brain-specific functions. Our results reveal versatile switching of non-catalytic and catalytic TET1 activities based on genomic context, lineage and developmental stage.
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Affiliation(s)
- Bernard K van der Veer
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
| | - Lehua Chen
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
| | - Colin Custers
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
| | - Paraskevi Athanasouli
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell Signaling, B-3000 Leuven, Belgium
| | - Mariana Schroiff
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
| | - Riet Cornelis
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
| | - Jonathan Sai-Hong Chui
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell Signaling, B-3000 Leuven, Belgium
| | - Richard H Finnell
- Baylor College of Medicine, Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Houston, TX 77030, USA
- Baylor College of Medicine, Department of Molecular and Human Genetics, Department of Medicine, Houston, TX 77030, USA
| | - Frederic Lluis
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell Signaling, B-3000 Leuven, Belgium
| | - Kian Peng Koh
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
- Baylor College of Medicine, Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Houston, TX 77030, USA
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13
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Bassal MA. The Interplay between Dysregulated Metabolism and Epigenetics in Cancer. Biomolecules 2023; 13:944. [PMID: 37371524 DOI: 10.3390/biom13060944] [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: 04/24/2023] [Revised: 05/21/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Cellular metabolism (or energetics) and epigenetics are tightly coupled cellular processes. It is arguable that of all the described cancer hallmarks, dysregulated cellular energetics and epigenetics are the most tightly coregulated. Cellular metabolic states regulate and drive epigenetic changes while also being capable of influencing, if not driving, epigenetic reprogramming. Conversely, epigenetic changes can drive altered and compensatory metabolic states. Cancer cells meticulously modify and control each of these two linked cellular processes in order to maintain their tumorigenic potential and capacity. This review aims to explore the interplay between these two processes and discuss how each affects the other, driving and enhancing tumorigenic states in certain contexts.
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Affiliation(s)
- Mahmoud Adel Bassal
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
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14
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Lo EK, Mears BM, Maurer HC, Idrizi A, Hansen KD, Thompson ED, Hruban RH, Olive KP, Feinberg AP. Comprehensive DNA Methylation Analysis Indicates That Pancreatic Intraepithelial Neoplasia Lesions Are Acinar-Derived and Epigenetically Primed for Carcinogenesis. Cancer Res 2023; 83:1905-1916. [PMID: 36989344 PMCID: PMC10239363 DOI: 10.1158/0008-5472.can-22-4052] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is believed to arise from the accumulation of a series of somatic mutations and is also frequently associated with pancreatic intraepithelial neoplasia (PanIN) lesions. However, there is still debate as to whether the cell type-of-origin of PanINs and PDACs in humans is acinar or ductal. As cell type identity is maintained epigenetically, DNA methylation changes during pancreatic neoplasia can provide a compelling perspective to examine this question. Here, we performed laser-capture microdissection on surgically resected specimens from 18 patients to isolate, with high purity, DNA for whole-genome bisulfite sequencing from four relevant cell types: acini, nonneoplastic ducts, PanIN lesions, and PDAC lesions. Differentially methylated regions (DMR) were identified using two complementary analytical approaches: bsseq, which identifies any DMRs but is particularly useful for large block-like DMRs, and informME, which profiles the potential energy landscape across the genome and is particularly useful for identifying differential methylation entropy. Both global methylation profiles and block DMRs clearly implicated an acinar origin for PanINs. At the gene level, PanIN lesions exhibited an intermediate acinar-ductal phenotype resembling acinar-to-ductal metaplasia. In 97.6% of PanIN-specific DMRs, PanIN lesions had an intermediate methylation level between normal and PDAC, which suggests from an information theory perspective that PanIN lesions are epigenetically primed to progress to PDAC. Thus, epigenomic analysis complements histopathology to define molecular progression toward PDAC. The shared epigenetic lineage between PanIN and PDAC lesions could provide an opportunity for prevention by targeting aberrantly methylated progression-related genes. SIGNIFICANCE Analysis of DNA methylation landscapes provides insights into the cell-of-origin of PanIN lesions, clarifies the role of PanIN lesions as metaplastic precursors to human PDAC, and suggests potential targets for chemoprevention.
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Affiliation(s)
- Emily K.W. Lo
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian M. Mears
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - H. Carlo Maurer
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kasper D. Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Elizabeth D. Thompson
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Baltimore, MD, USA
| | - Ralph H. Hruban
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Baltimore, MD, USA
| | - Kenneth P. Olive
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, MD, USA
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15
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Wang X, Dai L, Liu Y, Li C, Fan D, Zhou Y, Li P, Kong Q, Su J. Partial erosion on under-methylated regions and chromatin reprogramming contribute to oncogene activation in IDH mutant gliomas. Epigenetics Chromatin 2023; 16:13. [PMID: 37118755 PMCID: PMC10142198 DOI: 10.1186/s13072-023-00490-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/21/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND IDH1/2 hotspot mutations are well known to drive oncogenic mutations in gliomas and are well-defined in the WHO 2021 classification of central nervous system tumors. Specifically, IDH mutations lead to aberrant hypermethylation of under-methylated regions (UMRs) in normal tissues through the disruption of TET enzymes. However, the chromatin reprogramming and transcriptional changes induced by IDH-related hypermethylation in gliomas remain unclear. RESULTS Here, we have developed a precise computational framework based on Hidden Markov Model to identify altered methylation states of UMRs at single-base resolution. By applying this framework to whole-genome bisulfite sequencing data from 75 normal brain tissues and 15 IDH mutant glioma tissues, we identified two distinct types of hypermethylated UMRs in IDH mutant gliomas. We named them partially hypermethylated UMRs (phUMRs) and fully hypermethylated UMRs (fhUMRs), respectively. We found that the phUMRs and fhUMRs exhibit distinct genomic features and chromatin states. Genes related to fhUMRs were more likely to be repressed in IDH mutant gliomas. In contrast, genes related to phUMRs were prone to be up-regulated in IDH mutant gliomas. Such activation of phUMR genes is associated with the accumulation of active H3K4me3 and the loss of H3K27me3, as well as H3K36me3 accumulation in gene bodies to maintain gene expression stability. In summary, partial erosion on UMRs was accompanied by locus-specific changes in key chromatin marks, which may contribute to oncogene activation. CONCLUSIONS Our study provides a computational strategy for precise decoding of methylation encroachment patterns in IDH mutant gliomas, revealing potential mechanistic insights into chromatin reprogramming that contribute to oncogenesis.
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Affiliation(s)
- Xinyu Wang
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, China
| | - Lijun Dai
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, China
| | - Yang Liu
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, China
| | - Chenghao Li
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, China
| | - Dandan Fan
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, China
| | - Yue Zhou
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325011, Zhejiang, China
| | - Pengcheng Li
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, China
| | - Qingran Kong
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325011, Zhejiang, China
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, China.
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325011, Zhejiang, China.
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China.
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16
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Cao X, Xu J, Lin YL, Cabrera RM, Chen Q, Zhang C, Steele JW, Han X, Gross SS, Wlodarczyk BJ, Lupski JR, Li W, Wang H, Finnell RH, Lei Y. Excess folic acid intake increases DNA de novo point mutations. Cell Discov 2023; 9:22. [PMID: 36849450 PMCID: PMC9970956 DOI: 10.1038/s41421-022-00512-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/21/2022] [Indexed: 03/01/2023] Open
Affiliation(s)
- Xuanye Cao
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jianfeng Xu
- Division of Biostatistics, Dan L. Duncan Cancer and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Ying L Lin
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Robert M Cabrera
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA
| | - Chaofan Zhang
- Departments of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - John W Steele
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Xiao Han
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA
| | - Bogdan J Wlodarczyk
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Departments of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Wei Li
- Division of Biostatistics, Dan L. Duncan Cancer and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Hongyan Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Key Laboratory of Reproduction Regulation of NPFPC, Children Hospital, Fudan University, Shanghai, China.
| | - Richard H Finnell
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Departments of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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17
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Urabe A, Chi S, Minami Y. The Immuno-Oncology and Genomic Aspects of DNA-Hypomethylating Therapeutics in Acute Myeloid Leukemia. Int J Mol Sci 2023; 24:ijms24043727. [PMID: 36835136 PMCID: PMC9961620 DOI: 10.3390/ijms24043727] [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: 12/24/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Hypomethylating agents (HMAs) have been used for decades in the treatment of hematologic neoplasms, and now, have gathered attention again in terms of their combination with potent molecular-targeted agents such as a BCL-6 inhibitor venetoclax and an IDH1 inhibitor ivosidenib, as well as a novel immune-checkpoint inhibitor (anit-CD47 antibody) megrolimab. Several studies have shown that leukemic cells have a distinct immunological microenvironment, which is at least partially due to genetic alterations such as the TP53 mutation and epigenetic dysregulation. HMAs possibly improve intrinsic anti-leukemic immunity and sensitivity to immune therapies such as PD-1/PD-L1 inhibitors and anti-CD47 agents. This review describes the immuno-oncological backgrounds of the leukemic microenvironment and the therapeutic mechanisms of HMAs, as well as current clinical trials of HMAs and/or venetoclax-based combination therapies.
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Affiliation(s)
| | | | - Yosuke Minami
- Correspondence: ; Tel.: +81-4-7133-1111; Fax: +81-7133-6502
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18
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Feinberg AP, Levchenko A. Epigenetics as a mediator of plasticity in cancer. Science 2023; 379:eaaw3835. [PMID: 36758093 PMCID: PMC10249049 DOI: 10.1126/science.aaw3835] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 12/22/2022] [Indexed: 02/11/2023]
Abstract
The concept of an epigenetic landscape describing potential cellular fates arising from pluripotent cells, first advanced by Conrad Waddington, has evolved in light of experiments showing nondeterministic outcomes of regulatory processes and mathematical methods for quantifying stochasticity. In this Review, we discuss modern approaches to epigenetic and gene regulation landscapes and the associated ideas of entropy and attractor states, illustrating how their definitions are both more precise and relevant to understanding cancer etiology and the plasticity of cancerous states. We address the interplay between different types of regulatory landscapes and how their changes underlie cancer progression. We also consider the roles of cellular aging and intrinsic and extrinsic stimuli in modulating cellular states and how landscape alterations can be quantitatively mapped onto phenotypic outcomes and thereby used in therapy development.
