1
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Yoo J, Kim GW, Jeon YH, Lee SW, Kwon SH. Epigenetic roles of KDM3B and KDM3C in tumorigenesis and their therapeutic implications. Cell Death Dis 2024; 15:451. [PMID: 38926399 PMCID: PMC11208531 DOI: 10.1038/s41419-024-06850-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Advances in functional studies on epigenetic regulators have disclosed the vital roles played by diverse histone lysine demethylases (KDMs), ranging from normal development to tumorigenesis. Most of the KDMs are Jumonji C domain-containing (JMJD) proteins. Many of these KDMs remove methyl groups from histone tails to regulate gene transcription. There are more than 30 known KDM proteins, which fall into different subfamilies. Of the many KDM subfamilies, KDM3 (JMJD1) proteins specifically remove dimethyl and monomethyl marks from lysine 9 on histone H3 and other non-histone proteins. Dysregulation of KDM3 proteins leads to infertility, obesity, metabolic syndromes, heart diseases, and cancers. Among the KDM3 proteins, KDM3A has been largely studied in cancers. However, despite a number of studies pointing out their importance in tumorigenesis, KDM3B and KDM3C are relatively overlooked. KDM3B and KDM3C show context-dependent functions, showing pro- or anti-tumorigenic abilities in different cancers. Thus, this review provides a thorough understanding of the involvement of KDM3B and KDMC in oncology that should be helpful in determining the role of KDM3 proteins in preclinical studies for development of novel pharmacological methods to overcome cancer.
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Affiliation(s)
- Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea.
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2
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Tong D, Tang Y, Zhong P. The emerging roles of histone demethylases in cancers. Cancer Metastasis Rev 2024; 43:795-821. [PMID: 38227150 DOI: 10.1007/s10555-023-10160-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Modulation of histone methylation status is regarded as an important mechanism of epigenetic regulation and has substantial clinical potential for the therapy of diseases, including cancer and other disorders. The present study aimed to provide a comprehensive introduction to the enzymology of histone demethylases, as well as their cancerous roles, molecular mechanisms, therapeutic possibilities, and challenges for targeting them, in order to advance drug design for clinical therapy and highlight new insight into the mechanisms of these enzymes in cancer. A series of clinical trials have been performed to explore potential roles of histone demethylases in several cancer types. Numerous targeted inhibitors associated with immunotherapy, chemotherapy, radiotherapy, and targeted therapy have been used to exert anticancer functions. Future studies should evaluate the dynamic transformation of histone demethylases leading to carcinogenesis and explore individual therapy.
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Affiliation(s)
- Dali Tong
- Department of Urological Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, People's Republic of China.
| | - Ying Tang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China.
| | - Peng Zhong
- Department of Pathology, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, People's Republic of China.
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3
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Wang L, Xiao J, Zhang B, Hou A. Epigenetic modifications in the development of bronchopulmonary dysplasia: a review. Pediatr Res 2024:10.1038/s41390-024-03167-7. [PMID: 38570557 DOI: 10.1038/s41390-024-03167-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 02/25/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
While perinatal medicine advancements have bolstered survival outcomes for premature infants, bronchopulmonary dysplasia (BPD) continues to threaten their long-term health. Gene-environment interactions, mediated by epigenetic modifications such as DNA methylation, histone modification, and non-coding RNA regulation, take center stage in BPD pathogenesis. Recent discoveries link methylation variations across biological pathways with BPD. Also, the potential reversibility of histone modifications fuels new treatment avenues. The review also highlights the promise of utilizing mesenchymal stem cells and their exosomes as BPD therapies, given their ability to modulate non-coding RNA, opening novel research and intervention possibilities. IMPACT: The complexity and universality of epigenetic modifications in the occurrence and development of bronchopulmonary dysplasia were thoroughly discussed. Both molecular and cellular mechanisms contribute to the diverse nature of epigenetic changes, suggesting the need for deeper biochemical techniques to explore these molecular alterations. The utilization of innovative cell-specific drug delivery methods like exosomes and extracellular vesicles holds promise in achieving precise epigenetic regulation.
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Affiliation(s)
- Lichuan Wang
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Jun Xiao
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Bohan Zhang
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Ana Hou
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China.
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4
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Kim YY, Gryder BE, Sinniah R, Peach ML, Shern JF, Abdelmaksoud A, Pomella S, Woldemichael GM, Stanton BZ, Milewski D, Barchi JJ, Schneekloth JS, Chari R, Kowalczyk JT, Shenoy SR, Evans JR, Song YK, Wang C, Wen X, Chou HC, Gangalapudi V, Esposito D, Jones J, Procter L, O'Neill M, Jenkins LM, Tarasova NI, Wei JS, McMahon JB, O'Keefe BR, Hawley RG, Khan J. KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. Nat Commun 2024; 15:1703. [PMID: 38402212 PMCID: PMC10894237 DOI: 10.1038/s41467-024-45902-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/07/2024] [Indexed: 02/26/2024] Open
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) is an aggressive pediatric sarcoma driven primarily by the PAX3-FOXO1 fusion oncogene, for which therapies targeting PAX3-FOXO1 are lacking. Here, we screen 62,643 compounds using an engineered cell line that monitors PAX3-FOXO1 transcriptional activity identifying a hitherto uncharacterized compound, P3FI-63. RNA-seq, ATAC-seq, and docking analyses implicate histone lysine demethylases (KDMs) as its targets. Enzymatic assays confirm the inhibition of multiple KDMs with the highest selectivity for KDM3B. Structural similarity search of P3FI-63 identifies P3FI-90 with improved solubility and potency. Biophysical binding of P3FI-90 to KDM3B is demonstrated using NMR and SPR. P3FI-90 suppresses the growth of FP-RMS in vitro and in vivo through downregulating PAX3-FOXO1 activity, and combined knockdown of KDM3B and KDM1A phenocopies P3FI-90 effects. Thus, we report KDM inhibitors P3FI-63 and P3FI-90 with the highest specificity for KDM3B. Their potent suppression of PAX3-FOXO1 activity indicates a possible therapeutic approach for FP-RMS and other transcriptionally addicted cancers.
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Affiliation(s)
| | - Berkley E Gryder
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Megan L Peach
- Basic Science Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD, USA
| | - Jack F Shern
- Pediatric Oncology Branch, NCI, NIH, Bethesda, MD, USA
| | | | - Silvia Pomella
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Girma M Woldemichael
- Leidos Biomed Res Inc, FNLCR, Basic Sci Program, Frederick, MD, USA
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
| | - Benjamin Z Stanton
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Nationwide Children's Hospital, Center for Childhood Cancer Research, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Biological Chemistry & Pharmacology, The Ohio State University College of Medicine, Columbus, OH, USA
| | | | | | | | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, FNLCR, Frederick, MD, USA
| | | | - Shilpa R Shenoy
- Leidos Biomed Res Inc, FNLCR, Basic Sci Program, Frederick, MD, USA
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
| | - Jason R Evans
- Natural Products Branch, NCI, NIH, Frederick, MD, USA
| | | | - Chaoyu Wang
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | - Xinyu Wen
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | | | | | | | - Jane Jones
- Protein Expression Laboratory, FNLCR, NIH, Frederick, MD, USA
| | - Lauren Procter
- Protein Expression Laboratory, FNLCR, NIH, Frederick, MD, USA
| | - Maura O'Neill
- Protein Characterization Laboratory, FNLCR, NIH, Frederick, MD, USA
| | | | | | - Jun S Wei
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | | | - Barry R O'Keefe
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
- Natural Products Branch, NCI, NIH, Frederick, MD, USA
| | - Robert G Hawley
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Anatomy and Cell Biology, George Washington University, Washington, DC, USA
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, MD, USA.
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5
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Dillingham CM, Cormaty H, Morgan EC, Tak AI, Esgdaille DE, Boutz PL, Sridharan R. KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.31.543088. [PMID: 37398291 PMCID: PMC10312572 DOI: 10.1101/2023.05.31.543088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cell (ESC) identity is characterized by a lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 family of histone demethylases removes the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find that KDM3A and KDM3B interact with RNA processing factors such as EFTUD2 and PRMT5. Acute selective degradation of the endogenous KDM3A and KDM3B proteins resulted in altered splicing independent of H3K9me2 status or catalytic activity. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12. Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.
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Affiliation(s)
- Caleb M Dillingham
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Harshini Cormaty
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ellen C Morgan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Andrew I Tak
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Dakarai E Esgdaille
- Department of Biochemistry and Biophysics, Center for RNA Biology, Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry
| | - Paul L Boutz
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
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6
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Lewerissa EI, Nadif Kasri N, Linda K. Epigenetic regulation of autophagy-related genes: Implications for neurodevelopmental disorders. Autophagy 2024; 20:15-28. [PMID: 37674294 PMCID: PMC10761153 DOI: 10.1080/15548627.2023.2250217] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023] Open
Abstract
Macroautophagy/autophagy is an evolutionarily highly conserved catabolic process that is important for the clearance of cytosolic contents to maintain cellular homeostasis and survival. Recent findings point toward a critical role for autophagy in brain function, not only by preserving neuronal health, but especially by controlling different aspects of neuronal development and functioning. In line with this, mutations in autophagy-related genes are linked to various key characteristics and symptoms of neurodevelopmental disorders (NDDs), including autism, micro-/macrocephaly, and epilepsy. However, the group of NDDs caused by mutations in autophagy-related genes is relatively small. A significant proportion of NDDs are associated with mutations in genes encoding epigenetic regulatory proteins that modulate gene expression, so-called chromatinopathies. Intriguingly, several of the NDD-linked chromatinopathy genes have been shown to regulate autophagy-related genes, albeit in non-neuronal contexts. From these studies it becomes evident that tight transcriptional regulation of autophagy-related genes is crucial to control autophagic activity. This opens the exciting possibility that aberrant autophagic regulation might underly nervous system impairments in NDDs with disturbed epigenetic regulation. We here summarize NDD-related chromatinopathy genes that are known to regulate transcriptional regulation of autophagy-related genes. Thereby, we want to highlight autophagy as a candidate key hub mechanism in NDD-related chromatinopathies.Abbreviations: ADNP: activity dependent neuroprotector homeobox; ASD: autism spectrum disorder; ATG: AutTophaGy related; CpG: cytosine-guanine dinucleotide; DNMT: DNA methyltransferase; EHMT: euchromatic histone lysine methyltransferase; EP300: E1A binding protein p300; EZH2: enhancer of zeste 2 polycomb repressive complex 2 subunit; H3K4me3: histone 3 lysine 4 trimethylation; H3K9me1/2/3: histone 3 lysine 9 mono-, di-, or trimethylation; H3K27me2/3: histone 3 lysine 27 di-, or trimethylation; hiPSCs: human induced pluripotent stem cells; HSP: hereditary spastic paraplegia; ID: intellectual disability; KANSL1: KAT8 regulatory NSL complex subunit 1; KAT8: lysine acetyltransferase 8; KDM1A/LSD1: lysine demethylase 1A; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin complex 1; NDD: neurodevelopmental disorder; PHF8: PHD finger protein 8; PHF8-XLID: PHF8-X linked intellectual disability syndrome; PTM: post-translational modification; SESN2: sestrin 2; YY1: YY1 transcription factor; YY1AP1: YY1 associated protein 1.
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Affiliation(s)
- Elly I. Lewerissa
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Gelderland, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Gelderland, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behavior, Nijmegen, Gelderland, The Netherlands
| | - Katrin Linda
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Gelderland, The Netherlands
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Flemish Brabant, Belgium
- Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Flemish Brabant, Belgium
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7
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Gray ZH, Chakraborty D, Duttweiler RR, Alekbaeva GD, Murphy SE, Chetal K, Ji F, Ferman BI, Honer MA, Wang Z, Myers C, Sun R, Kaniskan HÜ, Toma MM, Bondarenko EA, Santoro JN, Miranda C, Dillingham ME, Tang R, Gozani O, Jin J, Skorski T, Duy C, Lee H, Sadreyev RI, Whetstine JR. Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement. Cell 2023; 186:4528-4545.e18. [PMID: 37788669 PMCID: PMC10591855 DOI: 10.1016/j.cell.2023.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 06/01/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023]
Abstract
MLL/KMT2A amplifications and translocations are prevalent in infant, adult, and therapy-induced leukemia. However, the molecular contributor(s) to these alterations are unclear. Here, we demonstrate that histone H3 lysine 9 mono- and di-methylation (H3K9me1/2) balance at the MLL/KMT2A locus regulates these amplifications and rearrangements. This balance is controlled by the crosstalk between lysine demethylase KDM3B and methyltransferase G9a/EHMT2. KDM3B depletion increases H3K9me1/2 levels and reduces CTCF occupancy at the MLL/KMT2A locus, in turn promoting amplification and rearrangements. Depleting CTCF is also sufficient to generate these focal alterations. Furthermore, the chemotherapy doxorubicin (Dox), which associates with therapy-induced leukemia and promotes MLL/KMT2A amplifications and rearrangements, suppresses KDM3B and CTCF protein levels. KDM3B and CTCF overexpression rescues Dox-induced MLL/KMT2A alterations. G9a inhibition in human cells or mice also suppresses MLL/KMT2A events accompanying Dox treatment. Therefore, MLL/KMT2A amplifications and rearrangements are controlled by epigenetic regulators that are tractable drug targets, which has clinical implications.
