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Yang Y, Chen BR, Ye XC, Ni LY, Zhang XY, Liu YZ, Lyu TJ, Tian Y, Fu YJ, Wang Y. The chromodomain protein CDYL confers forebrain identity to human cortical organoids by inhibiting neuronatin. Cell Rep 2024; 43:114814. [PMID: 39378153 DOI: 10.1016/j.celrep.2024.114814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 08/02/2024] [Accepted: 09/17/2024] [Indexed: 10/10/2024] Open
Abstract
Fate determination of neural stem cells (NSCs) is crucial for cortex development and is closely linked to neurodevelopmental disorders when gene expression networks are disrupted. The transcriptional corepressor chromodomain Y-like (CDYL) is widely expressed across diverse cell populations within the human embryonic cortex. However, its precise role in cortical development remains unclear. Here, we show that CDYL is critical for human cortical neurogenesis and that its deficiency leads to a substantial increase in gamma-aminobutyric acid (GABA)-ergic neurons in cortical organoids. Subsequently, neuronatin (NNAT) is identified as a significant target of CDYL, and its abnormal expression obviously influences the fate commitment of cortical NSCs. Cross-species comparisons of CDYL targets unravel a distinct developmental trajectory between human cortical organoids and the mouse cortex at an analogous stage. Collectively, our data provide insight into the evolutionary roles of CDYL in human cortex development, emphasizing its critical function in maintaining the fate of human cortical NSCs.
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Affiliation(s)
- Yaming Yang
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Bai-Rong Chen
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Xi-Chun Ye
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Liang-Yu Ni
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Xi-Yin Zhang
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Yun-Ze Liu
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Tian-Jie Lyu
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Yue Tian
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Yun-Jie Fu
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Yun Wang
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China.
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2
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Modafferi S, Esposito F, Tavella S, Gioia U, Francia S. Traffic light at DSB-transit regulation between gene transcription and DNA repair. FEBS Lett 2024. [PMID: 39333024 DOI: 10.1002/1873-3468.15024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 08/12/2024] [Accepted: 08/15/2024] [Indexed: 09/29/2024]
Abstract
Transcription of actively expressed genes is dampened for kilobases around DNA lesions via chromatin modifications. This is believed to favour repair and prevent genome instability. Nonetheless, mounting evidence suggests that transcription may be induced by DNA breakage, resulting in the local de novo synthesis of non-coding RNAs (ncRNAs). Such transcripts have been proposed to play important functions in both DNA damage signalling and repair. Here, we review the recently identified mechanistic details of transcriptional silencing at damaged chromatin, highlighting how post-translational histone modifications can also be modulated by the local synthesis of DNA damage-induced ncRNAs. Finally, we envision that these entangled transcriptional events at DNA breakages can be targeted to modulate DNA repair, with potential implications for locus-specific therapeutic strategies.
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Affiliation(s)
- Stefania Modafferi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli Sforza"- Consiglio Nazionale delle Ricerche, Pavia, Italy
- PhD Program in Biomolecular Sciences and Biotechnology (SBB), Istituto Universitario di Studi Superiori (IUSS), Pavia, Italy
| | - Francesca Esposito
- Istituto di Genetica Molecolare "Luigi Luca Cavalli Sforza"- Consiglio Nazionale delle Ricerche, Pavia, Italy
- PhD Program in Genetics, Molecular and Cellular Biology (GMCB), University of Pavia, Pavia, Italy
| | - Sara Tavella
- Istituto di Genetica Molecolare "Luigi Luca Cavalli Sforza"- Consiglio Nazionale delle Ricerche, Pavia, Italy
- IFOM-ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Ubaldo Gioia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli Sforza"- Consiglio Nazionale delle Ricerche, Pavia, Italy
- IFOM-ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Sofia Francia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli Sforza"- Consiglio Nazionale delle Ricerche, Pavia, Italy
- IFOM-ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
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3
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Xiang T, Li LZ, Li JX, Chen XY, Guo F, Liu J, Wu YT, Lin L, Xu RH, Wang HP, Ma L, Fu P. Chromodomain Y-like (CDYL) inhibition ameliorates acute kidney injury in mice by regulating tubular pyroptosis. Acta Pharmacol Sin 2024:10.1038/s41401-024-01345-1. [PMID: 39043969 DOI: 10.1038/s41401-024-01345-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/27/2024] [Indexed: 07/25/2024] Open
Abstract