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Affiliation(s)
- Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University Schools of Medicine, Biomedical Engineering, and Public Health, Baltimore, MD 21205, USA
| | - Andre Levchenko
- Yale Systems Biology Institute and Department of Biomedical Engineering, Yale University, West Haven, CT 06516, USA
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19
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Xu Y, Zhang Z, Zhao Y, Zhao C, Shi M, Dong X, Zhang J, Tan L, Zhang L, Zhao Y. TRAPPC1 is essential for the maintenance and differentiation of common myeloid progenitors in mice. EMBO Rep 2023; 24:e55503. [PMID: 36440617 PMCID: PMC9900341 DOI: 10.15252/embr.202255503] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022] Open
Abstract
Myeloid cell development in bone marrow is essential for the maintenance of peripheral immune homeostasis. However, the role of intracellular protein trafficking pathways during myeloid cell differentiation is currently unknown. By mining bioinformatics data, we identify trafficking protein particle complex subunit 1 (TRAPPC1) as continuously upregulated during myeloid cell development. Using inducible ER-TRAPPC1 knockout mice and bone marrow chimeric mouse models, we demonstrate that TRAPPC1 deficiency causes severe monocyte and neutrophil defects, accompanied by a selective decrease in common myeloid progenitors (CMPs) and subsequent cell subsets in bone marrow. TRAPPC1-deleted CMPs differentiate poorly into monocytes and neutrophils in vivo and in vitro, in addition to exhibiting enhanced endoplasmic reticulum stress and apoptosis via a Ca2+ -mitochondria-dependent pathway. Cell cycle arrest and senescence of TRAPPC1-deleted CMPs are mediated by the activation of pancreatic endoplasmic reticulum kinase and the upregulation of cyclin-dependent kinase inhibitor p21. This study reveals the essential role of TRAPPC1 in the maintenance and differentiation of CMPs and highlights the significance of protein processing and trafficking processes in myeloid cell development.
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Affiliation(s)
- Yanan Xu
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Zhaoqi Zhang
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Yang Zhao
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Chenxu Zhao
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Mingpu Shi
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Xue Dong
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Jiayu Zhang
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Liang Tan
- Kidney Transplantation DepartmentSecond Xiangya Hospital of Central South UniversityChangshaChina
| | - Lianfeng Zhang
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Laboratory Animal ScienceChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Yong Zhao
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
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20
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Poondi Krishnan V, Morone B, Toubiana S, Krzak M, Fioriniello S, Della Ragione F, Strazzullo M, Angelini C, Selig S, Matarazzo MR. The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory. Genome Res 2023; 33:169-183. [PMID: 36828588 PMCID: PMC10069469 DOI: 10.1101/gr.276986.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 01/12/2023] [Indexed: 02/26/2023]
Abstract
Bi-allelic hypomorphic mutations in DNMT3B disrupt DNA methyltransferase activity and lead to immunodeficiency, centromeric instability, facial anomalies syndrome, type 1 (ICF1). Although several ICF1 phenotypes have been linked to abnormally hypomethylated repetitive regions, the unique genomic regions responsible for the remaining disease phenotypes remain largely uncharacterized. Here we explored two ICF1 patient-derived induced pluripotent stem cells (iPSCs) and their CRISPR-Cas9-corrected clones to determine whether DNMT3B correction can globally overcome DNA methylation defects and related changes in the epigenome. Hypomethylated regions throughout the genome are highly comparable between ICF1 iPSCs carrying different DNMT3B variants, and significantly overlap with those in ICF1 patient peripheral blood and lymphoblastoid cell lines. These regions include large CpG island domains, as well as promoters and enhancers of several lineage-specific genes, in particular immune-related, suggesting that they are premarked during early development. CRISPR-corrected ICF1 iPSCs reveal that the majority of phenotype-related hypomethylated regions reacquire normal DNA methylation levels following editing. However, at the most severely hypomethylated regions in ICF1 iPSCs, which also display the highest increases in H3K4me3 levels and/or abnormal CTCF binding, the epigenetic memory persists, and hypomethylation remains uncorrected. Overall, we demonstrate that restoring the catalytic activity of DNMT3B can reverse the majority of the aberrant ICF1 epigenome. However, a small fraction of the genome is resilient to this rescue, highlighting the challenge of reverting disease states that are due to genome-wide epigenetic perturbations. Uncovering the basis for the persistent epigenetic memory will promote the development of strategies to overcome this obstacle.
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Affiliation(s)
- Varsha Poondi Krishnan
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
| | - Barbara Morone
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
| | - Shir Toubiana
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Monika Krzak
- Institute for Applied Computing (IAC) "Mauro Picone", CNR, Naples 80131 Italy
| | - Salvatore Fioriniello
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy.,IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia 86077, Italy
| | - Maria Strazzullo
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy;
| | - Claudia Angelini
- Institute for Applied Computing (IAC) "Mauro Picone", CNR, Naples 80131 Italy;
| | - Sara Selig
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel; .,Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
| | - Maria R Matarazzo
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
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21
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Lauria A, Meng G, Proserpio V, Rapelli S, Maldotti M, Polignano IL, Anselmi F, Incarnato D, Krepelova A, Donna D, Levra Levron C, Donati G, Molineris I, Neri F, Oliviero S. DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells. Nat Commun 2023; 14:367. [PMID: 36690616 PMCID: PMC9871038 DOI: 10.1038/s41467-023-35938-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
The correct establishment of DNA methylation patterns during mouse early development is essential for cell fate specification. However, the molecular targets as well as the mechanisms that determine the specificity of the de novo methylation machinery during differentiation are not completely elucidated. Here we show that the DNMT3B-dependent DNA methylation of key developmental regulatory regions at epiblast-like cells (EpiLCs) provides an epigenetic priming that ensures flawless commitment at later stages. Using in vitro stem cell differentiation and loss of function experiments combined with high-throughput genome-wide bisulfite-, bulk-, and single cell RNA-sequencing we dissected the specific role of DNMT3B in cell fate. We identify DNMT3B-dependent regulatory elements on the genome which, in Dnmt3b knockout (3BKO), impair the differentiation into meso-endodermal (ME) progenitors and redirect EpiLCs towards the neuro-ectodermal lineages. Moreover, ectopic expression of DNMT3B in 3BKO re-establishes the DNA methylation of the master regulator Sox2 super-enhancer, downmodulates its expression, and restores the expression of ME markers. Taken together, our data reveal that DNMT3B-dependent methylation at the epiblast stage is essential for the priming of the meso-endodermal lineages and provide functional characterization of the de novo DNMTs during EpiLCs lineage determination.
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Affiliation(s)
- Andrea Lauria
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Guohua Meng
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Valentina Proserpio
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Stefania Rapelli
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Mara Maldotti
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Isabelle Laurence Polignano
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Francesca Anselmi
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Anna Krepelova
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Daniela Donna
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Chiara Levra Levron
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Ivan Molineris
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Francesco Neri
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy.
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy.
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22
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Park HS, Im K, Shin D, Yoon S, Kwon S, Kim SW, Lee DS. Telomere integrated scoring system of myelodysplastic syndrome. J Clin Lab Anal 2023; 37:e24839. [PMID: 36658792 PMCID: PMC9978071 DOI: 10.1002/jcla.24839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/05/2022] [Accepted: 12/30/2022] [Indexed: 01/21/2023] Open
Abstract
INTRODUCTION Recently, multigene target sequencing is widely performed for the purpose of prognostic prediction and application of targeted therapy. Here, we proposed a new scoring system that encompasses gene variations, telomere length, and Revised International Prognostic Scoring System (IPSS-R) together in Asian myelodysplastic syndrome. METHODS We developed a new scoring model of these variables: age ≥ 65 years + IPSS-R score + ASXL1 mutation + TP53 mutation + Telomere length (<5.37). According to this new scoring system, patients were divided into four groups: very good score cutoff (≤3.0), good (3.0-4.5), poor (4.5-7.0), and very poor (>7.0). RESULTS The median OS was 170.1, 100.4, 46.0, and 12.0 months for very good, good, poor, and very poor, retrospectively (p < 0.001). Meanwhile, according to the conventional IPSS-R scoring system, the median OS was 141.3, 50.2, 93.0, 36.0, and 16.2 months for very low, low, intermediate, high, and very high, retrospectively (p < 0.001). CONCLUSIONS The newly developed model incorporating molecular variations and TL yielded more clear separations of the survival curves. By adding the presence of gene mutation and telomere length to the existing IPSS-R, its predictive ability can be further improved in myelodysplastic syndrome.
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Affiliation(s)
- Hee Sue Park
- Department of Laboratory MedicineChungbuk National University HospitalCheongju‐siKorea,Department of Laboratory MedicineChungbuk National University College of MedicineCheongju‐siKorea
| | - Kyongok Im
- Institute of Reproductive Medicine and Population Medical Research CenterSeoul National UniversitySeoulKorea,School of Health and Environmental Science, College of Health ScienceKorea UniversitySeoulKorea
| | - Dong‐Yeop Shin
- Department of Internal MedicineSeoul National University HospitalSeoulKorea
| | - Sung‐Soo Yoon
- Department of Internal MedicineSeoul National University HospitalSeoulKorea,Department of Internal MedicineSeoul National University College of MedicineSeoulKorea
| | - Sunghoon Kwon
- Department of Electrical and Computer EngineeringSeoul National UniversitySeoulKorea,Bio‐MAX InstituteSeoul National UniversitySeoulKorea
| | - Suhng Wook Kim
- School of Health and Environmental Science, College of Health ScienceKorea UniversitySeoulKorea,BK21 FOUR R&E Center for Learning Health SystemsKorea UniversitySeoulKorea
| | - Dong Soon Lee
- Department of Laboratory MedicineSeoul National University College of MedicineSeoulKorea
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23
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Epigenetic Modification of Cytosines in Hematopoietic Differentiation and Malignant Transformation. Int J Mol Sci 2023; 24:ijms24021727. [PMID: 36675240 PMCID: PMC9863985 DOI: 10.3390/ijms24021727] [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: 12/24/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The mammalian DNA methylation landscape is established and maintained by the combined activities of the two key epigenetic modifiers, DNA methyltransferases (DNMT) and Ten-eleven-translocation (TET) enzymes. Once DNMTs produce 5-methylcytosine (5mC), TET proteins fine-tune the DNA methylation status by consecutively oxidizing 5mC to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives. The 5mC and oxidized methylcytosines are essential for the maintenance of cellular identity and function during differentiation. Cytosine modifications with DNMT and TET enzymes exert pleiotropic effects on various aspects of hematopoiesis, including self-renewal of hematopoietic stem/progenitor cells (HSPCs), lineage determination, differentiation, and function. Under pathological conditions, these enzymes are frequently dysregulated, leading to loss of function. In particular, the loss of DNMT3A and TET2 function is conspicuous in diverse hematological disorders, including myeloid and lymphoid malignancies, and causally related to clonal hematopoiesis and malignant transformation. Here, we update recent advances in understanding how the maintenance of DNA methylation homeostasis by DNMT and TET proteins influences normal hematopoiesis and malignant transformation, highlighting the potential impact of DNMT3A and TET2 dysregulation on clonal dominance and evolution of pre-leukemic stem cells to full-blown malignancies. Clarification of the normal and pathological functions of DNA-modifying epigenetic regulators will be crucial to future innovations in epigenetic therapies for treating hematological disorders.