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Affiliation(s)
- Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Damayanti Chakraborty
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Reuben R Duttweiler
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Gulnaz D Alekbaeva
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sedona E Murphy
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Kashish Chetal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Zhentian Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Cynthia Myers
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Renhong Sun
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Monika Maria Toma
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, 3420 N. Broad Street, MRB 548, Philadelphia, PA 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - John N Santoro
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Christopher Miranda
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Megan E Dillingham
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Ran Tang
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA; School of Life Science and Technology, Harbin Institute of Technology, 150000 Harbin, China
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tomasz Skorski
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, 3420 N. Broad Street, MRB 548, Philadelphia, PA 19140, USA
| | - Cihangir Duy
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Hayan Lee
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA.
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8
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Song Y, Zhang J, Wang H, Wang H, Liu Y, Hu Z. Histone lysine demethylase 3B regulates autophagy via transcriptional regulation of GABARAPL1 in acute myeloid leukemia cells. Int J Oncol 2023; 63:87. [PMID: 37326062 PMCID: PMC10552699 DOI: 10.3892/ijo.2023.5535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Macroautophagy (hereafter referred to as autophagy) is a highly conserved self‑digestion process that is critical for maintaining homeostasis in response to various stresses. The autophagy‑related protein family, including the GABA type A receptor‑associated protein (GABARAP) and microtubule‑associated protein 1 light chain 3 subfamilies, is crucial for autophagosome biogenesis. Although the regulatory machinery of autophagy in the cytoplasm has been widely studied, its transcriptional and epigenetic regulatory mechanisms still require more targeted investigations. The present study identified histone lysine demethylase 3B (KDM3B) as a crucial component of autophagy on a panel of leukemia cell lines, including K562, THP1 and U937, resulting in transcriptional activation of the autophagy‑related gene GABA type A receptor‑associated protein like 1 (GABARAPL1). KDM3B expression promoted autophagosome formation and affected the autophagic flux in leukemia cells under the induction of external stimuli. Notably, RNA‑sequencing and reverse transcription‑quantitative PCR analysis showed that KDM3B knockout inhibited the expression of GABARAPL1. Chromatin immunoprecipitation‑quantitative PCR and luciferase assay showed that KDM3B was associated with the GABARAPL1 gene promoter under stimulation and enhanced its transcription. The present findings demonstrated that KDM3B was critical for regulating the GABARAPL1 gene and influencing the process of autophagy in leukemia cells. These results provide a new insight for exploring the association between autophagy and KDM3B epigenetic regulation in leukemia.
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Affiliation(s)
- Ying Song
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
| | - Jiaqi Zhang
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
- Granduate School, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Haihua Wang
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
- Granduate School, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Haiying Wang
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
| | - Yong Liu
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
| | - Zhenbo Hu
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
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9
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Casier K, Autaa J, Gueguen N, Delmarre V, Marie PP, Ronsseray S, Carré C, Brasset E, Teysset L, Boivin A. The histone demethylase Kdm3 prevents auto-immune piRNAs production in Drosophila. SCIENCE ADVANCES 2023; 9:eade3872. [PMID: 37027460 PMCID: PMC10081847 DOI: 10.1126/sciadv.ade3872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Genome integrity of the animal germline is protected from transposable element activity by PIWI-interacting RNAs (piRNAs). While piRNA biogenesis is intensively explored, little is known about the genetical determination of piRNA clusters, the genomic sources of piRNAs. Using a bimodal epigenetic state piRNA cluster (BX2), we identified the histone demethylase Kdm3 as being able to prevent a cryptic piRNA production. In the absence of Kdm3, dozens of coding gene-containing regions become genuine germline dual-strand piRNA clusters. Eggs laid by Kdm3 mutant females show developmental defects phenocopying loss of function of genes embedded into the additional piRNA clusters, suggesting an inheritance of functional ovarian "auto-immune" piRNAs. Antagonizing piRNA cluster determination through chromatin modifications appears crucial to prevent auto-immune genic piRNAs production.
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Affiliation(s)
- Karine Casier
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Julie Autaa
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Nathalie Gueguen
- iGReD, CNRS, INSERM, Faculté de Médecine, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Valérie Delmarre
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Pauline P. Marie
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Stéphane Ronsseray
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Clément Carré
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Emilie Brasset
- iGReD, CNRS, INSERM, Faculté de Médecine, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Laure Teysset
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Antoine Boivin
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
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10
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Cao J, Yan Q. Lysine Demethylation in Pathogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:1-14. [PMID: 37751133 DOI: 10.1007/978-3-031-38176-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Epigenetics has major impact on normal development and pathogenesis. Regulation of histone methylation on lysine and arginine residues is a major epigenetic mechanism and affects various processes including transcription and DNA repair. Histone lysine methylation is reversible and is added by histone lysine methyltransferases and removed by histone lysine demethylases. As these enzymes are also capable of writing or erasing lysine modifications on non-histone substrates, they were renamed to lysine demethylases (KDMs) in 2007. Since the discovery of the first lysine demethylase LSD1/KDM1A in 2004, eight more subfamilies of lysine demethylases have been identified and further characterized. The joint efforts by academia and industry have led to the development of potent and specific small molecule inhibitors of KDMs for treatment of cancer and several other diseases. Some of these inhibitors have already entered clinical trials since 2013, less than 10 years after the discovery of the first KDM. In this chapter, we briefly summarize the major roles of histone demethylases in normal development and human diseases and the efforts to target these enzymes to treat various diseases.
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Affiliation(s)
- Jian Cao
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| | - Qin Yan
- Department of Pathology, Yale Cancer Center, Yale Stem Cell Center, Yale Center for Immuno-Oncology, Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, 06520, USA.
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11
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Fan L, Sudeep K, Qi J. Histone Demethylase KDM3 (JMJD1) in Transcriptional Regulation and Cancer Progression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:69-86. [PMID: 37751136 PMCID: PMC11052651 DOI: 10.1007/978-3-031-38176-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Methylation of histone H3 lysine 9 (H3K9) is a repressive histone mark and associated with inhibition of gene expression. KDM3 is a subfamily of the JmjC histone demethylases. It specifically removes the mono- or di-methyl marks from H3K9 and thus contributes to activation of gene expression. KDM3 subfamily includes three members: KDM3A, KDM3B and KDM3C. As KDM3A (also known as JMJD1A or JHDM2A) is the best studied, this chapter will mainly focus on the role of KDM3A-mediated gene regulation in the biology of normal and cancer cells. Knockout mouse studies have revealed that KDM3A plays a role in the physiological processes such as spermatogenesis, metabolism and sex determination. KDM3A is upregulated in several types of cancers and has been shown to promote cancer development, progression and metastasis. KDM3A can enhance the expression or activity of transcription factors through its histone demethylase activity, thereby altering the transcriptional program and promoting cancer cell proliferation and survival. We conclude that KDM3A may serve as a promising target for anti-cancer therapies.
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Affiliation(s)
- Lingling Fan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 655 W Baltimore Street, Baltimore, MD, USA
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, 21201, USA
| | - Khadka Sudeep
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 655 W Baltimore Street, Baltimore, MD, USA
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, 21201, USA
| | - Jianfei Qi
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 655 W Baltimore Street, Baltimore, MD, USA.
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, 21201, USA.
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12
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JMJD family proteins in cancer and inflammation. Signal Transduct Target Ther 2022; 7:304. [PMID: 36050314 PMCID: PMC9434538 DOI: 10.1038/s41392-022-01145-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/22/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
The occurrence of cancer entails a series of genetic mutations that favor uncontrollable tumor growth. It is believed that various factors collectively contribute to cancer, and there is no one single explanation for tumorigenesis. Epigenetic changes such as the dysregulation of enzymes modifying DNA or histones are actively involved in oncogenesis and inflammatory response. The methylation of lysine residues on histone proteins represents a class of post-translational modifications. The human Jumonji C domain-containing (JMJD) protein family consists of more than 30 members. The JMJD proteins have long been identified with histone lysine demethylases (KDM) and histone arginine demethylases activities and thus could function as epigenetic modulators in physiological processes and diseases. Importantly, growing evidence has demonstrated the aberrant expression of JMJD proteins in cancer and inflammatory diseases, which might serve as an underlying mechanism for the initiation and progression of such diseases. Here, we discuss the role of key JMJD proteins in cancer and inflammation, including the intensively studied histone lysine demethylases, as well as the understudied group of JMJD members. In particular, we focused on epigenetic changes induced by each JMJD member and summarized recent research progress evaluating their therapeutic potential for the treatment of cancer and inflammatory diseases.
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13
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Diao W, Zheng J, Li Y, Wang J, Xu S. Targeting histone demethylases as a potential cancer therapy (Review). Int J Oncol 2022; 61:103. [PMID: 35801593 DOI: 10.3892/ijo.2022.5393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/15/2022] [Indexed: 11/06/2022] Open
Abstract
Post‑translational modifications of histones by histone demethylases have an important role in the regulation of gene transcription and are implicated in cancers. Recently, the family of lysine (K)‑specific demethylase (KDM) proteins, referring to histone demethylases that dynamically regulate histone methylation, were indicated to be involved in various pathways related to cancer development. To date, numerous studies have been conducted to explore the effects of KDMs on cancer growth, metastasis and drug resistance, and a majority of KDMs have been indicated to be oncogenes in both leukemia and solid tumors. In addition, certain KDM inhibitors have been developed and have become the subject of clinical trials to explore their safety and efficacy in cancer therapy. However, most of them focus on hematopoietic malignancy. This review summarizes the effects of KDMs on tumor growth, drug resistance and the current status of KDM inhibitors in clinical trials.
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Affiliation(s)
- Wenfei Diao
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Jiabin Zheng
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Yong Li
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Junjiang Wang
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Songhui Xu
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
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14
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Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat Rev Mol Cell Biol 2022; 23:623-640. [PMID: 35562425 PMCID: PMC9099300 DOI: 10.1038/s41580-022-00483-w] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 12/14/2022]
Abstract
Heterochromatin is characterized by dimethylated or trimethylated histone H3 Lys9 (H3K9me2 or H3K9me3, respectively) and is found at transposable elements, satellite repeats and genes, where it ensures their transcriptional silencing. The histone methyltransferases (HMTs) that methylate H3K9 — in mammals Suppressor of variegation 3–9 homologue 1 (SUV39H1), SUV39H2, SET domain bifurcated 1 (SETDB1), SETDB2, G9A and G9A-like protein (GLP) — and the ‘readers’ of H3K9me2 or H3K9me3 are highly conserved and show considerable redundancy. Despite their redundancy, genetic ablation or mistargeting of an individual H3K9 methyltransferase can correlate with impaired cell differentiation, loss of tissue identity, premature aging and/or cancer. In this Review, we discuss recent advances in understanding the roles of the known H3K9-specific HMTs in ensuring transcriptional homeostasis during tissue differentiation in mammals. We examine the effects of H3K9-methylation-dependent gene repression in haematopoiesis, muscle differentiation and neurogenesis in mammals, and compare them with mechanistic insights obtained from the study of model organisms, notably Caenorhabditis elegans and Drosophila melanogaster. In all these organisms, H3K9-specific HMTs have both unique and redundant roles that ensure the maintenance of tissue integrity by restricting the binding of transcription factors to lineage-specific promoters and enhancer elements. Histone H3 Lys9 (H3K9)-methylated heterochromatin ensures transcriptional silencing of repetitive elements and genes, and its deregulation leads to impaired cell and tissue identity, premature aging and cancer. Recent studies in mammals clarified the roles H3K9-specific histone methyltransferases in ensuring transcriptional homeostasis during tissue differentiation.