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24
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DNA methylation and gene expression analysis in adipose tissue to identify new loci associated with T2D development in obesity. Nutr Diabetes 2022; 12:50. [PMID: 36535927 PMCID: PMC9763387 DOI: 10.1038/s41387-022-00228-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Obesity is accompanied by excess adipose fat storage, which may lead to adipose dysfunction, insulin resistance, and type 2 diabetes (T2D). Currently, the tendency to develop T2D in obesity cannot be explained by genetic variation alone-epigenetic mechanisms, such as DNA methylation, might be involved. Here, we aimed to identify changes in DNA methylation and gene expression in visceral adipose tissue (VAT) that might underlie T2D susceptibility in patients with obesity. METHODS We investigated DNA methylation and gene expression in VAT biopsies from 19 women with obesity, without (OND = 9) or with T2D (OD = 10). Differences in genome-scale methylation (differentially methylated CpGs [DMCs], false discovery rate < 0.05; and differentially methylated regions [DMRs], p value < 0.05) and gene expression (DEGs, p value <0.05) between groups were assessed. We searched for overlap between altered methylation and expression and the impact of altered DNA methylation on gene expression, using bootstrap Pearson correlation. The relationship of altered DNA methylation to T2D-related traits was also tested. RESULTS We identified 11 120 DMCs and 96 DMRs distributed across all chromosomes, with the greatest density of epigenomic alterations at the MHC locus. These alterations were found in newly and previously T2D-related genes. Several of these findings were supported by validation and extended multi-ethnic analyses. Of 252 DEGs in the OD group, 68 genes contained DMCs (n = 88), of which 24 demonstrated a significant relationship between gene expression and methylation (p values <0.05). Of these, 16, including ATP11A, LPL and EHD2 also showed a significant correlation with fasting glucose and HbA1c levels. CONCLUSIONS Our results revealed novel candidate genes related to T2D pathogenesis in obesity. These genes show perturbations in DNA methylation and expression profiles in patients with obesity and diabetes. Methylation profiles were able to discriminate OND from OD individuals; DNA methylation is thus a potential biomarker.
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25
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Nam AS, Dusaj N, Izzo F, Murali R, Myers RM, Mouhieddine TH, Sotelo J, Benbarche S, Waarts M, Gaiti F, Tahri S, Levine R, Abdel-Wahab O, Godley LA, Chaligne R, Ghobrial I, Landau DA. Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation. Nat Genet 2022; 54:1514-1526. [PMID: 36138229 PMCID: PMC10068894 DOI: 10.1038/s41588-022-01179-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Somatic mutations in cancer genes have been detected in clonal expansions across healthy human tissue, including in clonal hematopoiesis. However, because mutated and wild-type cells are admixed, we have limited ability to link genotypes with phenotypes. To overcome this limitation, we leveraged multi-modality single-cell sequencing, capturing genotype, transcriptomes and methylomes in progenitors from individuals with DNMT3A R882 mutated clonal hematopoiesis. DNMT3A mutations result in myeloid over lymphoid bias, and an expansion of immature myeloid progenitors primed toward megakaryocytic-erythroid fate, with dysregulated expression of lineage and leukemia stem cell markers. Mutated DNMT3A leads to preferential hypomethylation of polycomb repressive complex 2 targets and a specific CpG flanking motif. Notably, the hypomethylation motif is enriched in binding motifs of key hematopoietic transcription factors, serving as a potential mechanistic link between DNMT3A mutations and aberrant transcriptional phenotypes. Thus, single-cell multi-omics paves the road to defining the downstream consequences of mutations that drive clonal mosaicism.
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Affiliation(s)
- Anna S Nam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville Dusaj
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Franco Izzo
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Rekha Murali
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tarek H Mouhieddine
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jesus Sotelo
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Salima Benbarche
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Waarts
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Federico Gaiti
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sabrin Tahri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lucy A Godley
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Ronan Chaligne
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Irene Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Dan A Landau
- New York Genome Center, New York, NY, USA.
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
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26
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Liang Y, Chiu PKF, Zhu Y, Wong CYP, Xiong Q, Wang L, Teoh JYC, Cao Q, Wei Y, Ye DW, Tsui SKW, Ng CF. Whole-exome sequencing reveals a comprehensive germline mutation landscape and identifies twelve novel predisposition genes in Chinese prostate cancer patients. PLoS Genet 2022; 18:e1010373. [PMID: 36095024 PMCID: PMC9499300 DOI: 10.1371/journal.pgen.1010373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/22/2022] [Accepted: 08/03/2022] [Indexed: 11/23/2022] Open
Abstract
Prostate cancer is the most inheritable cancer with approximately 42% of disease risk attributed to inherited factors by studies of twins, indicating the importance of additional genetic screening to identify predisposition variants. However, only DNA damage repair (DDR) genes have been investigated thoroughly in prostate cancer. To determine the comprehensive germline mutation landscape in Chinese prostate cancer patients, we performed whole exome sequencing in 100 Han Chinese patients with prostate cancer in Hong Kong and identified deleterious germline mutations. A total of 36 deleterious germline variants in 25 genes were identified in 29% patients. Variants were found in eight pathways, including DNA methylation, DDR, and tyrosine-protein kinase. These findings were validated in an independent Chinese cohort of 167 patients with prostate cancer in Shanghai. Seven common deleterious-variant-containing genes were found in discovery cohort (7/25, 28%) and validation cohort (7/28, 25%) with three genes not described before (LDLR, MYH7 and SUGCT) and four genes previously reported (FANCI, ITGA6, PABPC1 and RAD54B). When comparing with that of a cohort of East Asian healthy individuals, 12 non-DDR novel potential predisposition genes (ADGRG1, CHD4, DNMT3A, ERBB3, GRHL1, HMBS, LDLR, MYH7, MYO6, NT5C2, NUP98 and SUGCT) were identified using the discovery and validation cohorts, which have not been previously reported in prostate cancer patients in all ethnic groups. Taken together, this study reveals a comprehensive germline mutation landscape in Chinese prostate cancer patients and discovers 12 novel non-DDR predisposition genes to lay the groundwork for the optimization of genetic screening. Prostate cancer is the most inheritable cancer with about 42% of disease risk attributed to inherited factors, indicating the importance of additional genetic screening to identify predisposition variants. However, only DNA damage repair (DDR) genes have been studied thoroughly in prostate cancer. To determine the comprehensive germline mutation landscape in Chinese prostate cancer patients, we performed whole exome sequencing in 100 Han Chinese patients with prostate cancer in Hong Kong and identified deleterious germline mutations. A total of 36 deleterious germline variants in 25 genes were identified in 29% patients. Variants were found in eight pathways, including DNA methylation, DDR, and tyrosine-protein kinase. These findings were validated in an independent Chinese cohort of 167 patients with prostate cancer in Shanghai. Seven common deleterious-variant-containing genes were found in discovery cohort and validation cohort with three genes not described before (LDLR, MYH7 and SUGCT) and four genes previously reported. When comparing with that of a cohort of East Asian healthy individuals, 12 non-DDR novel potential predisposition genes were identified using the discovery and validation cohorts, which have not been previously reported in prostate cancer patients in all ethnic groups.
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Affiliation(s)
- Yonghao Liang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Peter Ka-Fung Chiu
- S.H. Ho Urology Centre, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Christine Yim-Ping Wong
- S.H. Ho Urology Centre, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Lin Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jeremy Yuen-Chun Teoh
- S.H. Ho Urology Centre, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Qin Cao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Wei
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
- * E-mail: (SK-WT); (C-FN)
| | - Chi-Fai Ng
- S.H. Ho Urology Centre, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- * E-mail: (SK-WT); (C-FN)
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27
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Hetzel S, Mattei AL, Kretzmer H, Qu C, Chen X, Fan Y, Wu G, Roberts KG, Luger S, Litzow M, Rowe J, Paietta E, Stock W, Mardis ER, Wilson RK, Downing JR, Mullighan CG, Meissner A. Acute lymphoblastic leukemia displays a distinct highly methylated genome. NATURE CANCER 2022; 3:768-782. [PMID: 35590059 PMCID: PMC9236905 DOI: 10.1038/s43018-022-00370-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 03/25/2022] [Indexed: 04/13/2023]
Abstract
DNA methylation is tightly regulated during development and is stably maintained in healthy cells. In contrast, cancer cells are commonly characterized by a global loss of DNA methylation co-occurring with CpG island hypermethylation. In acute lymphoblastic leukemia (ALL), the commonest childhood cancer, perturbations of CpG methylation have been reported to be associated with genetic disease subtype and outcome, but data from large cohorts at a genome-wide scale are lacking. Here, we performed whole-genome bisulfite sequencing across ALL subtypes, leukemia cell lines and healthy hematopoietic cells, and show that unlike most cancers, ALL samples exhibit CpG island hypermethylation but minimal global loss of methylation. This was most pronounced in T cell ALL and accompanied by an exceptionally broad range of hypermethylation of CpG islands between patients, which is influenced by TET2 and DNMT3B. These findings demonstrate that ALL is characterized by an unusually highly methylated genome and provide further insights into the non-canonical regulation of methylation in cancer.
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Affiliation(s)
- Sara Hetzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandra L Mattei
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Chunxu Qu
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiang Chen
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Selina Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jacob Rowe
- Department of Hematology, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - James R Downing
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Chemistry and Pharmacy, Freie Universität, Berlin, Germany.
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28
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Lyu Y, Ge Y. Toward Elucidating Epigenetic and Metabolic Regulation of Stem Cell Lineage Plasticity in Skin Aging. Front Cell Dev Biol 2022; 10:903904. [PMID: 35663405 PMCID: PMC9160930 DOI: 10.3389/fcell.2022.903904] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Skin is the largest organ in human body, harboring a plethora of cell types and serving as the organismal barrier. Skin aging such as wrinkling and hair graying is graphically pronounced, and the molecular mechanisms behind these phenotypic manifestations are beginning to unfold. As in many other organs and tissues, epigenetic and metabolic deregulations have emerged as key aging drivers. Particularly in the context of the skin epithelium, the epigenome and metabolome coordinately shape lineage plasticity and orchestrate stem cell function during aging. Our review discusses recent studies that proposed molecular mechanisms that drive the degeneration of hair follicles, a major appendage of the skin. By focusing on skin while comparing it to model organisms and adult stem cells of other tissues, we summarize literature on genotoxic stress, nutritional sensing, metabolic rewiring, mitochondrial activity, and epigenetic regulations of stem cell plasticity. Finally, we speculate about the rejuvenation potential of rate-limiting upstream signals during aging and the dominant role of the tissue microenvironment in dictating aged epithelial stem cell function.
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Affiliation(s)
| | - Yejing Ge
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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29
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The disordered N-terminal domain of DNMT3A recognizes H2AK119ub and is required for postnatal development. Nat Genet 2022; 54:625-636. [PMID: 35534561 PMCID: PMC9295050 DOI: 10.1038/s41588-022-01063-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/28/2022] [Indexed: 02/03/2023]
Abstract
DNA methyltransferase 3a (DNMT3A) plays a crucial role during mammalian development. Two isoforms of DNMT3A are differentially expressed from stem cells to somatic tissues, but their individual functions remain largely uncharacterized. Here we report that the long isoform DNMT3A1, but not the short DNMT3A2, is essential for mouse postnatal development. DNMT3A1 binds to and regulates bivalent neurodevelopmental genes in the brain. Strikingly, Dnmt3a1 knockout perinatal lethality could be partially rescued by DNMT3A1 restoration in the nervous system. We further show that the intrinsically disordered N terminus of DNMT3A1 is required for normal development and DNA methylation at DNMT3A1-enriched regions. Mechanistically, a ubiquitin-interacting motif embedded in a putative α-helix within the N terminus binds to mono-ubiquitinated histone H2AK119, probably mediating recruitment of DNMT3A1 to Polycomb-regulated regions. These data demonstrate an isoform-specific role for DNMT3A1 in mouse postnatal development and reveal the N terminus as a necessary regulatory domain for DNMT3A1 chromatin occupancy and functions in the nervous system.
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Zhang CR, Ostrander EL, Kukhar O, Mallaney C, Sun J, Haussler E, Celik H, Koh WK, King KY, Gontarz P, Challen GA. Txnip Enhances Fitness of Dnmt3a-Mutant Hematopoietic Stem Cells via p21. Blood Cancer Discov 2022; 3:220-239. [PMID: 35394496 PMCID: PMC9414740 DOI: 10.1158/2643-3230.bcd-21-0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 02/01/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022] Open
Abstract
Clonal hematopoiesis (CH) refers to the age-related expansion of specific clones in the blood system, and manifests from somatic mutations acquired in hematopoietic stem cells (HSCs). Most CH variants occur in the gene DNMT3A, but while DNMT3A-mutant CH becomes almost ubiquitous in aging humans, a unifying molecular mechanism to illuminate how DNMT3A-mutant HSCs outcompete their counterparts is lacking. Here, we used interferon gamma (IFNγ) as a model to study the mechanisms by which Dnmt3a mutations increase HSC fitness under hematopoietic stress. We found Dnmt3a-mutant HSCs resist IFNγ-mediated depletion, and IFNγ-signaling is required for clonal expansion of Dnmt3a-mutant HSCs in vivo. Mechanistically, DNA hypomethylation-associated overexpression of Txnip in Dnmt3a-mutant HSCs leads to p53 stabilization and upregulation of p21. This preserves the functional potential of Dnmt3a-mutant HSCs through increased quiescence and resistance to IFNγ-induced apoptosis. These data identify a previously undescribed mechanism to explain increased fitness of DNMT3A-mutant clones under hematopoietic stress. SIGNIFICANCE DNMT3A mutations are common variants in clonal hematopoiesis, and recurrent events in blood cancers. Yet the mechanisms by which these mutations provide hematopoietic stem cells a competitive advantage as a precursor to malignant transformation remain unclear. Here, we use inflammatory stress to uncover molecular mechanisms leading to this fitness advantage. See related article by De Dominici and James DeGregori .
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Affiliation(s)
- Christine R Zhang
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Elizabeth L Ostrander
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Ostap Kukhar
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Cates Mallaney
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jiameng Sun
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Emily Haussler
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Hamza Celik
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Won Kyun Koh
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Katherine Y King
- Section of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Paul Gontarz
- Center of Regenerative Medicine, Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Grant A Challen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
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31
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Mattei AL, Bailly N, Meissner A. DNA methylation: a historical perspective. Trends Genet 2022; 38:676-707. [DOI: 10.1016/j.tig.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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Watt SM, Hua P, Roberts I. Increasing Complexity of Molecular Landscapes in Human Hematopoietic Stem and Progenitor Cells during Development and Aging. Int J Mol Sci 2022; 23:ijms23073675. [PMID: 35409034 PMCID: PMC8999121 DOI: 10.3390/ijms23073675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
The past five decades have seen significant progress in our understanding of human hematopoiesis. This has in part been due to the unprecedented development of advanced technologies, which have allowed the identification and characterization of rare subsets of human hematopoietic stem and progenitor cells and their lineage trajectories from embryonic through to adult life. Additionally, surrogate in vitro and in vivo models, although not fully recapitulating human hematopoiesis, have spurred on these scientific advances. These approaches have heightened our knowledge of hematological disorders and diseases and have led to their improved diagnosis and therapies. Here, we review human hematopoiesis at each end of the age spectrum, during embryonic and fetal development and on aging, providing exemplars of recent progress in deciphering the increasingly complex cellular and molecular hematopoietic landscapes in health and disease. This review concludes by highlighting links between chronic inflammation and metabolic and epigenetic changes associated with aging and in the development of clonal hematopoiesis.
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Affiliation(s)
- Suzanne M. Watt
- Stem Cell Research, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9BQ, UK
- Myeloma Research Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide 5005, Australia
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide 5001, Australia
- Correspondence: or ; Tel.: +61-403-393-755
| | - Peng Hua
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China;
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, and NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK;
- Department of Paediatrics and NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford OX3 9DU, UK
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Yi Y, Ge S. Targeting the histone H3 lysine 79 methyltransferase DOT1L in MLL-rearranged leukemias. J Hematol Oncol 2022; 15:35. [PMID: 35331314 PMCID: PMC8944089 DOI: 10.1186/s13045-022-01251-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/09/2022] [Indexed: 01/28/2023] Open
Abstract
Disrupting the methylation of telomeric silencing 1-like (DOT1L)-mediated histone H3 lysine 79 has been implicated in MLL fusion-mediated leukemogenesis. Recently, DOT1L has become an attractive therapeutic target for MLL-rearranged leukemias. Rigorous studies have been performed, and much progress has been achieved. Moreover, one DOT1L inhibitor, EPZ-5676, has entered clinical trials, but its clinical activity is modest. Here, we review the recent advances and future trends of various therapeutic strategies against DOT1L for MLL-rearranged leukemias, including DOT1L enzymatic activity inhibitors, DOT1L degraders, protein-protein interaction (PPI) inhibitors, and combinatorial interventions. In addition, the limitations, challenges, and prospects of these therapeutic strategies are discussed. In summary, we present a general overview of DOT1L as a target in MLL-rearranged leukemias to provide valuable guidance for DOT1L-associated drug development in the future. Although a variety of DOT1L enzymatic inhibitors have been identified, most of them require further optimization. Recent advances in the development of small molecule degraders, including heterobifunctional degraders and molecular glues, provide valuable insights and references for DOT1L degraders. However, drug R&D strategies and platforms need to be developed and preclinical experiments need to be performed with the purpose of blocking DOT1L-associated PPIs. DOT1L epigenetic-based combination therapy is worth considering and exploring, but the therapy should be based on a thorough understanding of the regulatory mechanism of DOT1L epigenetic modifications.
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Affiliation(s)
- Yan Yi
- Departments of Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Shenglei Ge
- Departments of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Street, Changsha, 410011, Hunan, People's Republic of China.
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Al Adhami H, Bardet AF, Dumas M, Cleroux E, Guibert S, Fauque P, Acloque H, Weber M. A comparative methylome analysis reveals conservation and divergence of DNA methylation patterns and functions in vertebrates. BMC Biol 2022; 20:70. [PMID: 35317801 PMCID: PMC8941758 DOI: 10.1186/s12915-022-01270-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/04/2022] [Indexed: 12/24/2022] Open
Abstract
Background Cytosine DNA methylation is a heritable epigenetic mark present in most eukaryotic groups. While the patterns and functions of DNA methylation have been extensively studied in mouse and human, their conservation in other vertebrates remains poorly explored. In this study, we interrogated the distribution and function of DNA methylation in primary fibroblasts of seven vertebrate species including bio-medical models and livestock species (human, mouse, rabbit, dog, cow, pig, and chicken). Results Our data highlight both divergence and conservation of DNA methylation patterns and functions. We show that the chicken genome is hypomethylated compared to other vertebrates. Furthermore, compared to mouse, other species show a higher frequency of methylation of CpG-rich DNA. We reveal the conservation of large unmethylated valleys and patterns of DNA methylation associated with X-chromosome inactivation through vertebrate evolution and make predictions of conserved sets of imprinted genes across mammals. Finally, using chemical inhibition of DNA methylation, we show that the silencing of germline genes and endogenous retroviruses (ERVs) are conserved functions of DNA methylation in vertebrates. Conclusions Our data highlight conserved properties of DNA methylation in vertebrate genomes but at the same time point to differences between mouse and other vertebrate species. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01270-x.