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15
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Li X, Wang H, Yu X, Saha G, Kalafati L, Ioannidis C, Mitroulis I, Netea MG, Chavakis T, Hajishengallis G. Maladaptive innate immune training of myelopoiesis links inflammatory comorbidities. Cell 2022; 185:1709-1727.e18. [PMID: 35483374 PMCID: PMC9106933 DOI: 10.1016/j.cell.2022.03.043] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/22/2022] [Accepted: 03/30/2022] [Indexed: 12/30/2022]
Abstract
Bone marrow (BM)-mediated trained innate immunity (TII) is a state of heightened immune responsiveness of hematopoietic stem and progenitor cells (HSPC) and their myeloid progeny. We show here that maladaptive BM-mediated TII underlies inflammatory comorbidities, as exemplified by the periodontitis-arthritis axis. Experimental-periodontitis-related systemic inflammation in mice induced epigenetic rewiring of HSPC and led to sustained enhancement of production of myeloid cells with increased inflammatory preparedness. The periodontitis-induced trained phenotype was transmissible by BM transplantation to naive recipients, which exhibited increased inflammatory responsiveness and disease severity when subjected to inflammatory arthritis. IL-1 signaling in HSPC was essential for their maladaptive training by periodontitis. Therefore, maladaptive innate immune training of myelopoiesis underlies inflammatory comorbidities and may be pharmacologically targeted to treat them via a holistic approach.
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Affiliation(s)
- Xiaofei Li
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hui Wang
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiang Yu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gundappa Saha
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lydia Kalafati
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany
| | - Charalampos Ioannidis
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany
| | - Ioannis Mitroulis
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; First Department of Internal Medicine and Department of Haematology, Democritus University of Thrace, 681 00 Alexandroupolis, Greece
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525 XZ, the Netherlands; Department of Immunology and Metabolism, Life and Medical Science Institute, University of Bonn, 53115 Bonn, Germany
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK.
| | - George Hajishengallis
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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16
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Hansen AM, Ge Y, Schuster MB, Pundhir S, Jakobsen JS, Kalvisa A, Tapia MC, Gordon S, Ambri F, Bagger FO, Pandey D, Helin K, Porse BT. H3K9 dimethylation safeguards cancer cells against activation of the interferon pathway. SCIENCE ADVANCES 2022; 8:eabf8627. [PMID: 35302840 PMCID: PMC8932663 DOI: 10.1126/sciadv.abf8627] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Activation of interferon genes constitutes an important anticancer pathway able to restrict proliferation of cancer cells. Here, we demonstrate that the H3K9me3 histone methyltransferase (HMT) suppressor of variegation 3-9 homolog 1 (SUV39H1) is required for the proliferation of acute myeloid leukemia (AML) and find that its loss leads to activation of the interferon pathway. Mechanistically, we show that this occurs via destabilization of a complex composed of SUV39H1 and the two H3K9me2 HMTs, G9A and GLP. Indeed, loss of H3K9me2 correlated with the activation of key interferon pathway genes, and interference with the activities of G9A/GLP largely phenocopied loss of SUV39H1. Last, we demonstrate that inhibition of G9A/GLP synergized with DNA demethylating agents and that SUV39H1 constitutes a potential biomarker for the response to hypomethylation treatment. Collectively, we uncovered a clinically relevant role for H3K9me2 in safeguarding cancer cells against activation of the interferon pathway.
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Affiliation(s)
- Anne Meldgaard Hansen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ying Ge
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mikkel Bruhn Schuster
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sachin Pundhir
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Janus Schou Jakobsen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Adrija Kalvisa
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Marta Cecylia Tapia
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sandra Gordon
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Francesca Ambri
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Frederik Otzen Bagger
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Deo Pandey
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Microbiology, Oslo University Hospital, NO-0373 Oslo, Norway
| | - Kristian Helin
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Center, New York, NY 10065, USA
- The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Bo Torben Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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Goldenstein H, Shrem SB, Weiss O, Zeligson S, Segel R, Mory A, Weiss K. A rare rearrangement of 5q31.2 in a child with a neurodevelopmental syndrome. Clin Dysmorphol 2021; 30:181-185. [PMID: 34232135 DOI: 10.1097/mcd.0000000000000380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Hagit Goldenstein
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa
| | - Sara Beni Shrem
- Pediatric Neurodevelopment Service, Meuchedet Health Services
| | - Omri Weiss
- Medical Genetics Institute, Shaare Zedek Medical Center and Hebrew University-Hadassah School of Medicine, Jerusalem
| | - Sharon Zeligson
- Medical Genetics Institute, Shaare Zedek Medical Center and Hebrew University-Hadassah School of Medicine, Jerusalem
| | - Reeval Segel
- Medical Genetics Institute, Shaare Zedek Medical Center and Hebrew University-Hadassah School of Medicine, Jerusalem
| | - Adi Mory
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Karin Weiss
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
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18
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Wang Q, Liu P, Jing H, Zhou XF, Zhao B, Li Y, Jin JB. JMJ27-mediated histone H3K9 demethylation positively regulates drought-stress responses in Arabidopsis. THE NEW PHYTOLOGIST 2021; 232:221-236. [PMID: 34197643 DOI: 10.1111/nph.17593] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Dimethylation of histone H3 at lysine 9 (H3K9me2) is associated with heterochromatinization and transcriptional gene silencing in plants. The activation of sets of genes by drought stress is correlated with reduced H3K9me2 levels, but the role of H3K9 methylation in the regulation of drought-stress responses remains elusive. Here, we show that the Jumonji domain-containing H3K9 demethylase JMJ27 positively regulates drought-stress responses through its histone demethylase activity. RNA-seq analysis identified JMJ27-regulated genes, including positive regulators of drought stress GALACTINOL SYNTHASE 2 (GOLS2) and RESPONSE TO DESICCATION 20 (RD20). Genetic analysis demonstrated that JMJ27 positively regulates drought-stress responses at least partly through GOLS2 and RD20. JMJ27 directly associated with GOLS2 and RD20, and protected these loci from silencing by reducing H3K9me2 levels under normal conditions. REGULATORY PARTICLE NON-ATPASE 1a (RPN1a), a subunit of the 26S proteasome, interacted with JMJ27 and negatively regulated JMJ27 accumulation. Drought stress diminished RPN1a abundance, resulting in increased JMJ27 abundance. The drought stress-promoted occupancy of JMJ27 at GOLS2 and RD20 chromatin may reinforce their transcriptional induction by locally reducing the H3K9me2 levels. These results indicate that the RPN1a-JMJ27 module precisely regulates dynamic H3K9me2 deposition plasticity, ensuring proper adaptation to drought stress in Arabidopsis.
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Affiliation(s)
- Qiongli Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Peng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hua Jing
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Feng Zhou
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Bo Zhao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuan Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
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19
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Ren X, Ma L, Wang N, Zhou R, Wu J, Xie X, Zhang H, Liu D, Ma X, Dang C, Kang H, Zhou Z. Antioxidant Gene Signature Impacts the Immune Infiltration and Predicts the Prognosis of Kidney Renal Clear Cell Carcinoma. Front Genet 2021; 12:721252. [PMID: 34490047 PMCID: PMC8416991 DOI: 10.3389/fgene.2021.721252] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/30/2021] [Indexed: 01/05/2023] Open
Abstract
Background: Oxidative stress is related to oncogenic transformation in kidney renal clear cell carcinoma (KIRC). We intended to identify a prognostic antioxidant gene signature and investigate its relationship with immune infiltration in KIRC. Methods: With the support of The Cancer Genome Atlas (TCGA) database, we researched the gene expression and clinical data of KIRC patients. Antioxidant related genes with significant differences in expression between KIRC and normal samples were then identified. Through univariate and multivariate Cox analysis, a prognostic gene model was established and all patients were divided into high- and low-risk subgroups. Single sample gene set enrichment analysis was adopted to analyze the immune infiltration, HLA expression, and immune checkpoint genes in different risk groups. Finally, the prognostic nomogram model was established and evaluated. Results: We identified six antioxidant genes significantly correlated with the outcome of KIRC patients as independent predictors, namely DPEP1 (HR = 0.97, P < 0.05), GSTM3 (HR = 0.97, P < 0.05), IYD (HR = 0.33, P < 0.05), KDM3B (HR = 0.96, P < 0.05), PRDX2 (HR = 0.99, P < 0.05), and PRXL2A (HR = 0.96, P < 0.05). The high- and low-risk subgroups of KIRC patients were grouped according to the six-gene signature. Patients with higher risk scores had poorer prognosis, more advanced grade and stage, and more abundance of M0 macrophages, regulatory T cells, and follicular helper T cells. There were statistically significant differences in HLA and checkpoint gene expression between the two risk subgroups. The performance of the nomogram was favorable (concordance index = 0.766) and reliably predicted the 3-year (AUC = 0.792) and 5-year (AUC = 0.766) survival of patients with KIRC. Conclusion: The novel six antioxidant related gene signature could effectively forecast the prognosis of patients with KIRC, supply insights into the interaction between cellular antioxidant mechanisms and cancer, and is an innovative tool for selecting potential patients and targets for immunotherapy.
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Affiliation(s)
- Xueting Ren
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Li Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Nan Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ruina Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jianhua Wu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xin Xie
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hao Zhang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Di Liu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chengxue Dang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhangjian Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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20
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Zhu Z, Wu X, Li Q, Zhang J, Yu S, Shen Q, Zhou Z, Pan Q, Yue W, Qin D, Zhang Y, Zhao W, Zhang R, Peng S, Li N, Zhang S, Lei A, Miao YL, Liu Z, Chen X, Wang H, Liao M, Hua J. Histone demethylase complexes KDM3A and KDM3B cooperate with OCT4/SOX2 to define a pluripotency gene regulatory network. FASEB J 2021; 35:e21664. [PMID: 34042215 DOI: 10.1096/fj.202100230r] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/24/2021] [Accepted: 04/30/2021] [Indexed: 12/13/2022]
Abstract
The pluripotency gene regulatory network of porcine induced pluripotent stem cells(piPSCs), especially in epigenetics, remains elusive. To determine the biological function of epigenetics, we cultured piPSCs in different culture conditions. We found that activation of pluripotent gene- and pluripotency-related pathways requires the erasure of H3K9 methylation modification which was further influenced by mouse embryonic fibroblast (MEF) served feeder. By dissecting the dynamic change of H3K9 methylation during loss of pluripotency, we demonstrated that the H3K9 demethylases KDM3A and KDM3B regulated global H3K9me2/me3 level and that their co-depletion led to the collapse of the pluripotency gene regulatory network. Immunoprecipitation-mass spectrometry (IP-MS) provided evidence that KDM3A and KDM3B formed a complex to perform H3K9 demethylation. The genome-wide regulation analysis revealed that OCT4 (O) and SOX2 (S), the core pluripotency transcriptional activators, maintained the pluripotent state of piPSCs depending on the H3K9 hypomethylation. Further investigation revealed that O/S cooperating with histone demethylase complex containing KDM3A and KDM3B promoted pluripotency genes expression to maintain the pluripotent state of piPSCs. Together, these data offer a unique insight into the epigenetic pluripotency network of piPSCs.
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Affiliation(s)
- Zhenshuo Zhu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Xiaolong Wu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Qun Li
- College of Life Science, Northwest A&F University, Yangling, China
| | - Juqing Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Shuai Yu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Qiaoyan Shen
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Zhe Zhou
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Qin Pan
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Wei Yue
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Dezhe Qin
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Ying Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Wenxu Zhao
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Rui Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Sha Peng
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Na Li
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Shiqiang Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Anmin Lei
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, North-East Agricultural University, Harbin, China
| | - Xingqi Chen
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Huayan Wang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Mingzhi Liao
- College of Life Science, Northwest A&F University, Yangling, China
| | - Jinlian Hua
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
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21
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Kim YG, Bak MS, Kim A, Kim Y, Chae YC, Kim YL, Chun YS, An JY, Seo SB, Kim SJ, Lee YS. Kdm3b haploinsufficiency impairs the consolidation of cerebellum-dependent motor memory in mice. Mol Brain 2021; 14:106. [PMID: 34217333 PMCID: PMC8254933 DOI: 10.1186/s13041-021-00815-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/16/2021] [Indexed: 11/10/2022] Open
Abstract
Histone modifications are a key mechanism underlying the epigenetic regulation of gene expression, which is critically involved in the consolidation of multiple forms of memory. However, the roles of histone modifications in cerebellum-dependent motor learning and memory are not well understood. To test whether changes in histone methylation are involved in cerebellar learning, we used heterozygous Kdm3b knockout (Kdm3b+/-) mice, which show reduced lysine 9 on histone 3 (H3K9) demethylase activity. H3K9 di-methylation is significantly increased selectively in the granule cell layer of the cerebellum of Kdm3b+/- mice. In the cerebellum-dependent optokinetic response (OKR) learning, Kdm3b+/- mice show deficits in memory consolidation, whereas they are normal in basal oculomotor performance and OKR acquisition. In addition, RNA-seq analyses revealed that the expression levels of several plasticity-related genes were altered in the mutant cerebellum. Our study suggests that active regulation of histone methylation is critical for the consolidation of cerebellar motor memory.