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Affiliation(s)
- Hala Al Adhami
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Anaïs Flore Bardet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Elouan Cleroux
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Sylvain Guibert
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Patricia Fauque
- Université Bourgogne Franche-Comté, Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, 2 Rue Angélique Ducoudray, 21000, Dijon, France.,CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction - CECOS, 14 rue Gaffarel, 21000, Dijon, France
| | - Hervé Acloque
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Michael Weber
- University of Strasbourg, Strasbourg, France. .,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France.
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CD4 expression in effector T cells depends on DNA demethylation over a developmentally established stimulus-responsive element. Nat Commun 2022; 13:1477. [PMID: 35304452 PMCID: PMC8933563 DOI: 10.1038/s41467-022-28914-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 02/16/2022] [Indexed: 12/17/2022] Open
Abstract
The epigenetic patterns that are established during early thymic development might determine mature T cell physiology and function, but the molecular basis and topography of the genetic elements involved are not fully known. Here we show, using the Cd4 locus as a paradigm for early developmental programming, that DNA demethylation during thymic development licenses a novel stimulus-responsive element that is critical for the maintenance of Cd4 gene expression in effector T cells. We document the importance of maintaining high CD4 expression during parasitic infection and show that by driving transcription, this stimulus-responsive element allows for the maintenance of histone H3K4me3 levels during T cell replication, which is critical for preventing de novo DNA methylation at the Cd4 promoter. A failure to undergo epigenetic programming during development leads to gene silencing during effector T cell replication. Our study thus provides evidence of early developmental events shaping the functional fitness of mature effector T cells.
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Liao M, Chen R, Yang Y, He H, Xu L, Jiang Y, Guo Z, He W, Jiang H, Wang J. Aging-elevated inflammation promotes DNMT3A R878H-driven clonal hematopoiesis. Acta Pharm Sin B 2022; 12:678-691. [PMID: 35256939 PMCID: PMC8897035 DOI: 10.1016/j.apsb.2021.09.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/07/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Aging-elevated DNMT3A R882H-driven clonal hematopoiesis (CH) is a risk factor for myeloid malignancies remission and overall survival. Although some studies were conducted to investigate this phenomenon, the exact mechanism is still under debate. In this study, we observed that DNMT3A R878H bone marrow cells (human allele: DNMT3A R882H) displayed enhanced reconstitution capacity in aged bone marrow milieu and upon inflammatory insult. DNMT3A R878H protects hematopoietic stem and progenitor cells from the damage induced by chronic inflammation, especially TNFα insults. Mechanistically, we identified that RIPK1–RIPK3–MLKL-mediated necroptosis signaling was compromised in R878H cells in response to proliferation stress and TNFα insults. Briefly, we elucidated the molecular mechanism driving DNMT3A R878H-based clonal hematopoiesis, which raises clinical value for treating DNMT3A R882H-driven clonal hematopoiesis and myeloid malignancies with aging.
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37
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Czeh M, Stäble S, Krämer S, Tepe L, Talyan S, Carrelha J, Meng Y, Heitplatz B, Schwabenland M, Milsom MD, Plass C, Prinz M, Schlesner M, Andrade-Navarro MA, Nerlov C, Jacobsen SEW, Lipka DB, Rosenbauer F. DNMT1 Deficiency Impacts on Plasmacytoid Dendritic Cells in Homeostasis and Autoimmune Disease. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:358-370. [PMID: 34903641 PMCID: PMC7612220 DOI: 10.4049/jimmunol.2100624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/28/2021] [Indexed: 01/07/2023]
Abstract
Dendritic cells (DCs) are heterogeneous immune regulators involved in autoimmune diseases. Epigenomic mechanisms orchestrating DC development and DC subset diversification remain insufficiently understood but could be important to modulate DC fate for clinical purposes. By combining whole-genome methylation assessment with the analysis of mice expressing reduced DNA methyltransferase 1 levels, we show that distinct DNA methylation levels and patterns are required for the development of plasmacytoid DC and conventional DC subsets. We provide clonal in vivo evidence for DC lineage establishment at the stem cell level, and we show that a high DNA methylation threshold level is essential for Flt3-dependent survival of DC precursors. Importantly, reducing methylation predominantly depletes plasmacytoid DC and alleviates systemic lupus erythematosus in an autoimmunity mouse model. This study shows how DNA methylation regulates the production of DC subsets and provides a potential rationale for targeting autoimmune disease using hypomethylating agents.
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Affiliation(s)
- Melinda Czeh
- Institute of Molecular Tumor Biology, University of Münster, Münster, Germany
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Sina Stäble
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center and National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
| | - Stephen Krämer
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center and National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Germany
- Bioinformatics and Omics Data Analysis, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Lena Tepe
- Institute of Molecular Tumor Biology, University of Münster, Münster, Germany
| | - Sweta Talyan
- Faculty of Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Joana Carrelha
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Yiran Meng
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Barbara Heitplatz
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, University of Münster, Münster, Germany
| | - Marius Schwabenland
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael D Milsom
- Division of Experimental Hematology, German Cancer Research Center, Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Biological Signalling Studies and Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Schlesner
- Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Germany
- Bioinformatics and Omics Data Analysis, German Cancer Research Center, Heidelberg, Germany
| | | | - Claus Nerlov
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Sten Eirik W Jacobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Cell and Molecular Biology and Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; and
- Karolinska University Hospital, Stockholm, Sweden
| | - Daniel B Lipka
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center and National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, University of Münster, Münster, Germany;
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Merkel A, Esteller M. Experimental and Bioinformatic Approaches to Studying DNA Methylation in Cancer. Cancers (Basel) 2022; 14:349. [PMID: 35053511 PMCID: PMC8773752 DOI: 10.3390/cancers14020349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/26/2021] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
DNA methylation is an essential epigenetic mark. Alterations of normal DNA methylation are a defining feature of cancer. Here, we review experimental and bioinformatic approaches to showcase the breadth and depth of information that this epigenetic mark provides for cancer research. First, we describe classical approaches for interrogating bulk DNA from cell populations as well as more recently developed approaches for single cells and multi-Omics. Second, we focus on the computational analysis from primary data processing to the identification of unique methylation signatures. Additionally, we discuss challenges such as sparse data and cellular heterogeneity.
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Affiliation(s)
- Angelika Merkel
- Bioinformatics Unit, Josep Carreras Leukemia Research Institute (IJC), 08916 Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukemia Research Institute (IJC), 08916 Barcelona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Institucio Catalana de Recerca Avançats (ICREA), 08010 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Catalonia, 08017 Barcelona, Spain
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Gibson CJ, Kim HT, Zhao L, Murdock HM, Hambley B, Ogata A, Madero-Marroquin R, Wang S, Green L, Fleharty M, Dougan T, Cheng CA, Blumenstiel B, Cibulskis C, Tsuji J, Duran M, Gocke CD, Antin JH, Nikiforow S, DeZern AE, Chen YB, Ho VT, Jones RJ, Lennon NJ, Walt DR, Ritz J, Soiffer RJ, Gondek LP, Lindsley RC. Donor Clonal Hematopoiesis and Recipient Outcomes After Transplantation. J Clin Oncol 2022; 40:189-201. [PMID: 34793200 PMCID: PMC8718176 DOI: 10.1200/jco.21.02286] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Clonal hematopoiesis (CH) can be transmitted from a donor to a recipient during allogeneic hematopoietic cell transplantation. Exclusion of candidate donors with CH is controversial since its impact on recipient outcomes and graft alloimmune function is uncertain. PATIENTS AND METHODS We performed targeted error-corrected sequencing on samples from 1,727 donors age 40 years or older and assessed the effect of donor CH on recipient clinical outcomes. We measured long-term engraftment of 102 donor clones and cytokine levels in 256 recipients at 3 and 12 months after transplant. RESULTS CH was present in 22.5% of donors, with DNMT3A (14.6%) and TET2 (5.2%) mutations being most common; 85% of donor clones showed long-term engraftment in recipients after transplantation, including clones with a variant allele fraction < 0.01. DNMT3A-CH with a variant allele fraction ≥ 0.01, but not smaller clones, was associated with improved recipient overall (hazard ratio [HR], 0.79; P = .042) and progression-free survival (HR, 0.72; P = .003) after adjustment for significant clinical variables. In patients who received calcineurin-based graft-versus-host disease prophylaxis, donor DNMT3A-CH was associated with reduced relapse (subdistribution HR, 0.59; P = .014), increased chronic graft-versus-host disease (subdistribution HR, 1.36; P = .042), and higher interleukin-12p70 levels in recipients. No recipient of sole DNMT3A or TET2-CH developed donor cell leukemia (DCL). In seven of eight cases, DCL evolved from donor CH with rare TP53 or splicing factor mutations or from donors carrying germline DDX41 mutations. CONCLUSION Donor CH is closely associated with clinical outcomes in transplant recipients, with differential impact on graft alloimmune function and potential for leukemic transformation related to mutated gene and somatic clonal abundance. Donor DNMT3A-CH is associated with improved recipient survival because of reduced relapse risk and with an augmented network of inflammatory cytokines in recipients. Risk of DCL in allogeneic hematopoietic cell transplantation is driven by somatic myelodysplastic syndrome-associated mutations or germline predisposition in donors.