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Affiliation(s)
- Yong Gyu Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Myeong Seong Bak
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Ahbin Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Yujin Kim
- Department of Biosystems and Biomedical Sciences, College of Health Sciences, Korea University, Seoul, 02841, Korea
- Department of Integrated Biomedical and Life Sciences, College of Health Sciences, Korea University, Seoul, Korea
| | - Yun-Cheol Chae
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Korea
| | - Ye Lee Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Yang-Sook Chun
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Joon-Yong An
- Department of Biosystems and Biomedical Sciences, College of Health Sciences, Korea University, Seoul, 02841, Korea
- Department of Integrated Biomedical and Life Sciences, College of Health Sciences, Korea University, Seoul, Korea
| | - Sang-Beom Seo
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Korea
| | - Sang Jeong Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea.
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea.
| | - Yong-Seok Lee
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea.
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea.
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22
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Punnia-Moorthy G, Hersey P, Emran AA, Tiffen J. Lysine Demethylases: Promising Drug Targets in Melanoma and Other Cancers. Front Genet 2021; 12:680633. [PMID: 34220955 PMCID: PMC8242339 DOI: 10.3389/fgene.2021.680633] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic dysregulation has been implicated in a variety of pathological processes including carcinogenesis. A major group of enzymes that influence epigenetic modifications are lysine demethylases (KDMs) also known as "erasers" which remove methyl groups on lysine (K) amino acids of histones. Numerous studies have implicated aberrant lysine demethylase activity in a variety of cancers, including melanoma. This review will focus on the structure, classification and functions of KDMs in normal biology and the current knowledge of how KDMs are deregulated in cancer pathogenesis, emphasizing our interest in melanoma. We highlight the current knowledge gaps of KDMs in melanoma pathobiology and describe opportunities to increases our understanding of their importance in this disease. We summarize the progress of several pre-clinical compounds that inhibit KDMs and represent promising candidates for further investigation in oncology.
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Affiliation(s)
- Gaya Punnia-Moorthy
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Epigenetics Laboratory, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Peter Hersey
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Abdullah Al Emran
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Jessamy Tiffen
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Epigenetics Laboratory, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
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23
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KDM3B-ETF1 fusion gene downregulates LMO2 via the WNT/β-catenin signaling pathway, promoting metastasis of invasive ductal carcinoma. Cancer Gene Ther 2021; 29:215-224. [PMID: 33828234 DOI: 10.1038/s41417-021-00301-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 01/11/2021] [Accepted: 01/25/2021] [Indexed: 11/08/2022]
Abstract
Breast cancer is the most common malignancy for women, with invasive ductal carcinoma being the largest subtype of breast cancers, accounting for 75-80% of cases. However, the underlying mechanism of invasive ductal carcinoma remains unclear. In this study, we investigate the possible effects KDM3B-ETF1 fusion gene has on breast cancer cell metastasis, invasion and its downstream signaling mediators as revealed from RNA sequence data analysis. As predicted, KDM3B-ETF1 expression was increased in breast cancer tissues and cells. Overexpression of KDM3B-ETF1 in cancer cell lines promoted the growth and invasion of breast cancer cells, while KDM3B-ETF1 knockdown showed the opposite effects on malignant cell growth and invasion both in vivo and in vitro as evidenced by cell counting kit-8, Transwell assay and tumor xenograft in nude mice. On the contrary, LIM Domain Only 2 (LMO2) expression was significantly reduced in breast cancer tissues and cells. According to chromatin immunoprecipitation and Western blot analysis, KDM3B-ETF1 targets LMO2 and reduced the expression of LMO2, leading to an increase in WNT/β-catenin signaling pathway and thus promoting invasion. In conclusion, fusion gene KDM3B-ETF1 inhibits LMO2, activates the Wnt/β-catenin signaling pathway that leads to increased breast cancer cell invasion and metastasis, providing a novel insight into developing therapeutic strategies. These results provide novel insights into the molecular mechanism of invasive ductal carcinomas, which may lead to potential therapeutic targets.
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24
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Wang Z, Wang P, Li Y, Peng H, Zhu Y, Mohandas N, Liu J. Interplay between cofactors and transcription factors in hematopoiesis and hematological malignancies. Signal Transduct Target Ther 2021; 6:24. [PMID: 33468999 PMCID: PMC7815747 DOI: 10.1038/s41392-020-00422-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Hematopoiesis requires finely tuned regulation of gene expression at each stage of development. The regulation of gene transcription involves not only individual transcription factors (TFs) but also transcription complexes (TCs) composed of transcription factor(s) and multisubunit cofactors. In their normal compositions, TCs orchestrate lineage-specific patterns of gene expression and ensure the production of the correct proportions of individual cell lineages during hematopoiesis. The integration of posttranslational and conformational modifications in the chromatin landscape, nucleosomes, histones and interacting components via the cofactor–TF interplay is critical to optimal TF activity. Mutations or translocations of cofactor genes are expected to alter cofactor–TF interactions, which may be causative for the pathogenesis of various hematologic disorders. Blocking TF oncogenic activity in hematologic disorders through targeting cofactors in aberrant complexes has been an exciting therapeutic strategy. In this review, we summarize the current knowledge regarding the models and functions of cofactor–TF interplay in physiological hematopoiesis and highlight their implications in the etiology of hematological malignancies. This review presents a deep insight into the physiological and pathological implications of transcription machinery in the blood system.
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Affiliation(s)
- Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, 410011, ChangSha, Hunan, China. .,Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China.
| | - Pan Wang
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Yanan Li
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, 410011, ChangSha, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Narla Mohandas
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY, USA
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China.
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25
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He Y, Wang L, Tang J, Han Z. Genome-Wide Identification and Analysis of the Methylation of lncRNAs and Prognostic Implications in the Glioma. Front Oncol 2021; 10:607047. [PMID: 33489915 PMCID: PMC7820673 DOI: 10.3389/fonc.2020.607047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/24/2020] [Indexed: 12/23/2022] Open
Abstract
Glioma is characterized by rapid cell proliferation and extensive infiltration among brain tissues, but the molecular pathology has been still poorly understood. Previous studies found that DNA methylation modifications play a key role in contributing to the pathogenesis of glioma. On the other hand, long noncoding RNAs (lncRNAs) has been discovered to be associated with some key tumorigenic processes of glioma. Moreover, genomic methylation can influence expression and functions of lncRNAs, which contributes to the pathogenesis of many complex diseases. However, to date, no systematic study has been performed to detect the methylation of lncRNAs and its influences in glioma on a genome-wide scale. Here, we selected the methylation data, clinical information, expression of lncRNAs, and DNA methylation regulatory proteins of 537 glioma patients from TCGA and TANRIC databases. Then, we performed a differential analysis of lncRNA expression and methylated regions between low-grade glioma (LGG) and glioblastoma multiform (GBM) subjects, respectively. Next, we further identified and verified potential key lncRNAs contributing the pathogenesis of glioma involved in methylation modifications by an annotation and correlation analysis, respectively. In total, 18 such lncRNAs were identified, and 7 of them have been demonstrated to be functionally linked to the pathogenesis of glioma by previous studies. Finally, by the univariate Cox regression, LASSO regression, clinical correlation, and survival analysis, we found that all these 18 lncRNAs are high-risk factors for clinical prognosis of glioma. In summary, this study provided a strategy to explore the influence of lncRNA methylation on glioma, and our findings will be benefit to improve understanding of its pathogenesis.
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Affiliation(s)
- Yijie He
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Lidan Wang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.,Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing, China
| | - Jing Tang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.,Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing, China
| | - Zhijie Han
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
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26
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Hoyle RG, Wang H, Cen Y, Zhang Y, Li J. IOX1 Suppresses Wnt Target Gene Transcription and Colorectal Cancer Tumorigenesis through Inhibition of KDM3 Histone Demethylases. Mol Cancer Ther 2021; 20:191-202. [PMID: 33203729 PMCID: PMC7790990 DOI: 10.1158/1535-7163.mct-20-0328] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 09/02/2020] [Accepted: 10/21/2020] [Indexed: 11/16/2022]
Abstract
Epigenetic activation of Wnt/β-catenin signaling plays a critical role in Wnt-induced tumorigenesis, notably in colorectal cancers. KDM3 and KDM4 histone demethylases have been reported to promote oncogenic Wnt signaling through demethylation of H3K9 on Wnt target gene promoters and are suggested to be potential therapeutic targets. However, potent inhibitors for these regulators are still not available. In addition, which family is most responsible for activation of Wnt target genes and Wnt-induced oncogenesis is not well documented, specifically in colorectal cancer. In this study, we characterized the functional redundancy and differences between KDM3 and KDM4 in regard to regulating Wnt signaling. Our data suggest that KDM3 may play a more essential role than KDM4 in regulating oncogenic Wnt signaling in human colorectal cancer. We also identified that IOX1, a known histone demethylase inhibitor, significantly suppresses Wnt target gene transcription and colorectal cancer tumorigenesis. Mechanistically, IOX1 inhibits the enzymatic activity of KDM3 by binding to the Jumonji C domain and thereby preventing the demethylation of H3K9 on Wnt target gene promoters. Taken together, our data not only identified the critical mechanisms by which IOX1 suppressed Wnt/β-catenin signaling and colorectal cancer tumorigenesis through inhibition of KDM3, but also suggested that IOX1 may represent an attractive small molecule lead for future drug design and discovery.
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Affiliation(s)
- Rosalie G Hoyle
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia
| | - Huiqun Wang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Yana Cen
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia
| | - Yan Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Jiong Li
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia.
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
- Department of Oral and Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia
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27
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Das AB, Smith-Díaz CC, Vissers MCM. Emerging epigenetic therapeutics for myeloid leukemia: modulating demethylase activity with ascorbate. Haematologica 2021; 106:14-25. [PMID: 33099992 PMCID: PMC7776339 DOI: 10.3324/haematol.2020.259283] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2020] [Indexed: 12/23/2022] Open
Abstract
The past decade has seen a proliferation of drugs that target epigenetic pathways. Many of these drugs were developed to treat acute myeloid leukemia, a condition in which dysregulation of the epigenetic landscape is well established. While these drugs have shown promise, critical issues persist. Specifically, patients with the same mutations respond quite differently to treatment. This is true even with highly specific drugs that are designed to target the underlying oncogenic driver mutations. Furthermore, patients who do respond may eventually develop resistance. There is now evidence that epigenetic heterogeneity contributes, in part, to these issues. Cancer cells also have a remarkable capacity to ‘rewire’ themselves at the epigenetic level in response to drug treatment, and thereby maintain expression of key oncogenes. This epigenetic plasticity is a promising new target for drug development. It is therefore important to consider combination therapy in cases in which both driver mutations and epigenetic plasticity are targeted. Using ascorbate as an example of an emerging epigenetic therapeutic, we review the evidence for its potential use in both of these modes. We provide an overview of 2-oxoglutarate dependent dioxygenases with DNA, histone and RNA demethylase activity, focusing on those which require ascorbate as a cofactor. We also evaluate their role in the development and maintenance of acute myeloid leukemia. Using this information, we highlight situations in which the use of ascorbate to restore 2-oxoglutarate dependent dioxygenase activity could prove beneficial, in contrast to contexts in which targeted inhibition of specific enzymes might be preferred. Finally, we discuss how these insights could be incorporated into the rational design of future clinical trials.
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Affiliation(s)
- Andrew B Das
- Department of Pathology and Biomedical Science, University of Otago, Christchurch.
| | - Carlos C Smith-Díaz
- Department of Pathology and Biomedical Science, University of Otago, Christchurch
| | - Margreet C M Vissers
- Department of Pathology and Biomedical Science, University of Otago, Christchurch
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28
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Duddu S, Chakrabarti R, Ghosh A, Shukla PC. Hematopoietic Stem Cell Transcription Factors in Cardiovascular Pathology. Front Genet 2020; 11:588602. [PMID: 33193725 PMCID: PMC7596349 DOI: 10.3389/fgene.2020.588602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Transcription factors as multifaceted modulators of gene expression that play a central role in cell proliferation, differentiation, lineage commitment, and disease progression. They interact among themselves and create complex spatiotemporal gene regulatory networks that modulate hematopoiesis, cardiogenesis, and conditional differentiation of hematopoietic stem cells into cells of cardiovascular lineage. Additionally, bone marrow-derived stem cells potentially contribute to the cardiovascular cell population and have shown potential as a therapeutic approach to treat cardiovascular diseases. However, the underlying regulatory mechanisms are currently debatable. This review focuses on some key transcription factors and associated epigenetic modifications that modulate the maintenance and differentiation of hematopoietic stem cells and cardiac progenitor cells. In addition to this, we aim to summarize different potential clinical therapeutic approaches in cardiac regeneration therapy and recent discoveries in stem cell-based transplantation.
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Affiliation(s)
| | | | | | - Praphulla Chandra Shukla
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
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29
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The Histone Demethylase KDM3B Promotes Osteo-/Odontogenic Differentiation, Cell Proliferation, and Migration Potential of Stem Cells from the Apical Papilla. Stem Cells Int 2020; 2020:8881021. [PMID: 33082788 PMCID: PMC7563049 DOI: 10.1155/2020/8881021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/11/2020] [Accepted: 09/20/2020] [Indexed: 02/07/2023] Open
Abstract
Understanding the regulation mechanisms of mesenchymal stem cells (MSCs) can assist in tissue regeneration. The histone demethylase (KDM) family has a crucial role in differentiation and cell proliferation of MSCs, while the function of KDM3B in MSCs is not well understood. In this study, we used the stem cells from the apical papilla (SCAPs) to test whether KDM3B could regulate the function of MSCs. By an alkaline phosphatase (ALP) activity assay, Alizarin red staining, real-time RT-PCR, and western blot analysis, we found that KDM3B enhanced the ALP activity and mineralization of SCAPs and promoted the expression of runt-related transcription factor 2 (RUNX2), osterix (OSX), dentin sialophosphoprotein (DSPP), and osteocalcin (OCN). Additionally, the CFSE, CCK-8, and flow cytometry assays revealed that KDM3B improved cell proliferation by accelerating cell cycle transition from the G1 to S phase. Scratch and transwell migration assays displayed that KDM3B promoted the migration potential of SCAPs. Mechanically, microarray results displayed that 98 genes were upregulated, including STAT1, CCND1, and FGF5, and 48 genes were downregulated after KDM3B overexpression. Besides, we found that the Toll-like receptor and JAK-STAT signaling pathway may be involved in the regulating function of KDM3B in SCAPs. In brief, we discovered that KDM3B promoted the osteo-/odontogenic differentiation, cell proliferation, and migration potential of SCAPs and provided a novel target and theoretical basis for regenerative medicine.
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30
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Evolving insights on histone methylome regulation in human acute myeloid leukemia pathogenesis and targeted therapy. Exp Hematol 2020; 92:19-31. [PMID: 32950598 DOI: 10.1016/j.exphem.2020.09.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/09/2020] [Accepted: 09/14/2020] [Indexed: 12/25/2022]
Abstract
Acute myeloid leukemia (AML) is an aggressive, disseminated hematological malignancy associated with clonal selection of aberrant self-renewing hematopoietic stem cells and progenitors and poorly differentiated myeloid blasts. The most prevalent form of leukemia in adults, AML is predominantly an age-related disorder and accounts for more than 10,000 deaths per year in the United States alone. In comparison to solid tumors, AML has an overall low mutational burden, albeit more than 70% of AML patients harbor somatic mutations in genes encoding epigenetic modifiers and chromatin regulators. In the past decade, discoveries highlighting the role of DNA and histone modifications in determining cellular plasticity and lineage commitment have attested to the importance of epigenetic contributions to tumor cell de-differentiation and heterogeneity, tumor initiation, maintenance, and relapse. Orchestration in histone methylation levels regulates pluripotency and multicellular development. The increasing number of reversible methylation regulators being identified, including histone methylation writer, reader, and eraser enzymes, and their implications in AML pathogenesis have widened the scope of epigenetic reprogramming, with multiple drugs currently in various stages of preclinical and clinical trials. AML methylome also determines response to conventional chemotherapy, as well as AML cell interaction within a tumor-immune microenvironment ecosystem. Here we summarize the latest developments focusing on molecular derangements in histone methyltransferases (HMTs) and histone demethylases (HDMs) in AML pathogenesis. AML-associated HMTs and HDMs, through intricate crosstalk mechanisms, maintain an altered histone methylation code conducive to disease progression. We further discuss their importance in governing response to therapy, which can be used as a biomarker for treatment efficacy. Finally we deliberate on the therapeutic potential of targeting aberrant histone methylome in AML, examine available small molecule inhibitors in combination with immunomodulating therapeutic approaches and caveats, and discuss how future studies can enable posited epigenome-based targeted therapy to become a mainstay for AML treatment.
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31
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Jung H, Seo SB. Histone lysine demethylase 3B (KDM3B) regulates the propagation of autophagy via transcriptional activation of autophagy-related genes. PLoS One 2020; 15:e0236403. [PMID: 32716961 PMCID: PMC7384621 DOI: 10.1371/journal.pone.0236403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/05/2020] [Indexed: 12/14/2022] Open
Abstract
Autophagy, a self-degradative physiological process, is critical for homeostasis maintenance and energy source balancing in response to various stresses, including nutrient deprivation. It is a highly conserved catabolic process in eukaryotes and is indispensable for cell survival as it involves degradation of unessential or excessive components and their subsequent recycling as building blocks for the synthesis of necessary molecules. Although the dysregulation of autophagy has been reported to broadly contribute to various diseases, including cancers and neurodegenerative diseases, the molecular mechanisms underlying the epigenetic regulation of autophagy are poorly elucidated. Here, we report that the level of lysine demethylase 3B (KDM3B) increases in nutrient-deprived HCT116 cells, a colorectal carcinoma cell line, resulting in transcriptional activation of the autophagy-inducing genes. KDM3B was found to enhance the transcription by demethylating H3K9me2 on the promoter of these genes. Furthermore, we observed that the depletion of KDM3B inhibited the autophagic flux in HCT116 cells. Collectively, these data suggested the critical role of KDM3B in the regulation of autophagy-related genes via H3K9me2 demethylation and induction of autophagy in nutrient-starved HCT116 cells.
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Affiliation(s)
- Hyeonsoo Jung
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, Republic of Korea
| | - Sang-Beom Seo
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, Republic of Korea
- * E-mail:
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32
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Sui Y, Gu R, Janknecht R. Crucial Functions of the JMJD1/KDM3 Epigenetic Regulators in Cancer. Mol Cancer Res 2020; 19:3-13. [PMID: 32605929 DOI: 10.1158/1541-7786.mcr-20-0404] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 11/16/2022]
Abstract
Epigenetic changes are one underlying cause for cancer development and often due to dysregulation of enzymes modifying DNA or histones. Most Jumonji C domain-containing (JMJD) proteins are histone lysine demethylases (KDM) and therefore epigenetic regulators. One JMJD subfamily consists of JMJD1A/KDM3A, JMJD1B/KDM3B, and JMJD1C/KDM3C that are roughly 50% identical at the amino acid level. All three JMJD1 proteins are capable of removing dimethyl and monomethyl marks from lysine 9 on histone H3 and might also demethylate histone H4 on arginine 3 and nonhistone proteins. Analysis of knockout mice revealed critical roles for JMJD1 proteins in fertility, obesity, metabolic syndrome, and heart disease. Importantly, a plethora of studies demonstrated that especially JMJD1A and JMJD1C are overexpressed in various tumors, stimulate cancer cell proliferation and invasion, and facilitate efficient tumor growth. However, JMJD1A may also inhibit the formation of germ cell tumors. Likewise, JMJD1B appears to be a tumor suppressor in acute myeloid leukemia, but a tumor promoter in other cancers. Notably, by reducing methylation levels on histone H3 lysine 9, JMJD1 proteins can profoundly alter the transcriptome and thereby affect tumorigenesis, including through upregulating oncogenes such as CCND1, JUN, and MYC This epigenetic activity of JMJD1 proteins is sensitive to heavy metals, oncometabolites, oxygen, and reactive oxygen species, whose levels are frequently altered within cancer cells. In conclusion, inhibition of JMJD1 enzymatic activity through small molecules is predicted to be beneficial in many different cancers, but not in the few malignancies where JMJD1 proteins apparently exert tumor-suppressive functions.
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Affiliation(s)
- Yuan Sui
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Ruicai Gu
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Ralf Janknecht
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma. .,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
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33
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Wang Y, Zhao Y, Wang H, Zhang C, Wang M, Yang Y, Xu X, Hu Z. Histone demethylase KDM3B protects against ferroptosis by upregulating SLC7A11. FEBS Open Bio 2020; 10:637-643. [PMID: 32107878 PMCID: PMC7137800 DOI: 10.1002/2211-5463.12823] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/17/2020] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
Ferroptosis is a type of adaptive cell death driven by cellular metabolism and iron‐dependent lipid peroxidation. Though multiple genes (including SLC7A11 and GPX4) have been demonstrated to play key roles in ferroptosis, little is known about the epigenetic regulation of this process. Here, we report that KDM3B, a histone H3 lysine 9 demethylase, can protect against ferroptosis induced by Erastin, an inhibitor of SLC7A11. KDM3B overexpression in HT‐1080 cells results in decreased histone H3 lysine 9 methylation. Furthermore, KDM3B upregulates the expression of SLC7A11 through cooperation with the transcription factor ATF4. In summary, we identify here KDM3B as a potential epigenetic regulator of ferroptosis.
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Affiliation(s)
- Yishu Wang
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Yao Zhao
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Haihua Wang
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Chengliang Zhang
- College of Bioscience and Technology, Weifang Medical University, Shandong, China
| | - Meiqi Wang
- College of Bioscience and Technology, Weifang Medical University, Shandong, China
| | - Yong Yang
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Xin Xu
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, China.,College of Bioscience and Technology, Weifang Medical University, Shandong, China
| | - Zhenbo Hu
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, China
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34
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Saraç H, Morova T, Pires E, McCullagh J, Kaplan A, Cingöz A, Bagci-Onder T, Önder T, Kawamura A, Lack NA. Systematic characterization of chromatin modifying enzymes identifies KDM3B as a critical regulator in castration resistant prostate cancer. Oncogene 2020; 39:2187-2201. [PMID: 31822799 PMCID: PMC7056651 DOI: 10.1038/s41388-019-1116-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 12/28/2022]
Abstract
Androgen deprivation therapy (ADT) is the standard care for prostate cancer (PCa) patients who fail surgery or radiotherapy. While initially effective, the cancer almost always recurs as a more aggressive castration resistant prostate cancer (CRPC). Previous studies have demonstrated that chromatin modifying enzymes can play a critical role in the conversion to CRPC. However, only a handful of these potential pharmacological targets have been tested. Therefore, in this study, we conducted a focused shRNA screen of chromatin modifying enzymes previously shown to be involved in cellular differentiation. We found that altering the balance between histone methylation and demethylation impacted growth and proliferation. Of all genes tested, KDM3B, a histone H3K9 demethylase, was found to have the most antiproliferative effect. These results were phenocopied with a KDM3B CRISPR/Cas9 knockout. When tested in several PCa cell lines, the decrease in proliferation was remarkably specific to androgen-independent cells. Genetic rescue experiments showed that only the enzymatically active KDM3B could recover the phenotype. Surprisingly, despite the decreased proliferation of androgen-independent cell no alterations in the cell cycle distribution were observed following KDM3B knockdown. Whole transcriptome analyses revealed changes in the gene expression profile following loss of KDM3B, including downregulation of metabolic enzymes such as ARG2 and RDH11. Metabolomic analysis of KDM3B knockout showed a decrease in several critical amino acids. Overall, our work reveals, for the first time, the specificity and the dependence of KDM3B in CRPC proliferation.
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Affiliation(s)
- Hilal Saraç
- School of Medicine, Koç University, Istanbul, 34450, Turkey
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Tunç Morova
- School of Medicine, Koç University, Istanbul, 34450, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, V6H 3Z6, Canada
| | - Elisabete Pires
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - James McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Anıl Kaplan
- School of Medicine, Koç University, Istanbul, 34450, Turkey
| | - Ahmet Cingöz
- School of Medicine, Koç University, Istanbul, 34450, Turkey
| | | | - Tamer Önder
- School of Medicine, Koç University, Istanbul, 34450, Turkey
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Nathan A Lack
- School of Medicine, Koç University, Istanbul, 34450, Turkey.
- Vancouver Prostate Centre, University of British Columbia, Vancouver, V6H 3Z6, Canada.
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35
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Saavedra F, Gurard-Levin ZA, Rojas-Villalobos C, Vassias I, Quatrini R, Almouzni G, Loyola A. JMJD1B, a novel player in histone H3 and H4 processing to ensure genome stability. Epigenetics Chromatin 2020; 13:6. [PMID: 32070414 PMCID: PMC7027290 DOI: 10.1186/s13072-020-00331-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/05/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Maintaining a proper supply of soluble histones throughout the cell cycle is important to ensure chromatin and genome stability. Following their synthesis, histones undergo a series of maturation steps to prepare them for deposition onto chromatin. RESULTS Here, we identify the lysine demethylase JMJD1B as a novel player in the maturation cascade that contributes to regulate histone provision. We find that depletion of JMJD1B increases the protein levels of the histone chaperone tNASP leading to an accumulation of newly synthesized histones H3 and H4 at early steps of the histone maturation cascade, which perturbs chromatin assembly. Furthermore, we find a high rate of JMJD1B mutations in cancer patients, and a correlation with genomic instability. CONCLUSIONS Our data support a role for JMJD1B in fine-tuning histone supply to maintain genome integrity, opening novel avenues for cancer therapeutics.