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Affiliation(s)
- Christopher J. Gibson
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Haesook T. Kim
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA
| | - Lin Zhao
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD,Department of Hematology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - H. Moses Murdock
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Bryan Hambley
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Alana Ogata
- Department of Pathology, Brigham and Women's Hospital, Boston, MA,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | | | - Shiyu Wang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Lisa Green
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Mark Fleharty
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Tyler Dougan
- Department of Pathology, Brigham and Women's Hospital, Boston, MA,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Chi-An Cheng
- Department of Pathology, Brigham and Women's Hospital, Boston, MA,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | | | - Carrie Cibulskis
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Junko Tsuji
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Christopher D. Gocke
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD,Division of Molecular Pathology, Department of Pathology, Johns Hopkins University, Baltimore, MD
| | - Joseph H. Antin
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Sarah Nikiforow
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Amy E. DeZern
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Yi-Bin Chen
- Hematopoietic Cell Transplant and Cell Therapy Program, Massachusetts General Hospital, Boston, MA
| | - Vincent T. Ho
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Richard J. Jones
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Niall J. Lennon
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA
| | - David R. Walt
- Department of Pathology, Brigham and Women's Hospital, Boston, MA,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Jerome Ritz
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Robert J. Soiffer
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Lukasz P. Gondek
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - R. Coleman Lindsley
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA,R. Coleman Lindsley, MD, PhD, Dana-Farber Cancer Institute, 450 Brookline Ave – DA-530C, Boston, MA 02215; e-mail:
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40
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Gibson CJ, Kim HT, Zhao L, Murdock HM, Hambley B, Ogata A, Madero-Marroquin R, Wang S, Green L, Fleharty M, Dougan T, Cheng CA, Blumenstiel B, Cibulskis C, Tsuji J, Duran M, Gocke CD, Antin JH, Nikiforow S, DeZern AE, Chen YB, Ho VT, Jones RJ, Lennon NJ, Walt DR, Ritz J, Soiffer RJ, Gondek LP, Lindsley RC. Donor Clonal Hematopoiesis and Recipient Outcomes After Transplantation. J Clin Oncol 2022. [PMID: 34793200 DOI: 10.1200/jco.2021.39.15suppl.e16213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
PURPOSE Clonal hematopoiesis (CH) can be transmitted from a donor to a recipient during allogeneic hematopoietic cell transplantation. Exclusion of candidate donors with CH is controversial since its impact on recipient outcomes and graft alloimmune function is uncertain. PATIENTS AND METHODS We performed targeted error-corrected sequencing on samples from 1,727 donors age 40 years or older and assessed the effect of donor CH on recipient clinical outcomes. We measured long-term engraftment of 102 donor clones and cytokine levels in 256 recipients at 3 and 12 months after transplant. RESULTS CH was present in 22.5% of donors, with DNMT3A (14.6%) and TET2 (5.2%) mutations being most common; 85% of donor clones showed long-term engraftment in recipients after transplantation, including clones with a variant allele fraction < 0.01. DNMT3A-CH with a variant allele fraction ≥ 0.01, but not smaller clones, was associated with improved recipient overall (hazard ratio [HR], 0.79; P = .042) and progression-free survival (HR, 0.72; P = .003) after adjustment for significant clinical variables. In patients who received calcineurin-based graft-versus-host disease prophylaxis, donor DNMT3A-CH was associated with reduced relapse (subdistribution HR, 0.59; P = .014), increased chronic graft-versus-host disease (subdistribution HR, 1.36; P = .042), and higher interleukin-12p70 levels in recipients. No recipient of sole DNMT3A or TET2-CH developed donor cell leukemia (DCL). In seven of eight cases, DCL evolved from donor CH with rare TP53 or splicing factor mutations or from donors carrying germline DDX41 mutations. CONCLUSION Donor CH is closely associated with clinical outcomes in transplant recipients, with differential impact on graft alloimmune function and potential for leukemic transformation related to mutated gene and somatic clonal abundance. Donor DNMT3A-CH is associated with improved recipient survival because of reduced relapse risk and with an augmented network of inflammatory cytokines in recipients. Risk of DCL in allogeneic hematopoietic cell transplantation is driven by somatic myelodysplastic syndrome-associated mutations or germline predisposition in donors.
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Affiliation(s)
- Christopher J Gibson
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Haesook T Kim
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA
| | - Lin Zhao
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD.,Department of Hematology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - H Moses Murdock
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Bryan Hambley
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Alana Ogata
- Department of Pathology, Brigham and Women's Hospital, Boston, MA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | | | - Shiyu Wang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Lisa Green
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Mark Fleharty
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Tyler Dougan
- Department of Pathology, Brigham and Women's Hospital, Boston, MA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Chi-An Cheng
- Department of Pathology, Brigham and Women's Hospital, Boston, MA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | | | - Carrie Cibulskis
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Junko Tsuji
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Christopher D Gocke
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD.,Division of Molecular Pathology, Department of Pathology, Johns Hopkins University, Baltimore, MD
| | - Joseph H Antin
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Sarah Nikiforow
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Amy E DeZern
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Yi-Bin Chen
- Hematopoietic Cell Transplant and Cell Therapy Program, Massachusetts General Hospital, Boston, MA
| | - Vincent T Ho
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Richard J Jones
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Niall J Lennon
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA
| | - David R Walt
- Department of Pathology, Brigham and Women's Hospital, Boston, MA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Jerome Ritz
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Robert J Soiffer
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Lukasz P Gondek
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - R Coleman Lindsley
- Department of Medical Oncology, Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
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Stoyanova E, Riad M, Rao A, Heintz N. 5-Hydroxymethylcytosine-mediated active demethylation is required for mammalian neuronal differentiation and function. eLife 2021; 10:66973. [PMID: 34919053 PMCID: PMC8683082 DOI: 10.7554/elife.66973] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 11/02/2021] [Indexed: 01/02/2023] Open
Abstract
Although high levels of 5-hydroxymethylcytosine (5hmC) accumulate in mammalian neurons, our knowledge of its roles in terminal differentiation or as an intermediate in active DNA demethylation is incomplete. We report high-resolution mapping of DNA methylation and hydroxymethylation, chromatin accessibility, and histone marks in developing postmitotic Purkinje cells (PCs) in Mus musculus. Our data reveal new relationships between PC transcriptional and epigenetic programs, and identify a class of genes that lose both 5-methylcytosine (5mC) and 5hmC during terminal differentiation. Deletion of the 5hmC writers Tet1, Tet2, and Tet3 from postmitotic PCs prevents loss of 5mC and 5hmC in regulatory domains and gene bodies, and hinders transcriptional and epigenetic developmental transitions. Our data demonstrate that Tet-mediated active DNA demethylation occurs in vivo, and that acquisition of the precise molecular properties of adult PCs require continued oxidation of 5mC to 5hmC during the final phases of differentiation. At birth, the mammalian brain contains tens of billions of neurons. Although the number does not increase much as the animal grows, there are many dramatic changes to their size and structure. These changes allow the neurons to communicate with one another, develop into networks, and learn the tasks of the adult brain. One way that these changes occur is by the accumulation of chemical marks on each neuron’s DNA that help dictate which genes switch on, and which turn off. One of the most common ways that DNA can be marked is through the addition of a chemical group called a methyl group to one of the four DNA bases, cytosine. This process is called methylation. When methylation occurs, cytosine becomes 5-methylcytosine, or 5mC for short. In 2009, researchers found another modification present in the DNA in the brain: 5-hydroxymethylcytosine, or 5hmC. This modification appears when a group of proteins called the Tet hydroxylases turn 5mC into 5hmC. Converting 5mC to 5hmC normally helps cells remove marks on their DNA before they divide and expand. This is important because the newly generated cells need to be able to accumulate their own methylation marks to perform their roles properly. However, neurons in the brain accumulate 5hmC after birth, when the cells are no longer dividing, indicating that 5hmC may be required for the neurons to mature. Stoyanova et al. set out to determine whether mouse neurons need 5hmC to get their adult characteristics by tracking the chemical changes that occur in DNA from birth to adulthood. Some of the mice they tested produced 5hmC normally, while others lacked the genes necessary to make the Tet proteins in a specific class of neurons, preventing them from converting 5mC to 5hmC as they differentiate. The results reveal that neurons do not mature properly if 5hmC is not produced continuously following the first week of life. This is because neurons need to have the right genes switched on and off to differentiate correctly, and this only happens when 5hmC accumulates in some genes, while 5hmC and 5mC are removed from others. The data highlight the role of the Tet proteins, which convert 5mC into 5hmC, in preparing the marks for removal and demonstrate that active removal of these marks is essential for neuronal differentiation. Given the role of 5hmC in the development of neurons, it is possible that problems in this system could contribute to brain disorders. Further studies aimed at understanding how cells control 5hmC levels could lead to new ways to improve brain health. Research has also shown that if dividing cells lose the ability to make 5hmC, they can become cancerous. Future work could explain more about how and why this happens.
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Affiliation(s)
- Elitsa Stoyanova
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Michael Riad
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Anjana Rao
- Sanford Consortium for Regenerative Medicine, La Jolla, United States.,La Jolla Institute for Allergy and Immunology, La Jolla, United States.,Department of Pharmacology, University of California San Diego, La Jolla, United States
| | - Nathaniel Heintz
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
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42
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Kim PG, Niroula A, Shkolnik V, McConkey M, Lin AE, Słabicki M, Kemp JP, Bick A, Gibson CJ, Griffin G, Sekar A, Brooks DJ, Wong WJ, Cohen DN, Uddin MM, Shin WJ, Pirruccello J, Tsai JM, Agrawal M, Kiel DP, Bouxsein ML, Richards JB, Evans DM, Wein MN, Charles JF, Jaiswal S, Natarajan P, Ebert BL. Dnmt3a-mutated clonal hematopoiesis promotes osteoporosis. J Exp Med 2021; 218:e20211872. [PMID: 34698806 PMCID: PMC8552148 DOI: 10.1084/jem.20211872] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/18/2022] Open
Abstract
Osteoporosis is caused by an imbalance of osteoclasts and osteoblasts, occurring in close proximity to hematopoietic cells in the bone marrow. Recurrent somatic mutations that lead to an expanded population of mutant blood cells is termed clonal hematopoiesis of indeterminate potential (CHIP). Analyzing exome sequencing data from the UK Biobank, we found CHIP to be associated with increased incident osteoporosis diagnoses and decreased bone mineral density. In murine models, hematopoietic-specific mutations in Dnmt3a, the most commonly mutated gene in CHIP, decreased bone mass via increased osteoclastogenesis. Dnmt3a-/- demethylation opened chromatin and altered activity of inflammatory transcription factors. Bone loss was driven by proinflammatory cytokines, including Irf3-NF-κB-mediated IL-20 expression from Dnmt3a mutant macrophages. Increased osteoclastogenesis due to the Dnmt3a mutations was ameliorated by alendronate or IL-20 neutralization. These results demonstrate a novel source of osteoporosis-inducing inflammation.