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Affiliation(s)
- Francisco Saavedra
- Fundación Ciencia & Vida, 7780272, Santiago, Chile.,Universidad San Sebastián, 7510156, Santiago, Chile
| | - Zachary A Gurard-Levin
- CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, Paris, 75005, France.,UPMC Univ Paris 06, CNRS, UMR3664, Sorbonne Universités, Paris, 75005, France.,SAMDI Tech, Inc, Chicago, IL, 60616, USA
| | - Camila Rojas-Villalobos
- Fundación Ciencia & Vida, 7780272, Santiago, Chile.,Universidad San Sebastián, 7510156, Santiago, Chile
| | - Isabelle Vassias
- CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, Paris, 75005, France.,UPMC Univ Paris 06, CNRS, UMR3664, Sorbonne Universités, Paris, 75005, France
| | - Raquel Quatrini
- Fundación Ciencia & Vida, 7780272, Santiago, Chile.,Universidad San Sebastián, 7510156, Santiago, Chile
| | - Geneviève Almouzni
- CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, Paris, 75005, France.,UPMC Univ Paris 06, CNRS, UMR3664, Sorbonne Universités, Paris, 75005, France
| | - Alejandra Loyola
- Fundación Ciencia & Vida, 7780272, Santiago, Chile. .,Universidad San Sebastián, 7510156, Santiago, Chile.
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36
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Rahhal R, Seto E. Emerging roles of histone modifications and HDACs in RNA splicing. Nucleic Acids Res 2019; 47:4911-4926. [PMID: 31162605 PMCID: PMC6547430 DOI: 10.1093/nar/gkz292] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
Histone modifications and RNA splicing, two seemingly unrelated gene regulatory processes, greatly increase proteome diversity and profoundly influence normal as well as pathological eukaryotic cellular functions. Like many histone modifying enzymes, histone deacetylases (HDACs) play critical roles in governing cellular behaviors and are indispensable in numerous biological processes. While the association between RNA splicing and histone modifications is beginning to be recognized, a lack of knowledge exists regarding the role of HDACs in splicing. Recent studies however, reveal that HDACs interact with spliceosomal and ribonucleoprotein complexes, actively control the acetylation states of splicing-associated histone marks and splicing factors, and thereby unexpectedly could modulate splicing. Here, we review the role of histone/protein modifications and HDACs in RNA splicing and discuss the convergence of two parallel fields, which supports the argument that HDACs, and perhaps most histone modifying enzymes, are much more versatile and far more complicated than their initially proposed functions. Analogously, an HDAC-RNA splicing connection suggests that splicing is regulated by additional upstream factors and pathways yet to be defined or not fully characterized. Some human diseases share common underlying causes of aberrant HDACs and dysregulated RNA splicing and, thus, further support the potential link between HDACs and RNA splicing.
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Affiliation(s)
- Raneen Rahhal
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
| | - Edward Seto
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
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37
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Wang X, Fan H, Xu C, Jiang G, Wang H, Zhang J. KDM3B suppresses APL progression by restricting chromatin accessibility and facilitating the ATRA-mediated degradation of PML/RARα. Cancer Cell Int 2019; 19:256. [PMID: 31592194 PMCID: PMC6778369 DOI: 10.1186/s12935-019-0979-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/26/2019] [Indexed: 12/01/2022] Open
Abstract
Background A hallmark of acute promyelocytic leukemia (APL) is the expression of PML/RARα fusion protein. Treatment with all-trans retinoic acid (ATRA) results in the terminal differentiation of neutrophil granulocytes. However, the underlying mechanisms remain largely unknown. Here, we identify and elucidate a novel differentiation-suppressive model of APL involving the histone demethylase KDM3B, which has been identified as a suppressor of the tumor genes involved in hematopoietic malignancies. Methods First, we established a KDM3B knockdown NB4 cell model to determine the functional characteristics of KDM3B by cell proliferation assay and flow cytometry. Then, we performed ChIP-seq and ATAC-seq to search for potential relationships among KDM3B, histone modification (H3K9me1/me2) and the chromatin state. Finally, molecular biological techniques and a multi-omics analysis were used to explore the role of KDM3B in differentiation of the leukemia cells after ATRA treatment. Results We found that knocking down KDM3B contributed to the growth of NB4 APL cells via the promotion of cell-cycle progression and blocked granulocytic differentiation. Through global and molecular approaches, we provided futher evidence that knocking down KDM3B altered the global distribution of H3K9me1/me2 and increased the chromatin accessibility. Moreover, knocking down KDM3B inhibited the ATRA-induced degradation of the PML/RARα oncoprotein. Conclusion Our study suggested that KDM3B was able to inhibit APL progression by maintaining chromatin in a compact state and facilitating the ATRA-mediated degradation of PML/RARα. Taken together, the results show that KDM3B may be an alternative target for the treatment regimens and the targeted therapy for APL by sustaining the function of PML/RARα fusion protein.
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Affiliation(s)
- Xinrui Wang
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Huiyong Fan
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Congling Xu
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Guojuan Jiang
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Haiwei Wang
- 2Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate School, Chinese Academy of Sciences, Shanghai, 200025 China
| | - Ji Zhang
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
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38
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Li S, Ali S, Duan X, Liu S, Du J, Liu C, Dai H, Zhou M, Zhou L, Yang L, Chu P, Li L, Bhatia R, Schones DE, Wu X, Xu H, Hua Y, Guo Z, Yang Y, Zheng L, Shen B. JMJD1B Demethylates H4R3me2s and H3K9me2 to Facilitate Gene Expression for Development of Hematopoietic Stem and Progenitor Cells. Cell Rep 2019; 23:389-403. [PMID: 29641999 PMCID: PMC5933860 DOI: 10.1016/j.celrep.2018.03.051] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 01/23/2018] [Accepted: 03/13/2018] [Indexed: 12/23/2022] Open
Abstract
The arginine methylation status of histones dynamically changes during many cellular processes, including hematopoietic stem/progenitor cell (HSPC) development. The arginine methyltransferases and the readers that transduce the histone codes have been defined. However, whether arginine demethylation actively occurs in cells and what enzyme demethylates the methylarginine residues during various cellular processes are unknown. We report that JMJD1B, previously identified as a lysine demethylase for H3K9me2, mediates arginine demethylation of H4R3me2s and its intermediate, H4R3me1. We show that demethylation of H4R3me2s and H3K9me2s in promoter regions is correlated with active gene expression. Furthermore, knockout of JMJD1B blocks demethylation of H4R3me2s and/or H3K9me2 at distinct clusters of genes and impairs the activation of genes important for HSPC differentiation and development. Consequently, JMJD1B−/− mice show defects in hematopoiesis. Altogether, our study demonstrates that demethylase-mediated active arginine demethylation process exists in eukaryotes and that JMJD1B demethylates both H4R3me2s and H3K9me2 for epigenetic programming during hematopoiesis.
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Affiliation(s)
- Sihui Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Shafat Ali
- Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Xiaotao Duan
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Songbai Liu
- Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Juan Du
- Department of Diabetes Complications & Metabolism, Beckman Research Institute, City of Hope, Duarte, CA, USA; Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Changwei Liu
- Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Huifang Dai
- Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Mian Zhou
- Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Lina Zhou
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Lu Yang
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Peiguo Chu
- Department of Pathology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Ling Li
- Department of Hematologic Malignancy Translational Science, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Ravi Bhatia
- Department of Hematologic Malignancy Translational Science, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Dustin E Schones
- Department of Diabetes Complications & Metabolism, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Hong Xu
- Colleges of Life Sciences and Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuejin Hua
- Colleges of Life Sciences and Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhigang Guo
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Yanzhong Yang
- Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Li Zheng
- Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA.
| | - Binghui Shen
- Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA.
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39
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Huang M, Tailor J, Zhen Q, Gillmor AH, Miller ML, Weishaupt H, Chen J, Zheng T, Nash EK, McHenry LK, An Z, Ye F, Takashima Y, Clarke J, Ayetey H, Cavalli FMG, Luu B, Moriarity BS, Ilkhanizadeh S, Chavez L, Yu C, Kurian KM, Magnaldo T, Sevenet N, Koch P, Pollard SM, Dirks P, Snyder MP, Largaespada DA, Cho YJ, Phillips JJ, Swartling FJ, Morrissy AS, Kool M, Pfister SM, Taylor MD, Smith A, Weiss WA. Engineering Genetic Predisposition in Human Neuroepithelial Stem Cells Recapitulates Medulloblastoma Tumorigenesis. Cell Stem Cell 2019; 25:433-446.e7. [PMID: 31204176 PMCID: PMC6731167 DOI: 10.1016/j.stem.2019.05.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 03/15/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022]
Abstract
Human neural stem cell cultures provide progenitor cells that are potential cells of origin for brain cancers. However, the extent to which genetic predisposition to tumor formation can be faithfully captured in stem cell lines is uncertain. Here, we evaluated neuroepithelial stem (NES) cells, representative of cerebellar progenitors. We transduced NES cells with MYCN, observing medulloblastoma upon orthotopic implantation in mice. Significantly, transcriptomes and patterns of DNA methylation from xenograft tumors were globally more representative of human medulloblastoma compared to a MYCN-driven genetically engineered mouse model. Orthotopic transplantation of NES cells generated from Gorlin syndrome patients, who are predisposed to medulloblastoma due to germline-mutated PTCH1, also generated medulloblastoma. We engineered candidate cooperating mutations in Gorlin NES cells, with mutation of DDX3X or loss of GSE1 both accelerating tumorigenesis. These findings demonstrate that human NES cells provide a potent experimental resource for dissecting genetic causation in medulloblastoma.
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Affiliation(s)
- Miller Huang
- Department of Neurology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jignesh Tailor
- Wellcome Trust-MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Institute of Cancer Research, Sutton, London SM2 5NG, UK; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada
| | - Qiqi Zhen
- Department of Neurology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Aaron H Gillmor
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Matthew L Miller
- Department of Neurology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Holger Weishaupt
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Justin Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tina Zheng
- Department of Neurology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Emily K Nash
- Department of Neurology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lauren K McHenry
- Department of Neurology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zhenyi An
- Department of Neurology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Fubaiyang Ye
- Department of Neurology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yasuhiro Takashima
- Wellcome Trust-MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - James Clarke
- Wellcome Trust-MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Harold Ayetey
- Wellcome Trust-MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Florence M G Cavalli
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Betty Luu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Shirin Ilkhanizadeh
- Department of Neurology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lukas Chavez
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Chunying Yu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kathreena M Kurian
- Institute of Clinical Neurosciences, Level 1, Learning and Research Building, Southmead Hospital, University of Bristol, Bristol BS10 5NB, UK
| | - Thierry Magnaldo
- Institute for Research on Cancer and Aging, Nice UMR CNRS 7284 INSERM U1081 UNS/UCA, Nice, France
| | - Nicolas Sevenet
- Institut Bergonie & INSERM U1218, Universite de Bordeaux, 229 cours de l'Argonne, 33076 Bordeaux Cedex, France
| | - Philipp Koch
- Central Institute of Mental Health, University of Heidelberg/Medical Faculty Mannheim and Hector Institut for Translational Brain Research (HITBR gGmbH), Mannheim, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Peter Dirks
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A Largaespada
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yoon Jae Cho
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA; Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Joanna J Phillips
- Departments of Neurological Surgery and Pathology, University of California, San Francisco, CA 94158, USA
| | - Fredrik J Swartling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - A Sorana Morrissy
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marcel Kool
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael D Taylor
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Austin Smith
- Wellcome Trust-MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - William A Weiss
- Department of Neurology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Departments of Pediatrics, Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, CA 94158, USA.
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Hung KH, Woo YH, Lin IY, Liu CH, Wang LC, Chen HY, Chiang BL, Lin KI. The KDM4A/KDM4C/NF-κB and WDR5 epigenetic cascade regulates the activation of B cells. Nucleic Acids Res 2019; 46:5547-5560. [PMID: 29718303 PMCID: PMC6009645 DOI: 10.1093/nar/gky281] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
T follicular helper (Tfh) cell-derived signals promote activation and proliferation of antigen-primed B cells. It remains unclear whether epigenetic regulation is involved in the B cell responses to Tfh cell-derived signals. Here, we demonstrate that Tfh cell-mimicking signals induce the expression of histone demethylases KDM4A and KDM4C, and the concomitant global down-regulation of their substrates, H3K9me3/me2, in B cells. Depletion of KDM4A and KDM4C potentiates B cell activation and proliferation in response to Tfh cell-derived signals. ChIP-seq and de novo motif analysis reveals NF-κB p65 as a binding partner of KDM4A and KDM4C. Their co-targeting to Wdr5, a MLL complex member promoting H3K4 methylation, up-regulates cell cycle inhibitors Cdkn2c and Cdkn3. Thus, Tfh cell-derived signals trigger KDM4A/KDM4C - WDR5 - Cdkn2c/Cdkn3 cascade in vitro, an epigenetic mechanism regulating proper proliferation of activated B cells. This pathway is dysregulated in B cells from systemic lupus erythematosus patients and may represent a pathological link.
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Affiliation(s)
- Kuo-Hsuan Hung
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yong H Woo
- Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - I-Ying Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Hsiu Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.,PhD Program in Translational Medicine, Kaohsiung Medical University and Academia Sinica, Division of Allergy, Immunology and Rheumatology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 231, Taiwan
| | - Li-Chieh Wang
- Department of Pediatrics, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Hsin-Yu Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Bor-Luen Chiang
- Department of Pediatrics, National Taiwan University Hospital, Taipei 100, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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41
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Izaguirre-Carbonell J, Christiansen L, Burns R, Schmitz J, Li C, Mokry RL, Bluemn T, Zheng Y, Shen J, Carlson KS, Rao S, Wang D, Zhu N. Critical role of Jumonji domain of JMJD1C in MLL-rearranged leukemia. Blood Adv 2019; 3:1499-1511. [PMID: 31076406 PMCID: PMC6517669 DOI: 10.1182/bloodadvances.2018026054] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 03/31/2019] [Indexed: 12/30/2022] Open
Abstract
JMJD1C, a member of the lysine demethylase 3 family, is aberrantly expressed in mixed lineage leukemia (MLL) gene-rearranged (MLLr) leukemias. We have shown previously that JMJD1C is required for self-renewal of acute myeloid leukemia (AML) leukemia stem cells (LSCs) but not normal hematopoietic stem cells. However, the domains within JMJD1C that promote LSC self-renewal are unknown. Here, we used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9) negative-selection screening and identified a requirement for the catalytic Jumonji (JmjC) domain and zinc finger domain for leukemia cell survival in vitro and in vivo. In addition, we found that histone H3 lysine 36 methylation (H3K36me) is a marker for JMJD1C activity at gene loci. Moreover, we performed single cell transcriptome analysis of mouse leukemia cells harboring a single guide RNA (sgRNA) against the JmjC domain and identified increased activation of RAS/MAPK and the JAK-STAT pathway in cells harboring the JmjC sgRNA. We discovered that upregulation of interleukin 3 (IL-3) receptor genes mediates increased activation of IL-3 signaling upon JMJD1C loss or mutation. Along these lines, we observed resistance to JMJD1C loss in MLLr AML bearing activating RAS mutations, suggesting that RAS pathway activation confers resistance to JMJD1C loss. Overall, we discovered the functional importance of the JMJD1C JmjC domain in AML leukemogenesis and a novel interplay between JMJD1C and the IL-3 signaling pathway as a potential resistance mechanism to targeting JMJD1C catalytic activity.
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MESH Headings
- Animals
- CRISPR-Cas Systems/genetics
- Cell Line, Tumor
- Gene Editing
- Histone-Lysine N-Methyltransferase/genetics
- Histones/metabolism
- Humans
- Interleukin-3/metabolism
- Jumonji Domain-Containing Histone Demethylases/chemistry
- Jumonji Domain-Containing Histone Demethylases/genetics
- Jumonji Domain-Containing Histone Demethylases/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Myeloid-Lymphoid Leukemia Protein/genetics
- Oxidoreductases, N-Demethylating/chemistry
- Oxidoreductases, N-Demethylating/genetics
- Oxidoreductases, N-Demethylating/metabolism
- Protein Domains
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Signal Transduction
- Transplantation, Heterologous
- Zinc Fingers/genetics
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Affiliation(s)
| | - Luke Christiansen
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Cell Biology, Neurobiology, and Anatomy
| | - Robert Burns
- Blood Research Institute, Versiti, Milwaukee, WI; and
| | - Jesse Schmitz
- Blood Research Institute, Versiti, Milwaukee, WI; and
| | - Chenxuan Li
- Blood Research Institute, Versiti, Milwaukee, WI; and
| | | | - Theresa Bluemn
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Cell Biology, Neurobiology, and Anatomy
| | - Yongwei Zheng
- Blood Research Institute, Versiti, Milwaukee, WI; and
| | - Jian Shen
- Department of Microbiology and Immunology
| | - Karen-Sue Carlson
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Internal Medicine, and
| | - Sridhar Rao
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Cell Biology, Neurobiology, and Anatomy
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Demin Wang
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Microbiology and Immunology
| | - Nan Zhu
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Cell Biology, Neurobiology, and Anatomy
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42
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Diets IJ, van der Donk R, Baltrunaite K, Waanders E, Reijnders MRF, Dingemans AJM, Pfundt R, Vulto-van Silfhout AT, Wiel L, Gilissen C, Thevenon J, Perrin L, Afenjar A, Nava C, Keren B, Bartz S, Peri B, Beunders G, Verbeek N, van Gassen K, Thiffault I, Cadieux-Dion M, Huerta-Saenz L, Wagner M, Konstantopoulou V, Vodopiutz J, Griese M, Boel A, Callewaert B, Brunner HG, Kleefstra T, Hoogerbrugge N, de Vries BBA, Hwa V, Dauber A, Hehir-Kwa JY, Kuiper RP, Jongmans MCJ. De Novo and Inherited Pathogenic Variants in KDM3B Cause Intellectual Disability, Short Stature, and Facial Dysmorphism. Am J Hum Genet 2019; 104:758-766. [PMID: 30929739 PMCID: PMC6451728 DOI: 10.1016/j.ajhg.2019.02.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/21/2019] [Indexed: 01/17/2023] Open
Abstract
By using exome sequencing and a gene matching approach, we identified de novo and inherited pathogenic variants in KDM3B in 14 unrelated individuals and three affected parents with varying degrees of intellectual disability (ID) or developmental delay (DD) and short stature. The individuals share additional phenotypic features that include feeding difficulties in infancy, joint hypermobility, and characteristic facial features such as a wide mouth, a pointed chin, long ears, and a low columella. Notably, two individuals developed cancer, acute myeloid leukemia and Hodgkin lymphoma, in childhood. KDM3B encodes for a histone demethylase and is involved in H3K9 demethylation, a crucial part of chromatin modification required for transcriptional regulation. We identified missense and truncating variants, suggesting that KDM3B haploinsufficiency is the underlying mechanism for this syndrome. By using a hybrid facial-recognition model, we show that individuals with a pathogenic variant in KDM3B have a facial gestalt, and that they show significant facial similarity compared to control individuals with ID. In conclusion, pathogenic variants in KDM3B cause a syndrome characterized by ID, short stature, and facial dysmorphism.
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Affiliation(s)
- Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Roos van der Donk
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Kristina Baltrunaite
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Esmé Waanders
- Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Margot R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center, 6229HX Maastricht, the Netherlands
| | - Alexander J M Dingemans
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | | | - Laurens Wiel
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, Centre Hospitalier Universitaire de Dijon, 21079 Dijon, France; Equipe Génétique des Anomalies du Développement, Université de Bourgogne-France Comté, 21070 Dijon, France
| | - Laurence Perrin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, Centre Hospitalier Universitaire de Dijon, 21079 Dijon, France
| | - Alexandra Afenjar
- APHP, Département de Génétique et Embryologie Médicale, Centre de Référence Déficiences Intellectuelles de Causes Rares, GRC n°19, ConCer-LD, Hôpital Armand Trousseau, 75012 Paris, France
| | - Caroline Nava
- APHP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France; Sorbonne Universités, Institut du Cerveau et de la Moelle épinière, ICM, Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique UMR 7225, 75013, Paris, France
| | - Boris Keren
- APHP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
| | - Sarah Bartz
- Division of Endocrinology, Children's Hospital of Colorado, Aurora, CO 80045, USA
| | - Bethany Peri
- Division of Endocrinology, Children's Hospital of Colorado, Aurora, CO 80045, USA
| | - Gea Beunders
- Department of Clinical Genetics, VU University Medical Center, 1081HV Amsterdam, the Netherlands
| | - Nienke Verbeek
- Department of Genetics, University Medical Center Utrecht, 3508AB Utrecht, the Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, 3508AB Utrecht, the Netherlands
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA; University of Missouri, Kansas City School of Medicine, Kansas City, MO 66211, USA
| | - Maxime Cadieux-Dion
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA
| | - Lina Huerta-Saenz
- Children's Mercy Hospital, Kansas City, MO 66211, USA; Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics, Penn State Hershey Children's Hospital, Hershey, PA 17033, USA
| | - Matias Wagner
- Institute of Human Genetics, Technische Universität München, 80333 Munich, Germany; Institute for Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Vassiliki Konstantopoulou
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Julia Vodopiutz
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Matthias Griese
- Dr. von Hauner Children's Hospital, Division of Pediatric Pneumology, University Hospital Munich, German Center for Lung Research, 80333 Munich, Germany
| | - Annekatrien Boel
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202AZ Maastricht, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Vivian Hwa
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Andrew Dauber
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Endocrinology, Children's National Health System, Washington, DC 20010, USA
| | - Jayne Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Marjolijn C J Jongmans
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, 3508AB Utrecht, the Netherlands.
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43
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McCann TS, Sobral LM, Self C, Hsieh J, Sechler M, Jedlicka P. Biology and targeting of the Jumonji-domain histone demethylase family in childhood neoplasia: a preclinical overview. Expert Opin Ther Targets 2019; 23:267-280. [PMID: 30759030 DOI: 10.1080/14728222.2019.1580692] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
INTRODUCTION Epigenetic mechanisms of gene regulatory control play fundamental roles in developmental morphogenesis, and, as more recently appreciated, are heavily implicated in the onset and progression of neoplastic disease, including cancer. Many epigenetic mechanisms are therapeutically targetable, providing additional incentive for understanding of their contribution to cancer and other types of neoplasia. Areas covered: The Jumonji-domain histone demethylase (JHDM) family exemplifies many of the above traits. This review summarizes the current state of knowledge of the functions and pharmacologic targeting of JHDMs in cancer and other neoplastic processes, with an emphasis on diseases affecting the pediatric population. Expert opinion: To date, the JHDM family has largely been studied in the context of normal development and adult cancers. In contrast, comparatively few studies have addressed JHDM biology in cancer and other neoplastic diseases of childhood, especially solid (non-hematopoietic) neoplasms. Encouragingly, the few available examples support important roles for JHDMs in pediatric neoplasia, as well as potential roles for JHDM pharmacologic inhibition in disease management. Further investigations of JHDMs in cancer and other types of neoplasia of childhood can be expected to both enlighten disease biology and inform new approaches to improve disease outcomes.
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Affiliation(s)
- Tyler S McCann
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Lays M Sobral
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Chelsea Self
- b Department of Pediatrics , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Joseph Hsieh
- c Medical Scientist Training Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Marybeth Sechler
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA.,d Cancer Biology Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Paul Jedlicka
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA.,c Medical Scientist Training Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA.,d Cancer Biology Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
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Lamadema N, Burr S, Brewer AC. Dynamic regulation of epigenetic demethylation by oxygen availability and cellular redox. Free Radic Biol Med 2019; 131:282-298. [PMID: 30572012 DOI: 10.1016/j.freeradbiomed.2018.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/04/2018] [Accepted: 12/10/2018] [Indexed: 02/07/2023]
Abstract
The chromatin structure of the mammalian genome must facilitate both precisely-controlled DNA replication together with tightly-regulated gene transcription. This necessarily involves complex mechanisms and processes which remain poorly understood. It has long been recognised that the epigenetic landscape becomes established during embryonic development and acts to specify and determine cell fate. In addition, the chromatin structure is highly dynamic and allows for both cellular reprogramming and homeostatic modulation of cell function. In this respect, the functions of epigenetic "erasers", which act to remove covalently-linked epigenetic modifications from DNA and histones are critical. The enzymatic activities of the TET and JmjC protein families have been identified as demethylases which act to remove methyl groups from DNA and histones, respectively. Further, they are characterised as members of the Fe(II)- and 2-oxoglutarate-dependent dioxygenase superfamily. This provides the intriguing possibility that their enzymatic activities may be modulated by cellular metabolism, oxygen availability and redox-based mechanisms, all of which are likely to display dynamic cell- and tissue-specific patterns of flux. Here we discuss the current evidence for such [O2]- and redox-dependent regulation of the TET and Jmjc demethylases and the potential physiological and pathophysiological functional consequences of such regulation.
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Affiliation(s)
- Nermina Lamadema
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom
| | - Simon Burr
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom
| | - Alison C Brewer
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom.