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Affiliation(s)
- Peter Geon Kim
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Abhishek Niroula
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Veronica Shkolnik
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Marie McConkey
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Amy E. Lin
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - John P. Kemp
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Alexander Bick
- Division of Genetic Medicine, Vanderbilt University, Nashville, TN
| | | | - Gabriel Griffin
- Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Aswin Sekar
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Daniel J. Brooks
- Center for Advanced Orthopedic Studies, Beth Israel Deaconess Medical Center, Boston, MA
| | - Waihay J. Wong
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Drew N. Cohen
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Md Mesbah Uddin
- Broad Institute of Harvard and MIT, Cambridge, MA
- Center for Genomic Medicine, Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Wesley J. Shin
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - James Pirruccello
- Center for Genomic Medicine, Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Jonathan M. Tsai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Mridul Agrawal
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Douglas P. Kiel
- Broad Institute of Harvard and MIT, Cambridge, MA
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA
| | - Mary L. Bouxsein
- Center for Advanced Orthopedic Studies, Beth Israel Deaconess Medical Center, Boston, MA
| | - J. Brent Richards
- Centre for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital, and Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - David M. Evans
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Marc N. Wein
- Broad Institute of Harvard and MIT, Cambridge, MA
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Julia F. Charles
- Department of Orthopaedic Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Siddhartha Jaiswal
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA
| | - Pradeep Natarajan
- Broad Institute of Harvard and MIT, Cambridge, MA
- Center for Genomic Medicine, Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
- Howard Hughes Medical Institute, Boston, MA
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43
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Angeles AK, Janke F, Bauer S, Christopoulos P, Riediger AL, Sültmann H. Liquid Biopsies beyond Mutation Calling: Genomic and Epigenomic Features of Cell-Free DNA in Cancer. Cancers (Basel) 2021; 13:5615. [PMID: 34830770 PMCID: PMC8616179 DOI: 10.3390/cancers13225615] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/12/2023] Open
Abstract
Cell-free DNA (cfDNA) analysis using liquid biopsies is a non-invasive method to gain insights into the biology, therapy response, mechanisms of acquired resistance and therapy escape of various tumors. While it is well established that individual cancer treatment options can be adjusted by panel next-generation sequencing (NGS)-based evaluation of driver mutations in cfDNA, emerging research additionally explores the value of deep characterization of tumor cfDNA genomics and fragmentomics as well as nucleosome modifications (chromatin structure), and methylation patterns (epigenomics) for comprehensive and multi-modal assessment of cfDNA. These tools have the potential to improve disease monitoring, increase the sensitivity of minimal residual disease identification, and detection of cancers at earlier stages. Recent progress in emerging technologies of cfDNA analysis is summarized, the added potential clinical value is highlighted, strengths and limitations are identified and compared with conventional targeted NGS analysis, and current challenges and future directions are discussed.
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Affiliation(s)
- Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Simone Bauer
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Petros Christopoulos
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
- Department of Oncology, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Anja Lisa Riediger
- Helmholtz Young Investigator Group, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Department of Urology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
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44
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Krishnan V, Kim DDH, Hughes TP, Branford S, Ong ST. Integrating genetic and epigenetic factors in chronic myeloid leukemia risk assessment: toward gene expression-based biomarkers. Haematologica 2021; 107:358-370. [PMID: 34615339 PMCID: PMC8804571 DOI: 10.3324/haematol.2021.279317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Indexed: 11/17/2022] Open
Abstract
Cancer treatment is constantly evolving from a one-size-fits-all towards bespoke approaches for each patient. In certain solid cancers, including breast and lung, tumor genome profiling has been incorporated into therapeutic decision-making. For chronic phase chronic myeloid leukemia (CML), while tyrosine kinase inhibitor therapy is the standard treatment, current clinical scoring systems cannot accurately predict the heterogeneous treatment outcomes observed in patients. Biomarkers capable of segregating patients according to outcome at diagnosis are needed to improve management, and facilitate enrollment in clinical trials seeking to prevent blast crisis transformation and improve the depth of molecular responses. To this end, gene expression (GE) profiling studies have evaluated whether GE signatures at diagnosis are clinically informative. Patient material from a variety of sources has been profiled using microarrays, RNA sequencing and, more recently, single-cell RNA sequencing. However, differences in the cell types profiled, the technologies used, and the inherent complexities associated with the interpretation of genomic data pose challenges in distilling GE datasets into biomarkers with clinical utility. The goal of this paper is to review previous studies evaluating GE profiling in CML, and explore their potential as risk assessment tools for individualized CML treatment. We also review the contribution that acquired mutations, including those seen in clonal hematopoiesis, make to GE profiles, and how a model integrating contributions of genetic and epigenetic factors in resistance to tyrosine kinase inhibitors and blast crisis transformation can define a route to GE-based biomarkers. Finally, we outline a four-stage approach for the development of GE-based biomarkers in CML.
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Affiliation(s)
- Vaidehi Krishnan
- Cancer and Stem Cell Biology Signature Research Program, Duke-NUS Medical School, Singapore, Singapore; International Chronic Myeloid Leukemia Foundation
| | - Dennis Dong Hwan Kim
- International Chronic Myeloid Leukemia Foundation; Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto
| | - Timothy P Hughes
- International Chronic Myeloid Leukemia Foundation; School of Medicine, University of Adelaide, Adelaide, Australia; South Australian Health and Medical Research Institute, Adelaide, Australia; Department of Haematology, Royal Adelaide Hospital, Adelaide
| | - Susan Branford
- International Chronic Myeloid Leukemia Foundation; School of Medicine, University of Adelaide, Adelaide, Australia; Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, Australia; School of Pharmacy and Medical Science, University of South Australia, Adelaide
| | - S Tiong Ong
- Cancer and Stem Cell Biology Signature Research Program, Duke-NUS Medical School, Singapore, Singapore; International Chronic Myeloid Leukemia Foundation; Department of Haematology, Singapore General Hospital, Singapore, Singapore; Department of Medical Oncology, National Cancer Centre Singapore; Department of Medicine, Duke University Medical Center, Durham, NC.
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45
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Shi J, Xu J, Chen YE, Li JS, Cui Y, Shen L, Li JJ, Li W. The concurrence of DNA methylation and demethylation is associated with transcription regulation. Nat Commun 2021; 12:5285. [PMID: 34489442 PMCID: PMC8421433 DOI: 10.1038/s41467-021-25521-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
The mammalian DNA methylome is formed by two antagonizing processes, methylation by DNA methyltransferases (DNMT) and demethylation by ten-eleven translocation (TET) dioxygenases. Although the dynamics of either methylation or demethylation have been intensively studied in the past decade, the direct effects of their interaction on gene expression remain elusive. Here, we quantify the concurrence of DNA methylation and demethylation by the percentage of unmethylated CpGs within a partially methylated read from bisulfite sequencing. After verifying ‘methylation concurrence’ by its strong association with the co-localization of DNMT and TET enzymes, we observe that methylation concurrence is strongly correlated with gene expression. Notably, elevated methylation concurrence in tumors is associated with the repression of 40~60% of tumor suppressor genes, which cannot be explained by promoter hypermethylation alone. Furthermore, methylation concurrence can be used to stratify large undermethylated regions with negligible differences in average methylation into two subgroups with distinct chromatin accessibility and gene regulation patterns. Together, methylation concurrence represents a unique methylation metric important for transcription regulation and is distinct from conventional metrics, such as average methylation and methylation variation. The global pattern of the mammalian methylome is formed by changes in methylation and demethylation. Here the authors describe a metric methylation concurrence that measures the ratio of unmethylated CpGs inside the partially methylated reads and show that methylation concurrence is associated with epigenetically regulated tumour suppressor genes.
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Affiliation(s)
- Jiejun Shi
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Jianfeng Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yiling Elaine Chen
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Jason Sheng Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Lanlan Shen
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA.
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46
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Meng FJ, Guo F, Sun ZN, Wang SJ, Yang CR, Wang CY, Zhang WC, Gao ZY, Ji LL, Feng FK, Guan ZY, Wang GS. Downregulation of DNMT3a expression by RNAi and its effect on NF-κBs expression of thymic epithelial cells. Immunol Lett 2021; 237:17-26. [PMID: 34192561 DOI: 10.1016/j.imlet.2021.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/11/2021] [Accepted: 06/23/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To understand the characteristics of DNA methyltransferase 3a (DNMT3a) in thymoma associated Myasthenia Gravis reveal its transcriptional regulator network as while as analyze the effect of DNMT3a on Rel/ nuclear factor-kappaB family (RelA/RelB) and its downstream autoimmune regulatory factor (Aire). METHODS Tissues of 30 patients with thymoma, with or without myasthenia gravis (MG), were collected and the DNMT3a protein expression were evaluated through immunohistochemistry. We performed mRNA expression profiling microarray detection and analysis, and integrated the analysis by constructing protein-protein interaction networks and the integration with other database. We identified molecular difference between low and high DNMT3a in the thymoma by heatmap. We also performed PCR validation in thymoma tissues. The DNMT3a-shRNA plasmid was transfected into TEC cells, and these cells were treated with 5-aza-2-deoxycytidine, a blocker of DNMT3a. After the down-regulation of DNMT3a in TEC cells, the transcript and protein levels of RelA, RelB, Aire, and CHRNA3 were evaluated by western blotting. In addition, changes in gene expression profiles were screened through microarray technology. We performed differential gene analysis in the thymoma cohort by heatmap with R (v.4.3.0) software. RESULTS In 30 matched tissue specimens, the expression of DNMT3a protein in thymoma with MG was lower than that in thymoma. Through mRNA expression profiling analysis, we constructed a co-expression network of DNMT3a and found direct interaction between IKZF1 and DNMT3a, and this co-expression relationship was overlappted with Cistrome DB database. We found up-regulation of 149 mRNAs and repression of 177 mRNAs in thymoma with MG compared with thymoma. Gene ontology and pathway analysis show the involvement of a multitude of genes in the mis-regulation of MG-related pathways. RNA interference significantly reduced the level of mRNA of DNMT3a, which proved that plasmid DNMT3a was effective. In comparison to the control group, the levels of DNMT3a, Aire, and CHRNA3 mRNA and protein in TEC cells transfected with DNMT3a-shRNA interference plasmid were significantly decreased, while the expression level of RelA and RelA/RelB was significantly increased. CONCLUSIONS Our study reveals the DNMT3a-NF-κB pathway has a major effect on MG, and can be used as a marker for diagnosis as well as a target for MG treatment.
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Affiliation(s)
- Fan-Jie Meng
- Baodi Clinical College of Tianjin Medical University, Tianjin Baodi Hospital, Tianjin 301800, China
| | - Feng Guo
- Department of Endoscopy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Zhao-Nan Sun
- Tianjin Medical University General Hospital, Tianjin 300052, China
| | | | - Chun-Rui Yang
- The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Chun-Yang Wang
- Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Wen-Cheng Zhang
- Baodi Clinical College of Tianjin Medical University, Tianjin Baodi Hospital, Tianjin 301800, China
| | - Zhou-Yong Gao
- Baodi Clinical College of Tianjin Medical University, Tianjin Baodi Hospital, Tianjin 301800, China
| | - Lin-Lin Ji
- Baodi Clinical College of Tianjin Medical University, Tianjin Baodi Hospital, Tianjin 301800, China
| | - Fu-Kai Feng
- Baodi Clinical College of Tianjin Medical University, Tianjin Baodi Hospital, Tianjin 301800, China
| | - Zhi-Yu Guan
- The Second Hospital of Tianjin Medical University, Tianjin 300211, China.
| | - Guang-Shun Wang
- Baodi Clinical College of Tianjin Medical University, Tianjin Baodi Hospital, Tianjin 301800, China.
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Hormaechea-Agulla D, Matatall KA, Le DT, Kain B, Long X, Kus P, Jaksik R, Challen GA, Kimmel M, King KY. Chronic infection drives Dnmt3a-loss-of-function clonal hematopoiesis via IFNγ signaling. Cell Stem Cell 2021; 28:1428-1442.e6. [PMID: 33743191 PMCID: PMC8349829 DOI: 10.1016/j.stem.2021.03.002] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 01/08/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023]
Abstract
Age-related clonal hematopoiesis (CH) is a risk factor for malignancy, cardiovascular disease, and all-cause mortality. Somatic mutations in DNMT3A are drivers of CH, but decades may elapse between the acquisition of a mutation and CH, suggesting that environmental factors contribute to clonal expansion. We tested whether infection provides selective pressure favoring the expansion of Dnmt3a mutant hematopoietic stem cells (HSCs) in mouse chimeras. We created Dnmt3a-mosaic mice by transplanting Dnmt3a-/- and WT HSCs into WT mice and observed the substantial expansion of Dnmt3a-/- HSCs during chronic mycobacterial infection. Injection of recombinant IFNγ alone was sufficient to phenocopy CH by Dnmt3a-/- HSCs upon infection. Transcriptional and epigenetic profiling and functional studies indicate reduced differentiation associated with widespread methylation alterations, and reduced secondary stress-induced apoptosis accounts for Dnmt3a-/- clonal expansion during infection. DNMT3A mutant human HSCs similarly exhibit defective IFNγ-induced differentiation. We thus demonstrate that IFNγ signaling induced during chronic infection can drive DNMT3A-loss-of-function CH.
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Affiliation(s)
- Daniel Hormaechea-Agulla
- Department of Pediatrics, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX 77030, USA
| | - Katie A Matatall
- Department of Pediatrics, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX 77030, USA
| | - Duy T Le
- Program in Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bailee Kain
- Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaochen Long
- Department of Statistics, Rice University, Houston, TX 77030, USA
| | - Pawel Kus
- Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Roman Jaksik
- Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Grant A Challen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, TX 77030, USA; Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Katherine Y King
- Department of Pediatrics, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX 77030, USA; Program in Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA.
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48
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Choi S, Choi D, Lee YK, Ahn SH, Seong JK, Chi SW, Oh TJ, Choi SH, Koo SH. Depletion of Prmt1 in Adipocytes Impairs Glucose Homeostasis in Diet-Induced Obesity. Diabetes 2021; 70:1664-1678. [PMID: 34039627 DOI: 10.2337/db20-1050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/21/2021] [Indexed: 11/13/2022]
Abstract
Protein arginine methyltransferase (PRMT) 1 is involved in the regulation of various metabolic pathways such as glucose metabolism in liver and atrophy in the skeletal muscle. However, the role of PRMT1 in the fat tissues under the disease state has not been elucidated to date. In this study, we delineate the function of this protein in adipocytes in vivo. PRMT1 expression was abundant in the white adipose tissues (WAT), which was induced upon a high-fat diet in mice and by obesity in humans. We found that adipocyte-specific depletion of Prmt1 resulted in decreased fat mass without overall changes in body weight in mice. Mechanistically, the depletion of Prmt1 in WAT led to the activation of the AMPK pathway, which was causal to the increased lipophagy, mitochondrial lipid catabolism, and the resultant reduction in lipid droplet size in WAT in vivo. Interestingly, despite the increased energy expenditure, we observed a promotion of adipose tissue inflammation and an ectopic accumulation of triglycerides in the peripheral tissues in Prmt1 adipocyte-specific knockout mice, which promoted the impaired insulin tolerance that is reminiscent of mouse models of lipodystrophy. These data collectively suggest that PRMT1 prevents WAT from excessive degradation of triglycerides by limiting AMPK-mediated lipid catabolism to control whole-body metabolic homeostasis in diet-induced obesity conditions.
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Affiliation(s)
- Seri Choi
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Dahee Choi
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Yun-Kyung Lee
- Department of Internal Medicine, Seoul National University College of Medicine and Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seung Hyun Ahn
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, Korea
| | - Sung Wook Chi
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Tae Jung Oh
- Department of Internal Medicine, Seoul National University College of Medicine and Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sung Hee Choi
- Department of Internal Medicine, Seoul National University College of Medicine and Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seung-Hoi Koo
- Division of Life Sciences, Korea University, Seoul, Korea
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49
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Smith AM, LaValle TA, Shinawi M, Ramakrishnan SM, Abel HJ, Hill CA, Kirkland NM, Rettig MP, Helton NM, Heath SE, Ferraro F, Chen DY, Adak S, Semenkovich CF, Christian DL, Martin JR, Gabel HW, Miller CA, Ley TJ. Functional and epigenetic phenotypes of humans and mice with DNMT3A Overgrowth Syndrome. Nat Commun 2021; 12:4549. [PMID: 34315901 PMCID: PMC8316576 DOI: 10.1038/s41467-021-24800-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/08/2021] [Indexed: 01/02/2023] Open
Abstract
Germline pathogenic variants in DNMT3A were recently described in patients with overgrowth, obesity, behavioral, and learning difficulties (DNMT3A Overgrowth Syndrome/DOS). Somatic mutations in the DNMT3A gene are also the most common cause of clonal hematopoiesis, and can initiate acute myeloid leukemia (AML). Using whole genome bisulfite sequencing, we studied DNA methylation in peripheral blood cells of 11 DOS patients and found a focal, canonical hypomethylation phenotype, which is most severe with the dominant negative DNMT3AR882H mutation. A germline mouse model expressing the homologous Dnmt3aR878H mutation phenocopies most aspects of the human DOS syndrome, including the methylation phenotype and an increased incidence of spontaneous hematopoietic malignancies, suggesting that all aspects of this syndrome are caused by this mutation.
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Affiliation(s)
- Amanda M Smith
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Taylor A LaValle
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sai M Ramakrishnan
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Haley J Abel
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cheryl A Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO, USA
| | - Nicole M Kirkland
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO, USA
| | - Michael P Rettig
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Nichole M Helton
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sharon E Heath
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Francesca Ferraro
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - David Y Chen
- Division of Dermatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sangeeta Adak
- Division of Endocrinology, Metabolism & Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Clay F Semenkovich
- Division of Endocrinology, Metabolism & Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Diana L Christian
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Miller
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Timothy J Ley
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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50
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Liu P, Liu JP, Sun SJ, Gao Y, Ai Y, Chen X, Sun Y, Zhou M, Liu Y, Xiong Y, Yuan HX. CBFB-MYH11 Fusion Sequesters RUNX1 in Cytoplasm to Prevent DNMT3A Recruitment to Target Genes in AML. Front Cell Dev Biol 2021; 9:675424. [PMID: 34336831 PMCID: PMC8321512 DOI: 10.3389/fcell.2021.675424] [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: 03/03/2021] [Accepted: 06/16/2021] [Indexed: 12/11/2022] Open
Abstract
A growing number of human diseases have been found to be associated with aberrant DNA methylation, including cancer. Mutations targeting genes encoding DNA methyltransferase (DNMT), TET family of DNA demethylases, and isocitrate dehydrogenase (IDH1, IDH2) that produce TET inhibitory metabolite, 2-hyoxyglutarate (2-HG), are found in more than half of acute myeloid leukemia (AML). To gain new insights into the regulation of DNA de/methylation and consequence of its alteration in cancer development, we searched for genes which are mutated in a manner that is linked with gene mutations involved in DNA de/methylation in multiple cancer types. We found that recurrent CBFB-MYH11 fusions, which result in the expression of fusion protein comprising core-binding factor β (CBFB) and myosin heavy chain 11 (MYH11) and are found in 6∼8% of AML patients, occur mutually exclusively with DNMT3A mutations. Tumors bearing CBFB-MYH11 fusion show DNA hypomethylation patterns similar to those with loss-of-function mutation of DNMT3A. Expression of CBFB-MYH11 fusion or inhibition of DNMT3A similarly impairs the methylation and expression of target genes of Runt related transcription factor 1 (RUNX1), a functional partner of CBFB. We demonstrate that RUNX1 directly interacts with DNMT3A and that CBFB-MYH11 fusion protein sequesters RUNX1 in the cytoplasm, thereby preventing RUNX1 from interacting with and recruiting DNMT3A to its target genes. Our results identify a novel regulation of DNA methylation and provide a molecular basis how CBFB-MYH11 fusion contributes to leukemogenesis.
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Affiliation(s)
- Peng Liu
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jin-Pin Liu
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Si-Jia Sun
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yun Gao
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yingjie Ai
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Xiufei Chen
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yiping Sun
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mengyu Zhou
- Ministry of Education (MOE) Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yun Liu
- Ministry of Education (MOE) Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yue Xiong
- Cullgen Inc., San Diego, CA, United States
| | - Hai-Xin Yuan
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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