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45
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An MJ, Kim DH, Kim CH, Kim M, Rhee S, Seo SB, Kim JW. Histone demethylase KDM3B regulates the transcriptional network of cell-cycle genes in hepatocarcinoma HepG2 cells. Biochem Biophys Res Commun 2018; 508:576-582. [PMID: 30514438 DOI: 10.1016/j.bbrc.2018.11.179] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer and the third most lethal cancer worldwide. Although gene mutations associated with HCC development have been intensively studied, how epigenetic factors specifically modulate the functional properties of HCC by regulating target gene expression is unclear. Here we demonstrated the overexpression of KDM3B in liver tissue of HCC patients using public RNA-seq data. Ablation of KDM3B by CRISPR/Cas9 retarded the cell cycle and proliferation of hepatocarcinoma HepG2 cells. Approximately 30% of KDM3B knockout cells exhibited mitotic spindle multipolarity as a chromosome instability (CIN) phenotype. RNA-seq analysis of KDM3B knockout revealed significantly down-regulated expression of cell cycle related genes, especially cell proliferation factor CDC123. Furthermore, the expression level of Cyclin D1 was reduced in KDM3B knockout by proteosomal degradation without any change in the expression of CCND1, which encodes Cyclin D1. The results implicate KDM3B as a crucial epigenetic factor in cell cycle regulation that manipulates chromatin dynamics and transcription in HCC, and identifies a potential gene therapy target for effective treatment of HCC.
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Affiliation(s)
- Mi-Jin An
- Department of Life Science, College of Natural Sciences, Chung-Ang University, 06974, Seoul, Republic of Korea
| | - Dae-Hyun Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, 06974, Seoul, Republic of Korea
| | - Chul-Hong Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, 06974, Seoul, Republic of Korea
| | - Mijin Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, 06974, Seoul, Republic of Korea
| | - Sangmyung Rhee
- Department of Life Science, College of Natural Sciences, Chung-Ang University, 06974, Seoul, Republic of Korea
| | - Sang-Beom Seo
- Department of Life Science, College of Natural Sciences, Chung-Ang University, 06974, Seoul, Republic of Korea
| | - Jung-Woong Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, 06974, Seoul, Republic of Korea.
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46
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Deacetylase activity-independent transcriptional activation by HDAC2 during TPA-induced HL-60 cell differentiation. PLoS One 2018; 13:e0202935. [PMID: 30142192 PMCID: PMC6108480 DOI: 10.1371/journal.pone.0202935] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/10/2018] [Indexed: 12/22/2022] Open
Abstract
The human myeloid leukemia cell line HL-60 differentiate into monocytes following treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA). However, the mechanism underlying the differentiation of these cells in response to TPA has not been fully elucidated. In this study, we performed ChIP-seq profiling of RNA Pol II, HDAC2, Acetyl H3 (AcH3), and H3K27me3 and analyzed differential chromatin state changes during TPA-induced differentiation of HL-60 cells. We focused on atypically active genes, which showed enhanced H3 acetylation despite increased HDAC2 recruitment. We found that HDAC2 positively regulates the expression of these genes in a histone deacetylase activity-independent manner. HDAC2 interacted with and recruited paired box 5 (PAX5) to the promoters of the target genes and regulated HL-60 cell differentiation by PAX5-mediated gene activation. Taken together, these data elucidated the specific-chromatin status during HL-60 cell differentiation following TPA exposure and suggested that HDAC2 can activate transcription of certain genes through interactions with PAX5 in a deacetylase activity-independent pathway.
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Abstract
Puberty involves a series of morphological, physiological and behavioural changes during the last part of the juvenile period that culminates in the attainment of fertility. The activation of the pituitary-gonadal axis by increased hypothalamic secretion of gonadotrophin-releasing hormone (GnRH) is an essential step in the process. The current hypothesis postulates that a loss of transsynaptic inhibition and a rise in excitatory inputs are responsible for the activation of GnRH release. Similarly, a shift in the balance in the expression of puberty activating and puberty inhibitory genes exists during the pubertal transition. In addition, recent evidence suggests that the epigenetic machinery controls this genetic balance, giving rise to the tantalising possibility that epigenetics serves as a relay of environmental signals known for many years to modulate pubertal development. Here, we review the contribution of epigenetics as a regulatory mechanism in the hypothalamic control of female puberty.
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Affiliation(s)
- C A Toro
- Primate Genetics Section/Division of Neuroscience, Oregon National Primate Research Center/Oregon Health & Science University, Beaverton, OR, USA
| | - C F Aylwin
- Primate Genetics Section/Division of Neuroscience, Oregon National Primate Research Center/Oregon Health & Science University, Beaverton, OR, USA
| | - A Lomniczi
- Primate Genetics Section/Division of Neuroscience, Oregon National Primate Research Center/Oregon Health & Science University, Beaverton, OR, USA
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48
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Kuroki S, Nakai Y, Maeda R, Okashita N, Akiyoshi M, Yamaguchi Y, Kitano S, Miyachi H, Nakato R, Ichiyanagi K, Shirahige K, Kimura H, Shinkai Y, Tachibana M. Combined Loss of JMJD1A and JMJD1B Reveals Critical Roles for H3K9 Demethylation in the Maintenance of Embryonic Stem Cells and Early Embryogenesis. Stem Cell Reports 2018. [PMID: 29526734 PMCID: PMC5998703 DOI: 10.1016/j.stemcr.2018.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Histone H3 lysine 9 (H3K9) methylation is unevenly distributed in mammalian chromosomes. However, the molecular mechanism controlling the uneven distribution and its biological significance remain to be elucidated. Here, we show that JMJD1A and JMJD1B preferentially target H3K9 demethylation of gene-dense regions of chromosomes, thereby establishing an H3K9 hypomethylation state in euchromatin. JMJD1A/JMJD1B-deficient embryos died soon after implantation accompanying epiblast cell death. Furthermore, combined loss of JMJD1A and JMJD1B caused perturbed expression of metabolic genes and rapid cell death in embryonic stem cells (ESCs). These results indicate that JMJD1A/JMJD1B-meditated H3K9 demethylation has critical roles for early embryogenesis and ESC maintenance. Finally, genetic rescue experiments clarified that H3K9 overmethylation by G9A was the cause of the cell death and perturbed gene expression of JMJD1A/JMJD1B-depleted ESCs. We summarized that JMJD1A and JMJD1B, in combination, ensure early embryogenesis and ESC viability by establishing the correct H3K9 methylated epigenome.
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Affiliation(s)
- Shunsuke Kuroki
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Yuji Nakai
- Institute for Food Sciences, Hirosaki University, 2-1-1 Yanagawa, Aomori 038-0012, Japan
| | - Ryo Maeda
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Naoki Okashita
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Mika Akiyoshi
- Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8597, Japan
| | - Yutaro Yamaguchi
- Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8597, Japan
| | - Satsuki Kitano
- Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8597, Japan
| | - Hitoshi Miyachi
- Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8597, Japan
| | - Ryuichiro Nakato
- Research Center for Epigenetic Disease, The University of Tokyo, 1-1-1 Yayoi, Bonkyo-ku, Tokyo 113-0032, Japan
| | - Kenji Ichiyanagi
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, The University of Tokyo, 1-1-1 Yayoi, Bonkyo-ku, Tokyo 113-0032, Japan
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Makoto Tachibana
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan; Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8597, Japan.
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49
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Dalvi MP, Wang L, Zhong R, Kollipara RK, Park H, Bayo J, Yenerall P, Zhou Y, Timmons BC, Rodriguez-Canales J, Behrens C, Mino B, Villalobos P, Parra ER, Suraokar M, Pataer A, Swisher SG, Kalhor N, Bhanu NV, Garcia BA, Heymach JV, Coombes K, Xie Y, Girard L, Gazdar AF, Kittler R, Wistuba II, Minna JD, Martinez ED. Taxane-Platin-Resistant Lung Cancers Co-develop Hypersensitivity to JumonjiC Demethylase Inhibitors. Cell Rep 2018; 19:1669-1684. [PMID: 28538184 DOI: 10.1016/j.celrep.2017.04.077] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 03/06/2017] [Accepted: 04/27/2017] [Indexed: 12/30/2022] Open
Abstract
Although non-small cell lung cancer (NSCLC) patients benefit from standard taxane-platin chemotherapy, many relapse, developing drug resistance. We established preclinical taxane-platin-chemoresistance models and identified a 35-gene resistance signature, which was associated with poor recurrence-free survival in neoadjuvant-treated NSCLC patients and included upregulation of the JumonjiC lysine demethylase KDM3B. In fact, multi-drug-resistant cells progressively increased the expression of many JumonjiC demethylases, had altered histone methylation, and, importantly, showed hypersensitivity to JumonjiC inhibitors in vitro and in vivo. Increasing taxane-platin resistance in progressive cell line series was accompanied by progressive sensitization to JIB-04 and GSK-J4. These JumonjiC inhibitors partly reversed deregulated transcriptional programs, prevented the emergence of drug-tolerant colonies from chemo-naive cells, and synergized with standard chemotherapy in vitro and in vivo. Our findings reveal JumonjiC inhibitors as promising therapies for targeting taxane-platin-chemoresistant NSCLCs.
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Affiliation(s)
- Maithili P Dalvi
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lei Wang
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rui Zhong
- Department of Clinical Science, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hyunsil Park
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Juan Bayo
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paul Yenerall
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunyun Zhou
- Department of Clinical Science, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brenda C Timmons
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Barbara Mino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pamela Villalobos
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Milind Suraokar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Apar Pataer
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Natarajan V Bhanu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kevin Coombes
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Yang Xie
- Department of Clinical Science, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralf Kittler
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elisabeth D Martinez
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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50
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Diets IJ, Waanders E, Ligtenberg MJ, van Bladel DAG, Kamping EJ, Hoogerbrugge PM, Hopman S, Olderode-Berends MJ, Gerkes EH, Koolen DA, Marcelis C, Santen GW, van Belzen MJ, Mordaunt D, McGregor L, Thompson E, Kattamis A, Pastorczak A, Mlynarski W, Ilencikova D, van Silfhout AV, Gardeitchik T, de Bont ES, Loeffen J, Wagner A, Mensenkamp AR, Kuiper RP, Hoogerbrugge N, Jongmans MC. High Yield of Pathogenic Germline Mutations Causative or Likely Causative of the Cancer Phenotype in Selected Children with Cancer. Clin Cancer Res 2018; 24:1594-1603. [PMID: 29351919 DOI: 10.1158/1078-0432.ccr-17-1725] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/11/2017] [Accepted: 01/12/2018] [Indexed: 11/16/2022]
Abstract
Purpose: In many children with cancer and characteristics suggestive of a genetic predisposition syndrome, the genetic cause is still unknown. We studied the yield of pathogenic mutations by applying whole-exome sequencing on a selected cohort of children with cancer.Experimental Design: To identify mutations in known and novel cancer-predisposing genes, we performed trio-based whole-exome sequencing on germline DNA of 40 selected children and their parents. These children were diagnosed with cancer and had at least one of the following features: (1) intellectual disability and/or congenital anomalies, (2) multiple malignancies, (3) family history of cancer, or (4) an adult type of cancer. We first analyzed the sequence data for germline mutations in 146 known cancer-predisposing genes. If no causative mutation was found, the analysis was extended to the whole exome.Results: Four patients carried causative mutations in a known cancer-predisposing gene: TP53 and DICER1 (n = 3). In another 4 patients, exome sequencing revealed mutations causing syndromes that might have contributed to the malignancy (EP300-based Rubinstein-Taybi syndrome, ARID1A-based Coffin-Siris syndrome, ACTB-based Baraitser-Winter syndrome, and EZH2-based Weaver syndrome). In addition, we identified two genes, KDM3B and TYK2, which are possibly involved in genetic cancer predisposition.Conclusions: In our selected cohort of patients, pathogenic germline mutations causative or likely causative of the cancer phenotype were found in 8 patients, and two possible novel cancer-predisposing genes were identified. Therewith, our study shows the added value of sequencing beyond a cancer gene panel in selected patients, to recognize childhood cancer predisposition. Clin Cancer Res; 24(7); 1594-603. ©2018 AACR.
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Affiliation(s)
- Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Esmé Waanders
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marjolijn J Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Diede A G van Bladel
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | | | - Saskia Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Maran J Olderode-Berends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carlo Marcelis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gijs W Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Martine J van Belzen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dylan Mordaunt
- Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, Australia
| | - Lesley McGregor
- Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, Australia
| | - Elizabeth Thompson
- Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, Australia
| | - Antonis Kattamis
- First Department of Pediatrics, Athens University Medical School, Athens, Greece
| | - Agata Pastorczak
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - Denisa Ilencikova
- 2nd Pediatric Department, Children's University Hospital, Comenius University, Bratislava, Slovakia
| | | | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Eveline S de Bont
- Department of Pediatric Oncology and Hematology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, the Netherlands
| | - Jan Loeffen
- Department of Pediatric Oncology and Hematology, Sophia Children's Hospital, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Marjolijn C Jongmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands. .,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
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