Acute kidney injury (AKI) is a common disease, but lacking effective drug treatments. Chromodomain Y-like (CDYL) is a kind of chromodomain protein that has been implicated in transcription regulation of autosomal dominant polycystic kidney disease. Benzo[d]oxazol-2(3H)-one derivative (compound D03) is the first potent and selective small-molecule inhibitor of CDYL (KD = 0.5 μM). In this study, we investigated the expression of CDYL in three different models of cisplatin (Cis)-, lipopolysaccharide (LPS)- and ischemia/reperfusion injury (IRI)-induced AKI mice. By conducting RNA sequencing and difference analysis of kidney samples, we found that tubular CDYL was abnormally and highly expressed in injured kidneys of AKI patients and mice. Overexpression of CDYL in cisplatin-induced AKI mice aggravated tubular injury and pyroptosis via regulating fatty acid binding protein 4 (FABP4)-mediated reactive oxygen species production. Treatment of cisplatin-induced AKI mice with compound D03 (2.5 mg·kg-1·d-1, i.p.) effectively attenuated the kidney dysfunction, pathological damages and tubular pyroptosis without side effects on liver or kidney function and other tissue injuries. Collectively, this study has, for the first time, explored a novel aspect of CDYL for tubular epithelial cell pyroptosis in kidney injury, and confirmed that inhibition of CDYL might be a promising therapeutic strategy against AKI.
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Affiliation(s)
- Ting Xiang
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, 610041, China
| | - Ling-Zhi Li
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, 610041, China
| | - Jin-Xi Li
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, 610041, China
| | - Xin-Yun Chen
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, 610041, China
| | - Fan Guo
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, 610041, China
| | - Jing Liu
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, 610041, China
| | - Yi-Ting Wu
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, 610041, China
| | - Lin Lin
- West-District Outpatient Department, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Rui-Han Xu
- West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Hui-Ping Wang
- West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Liang Ma
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, 610041, China.
| | - Ping Fu
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, 610041, China
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Becker TJ, Enkhmandakh B, Bayarsaihan D. Single-cell RNA analysis of chromodomain-encoding genes in mesenchymal stromal cells of the mouse dental pulp. J Cell Biochem 2024. [PMID: 38779967 DOI: 10.1002/jcb.30608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
The chromodomain helicase DNA-binding (CHD) and chromobox (CBX) families of proteins play crucial roles in cell fate decisions, differentiation, and cell proliferation in a broad variety of tissues and cell types. CHD proteins are ATP-dependent epigenetic enzymes actively engaged in transcriptional regulation, DNA replication, and DNA damage repair, whereas CBX proteins are transcriptional repressors mainly involved in the formation of heterochromatin. The pleiotropic effects of CHD and CBX proteins are largely dependent on their versatility to interact with other key components of the epigenetic and transcriptional machinery. Although the function and regulatory modes of CHD and CBX factors are well established in many cell types, little is known about their roles during osteogenic differentiation. A single-cell RNA-sequencing analysis of the mouse incisor dental pulp revealed distinct spatiotemporal expression patterns of CHD- and CBX-encoding genes within different clusters of mesenchymal stromal cells (MSCs) representing various stages of osteogenic differentiation. Additionally, genes encoding interaction partners of CHD and CBX proteins, such as subunits of the trithorax-COMPASS and polycomb chromatin remodeling complexes, exhibited differential co-expression behaviors within MSC subpopulations. Thus, CHD- and CBX-encoding genes show partially overlapping but distinct expression patterns in MSCs, suggesting their differential roles in osteogenic cell fate decisions.
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Affiliation(s)
- Timothy James Becker
- Department of Computer Science, Connecticut College, New London, Connecticut, USA
| | - Badam Enkhmandakh
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Dashzeveg Bayarsaihan
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, Connecticut, USA
- Institute for System Genomics, University of Connecticut, Storrs, Connecticut, USA
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5
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Hao H, Ren C, Lian Y, Zhao M, Bo T, Xu J, Wang W. Independent and Complementary Functions of Caf1b and Hir1 for Chromatin Assembly in Tetrahymena thermophila. Cells 2023; 12:2828. [PMID: 38132148 PMCID: PMC10741905 DOI: 10.3390/cells12242828] [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: 11/17/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Histones and DNA associate to form the nucleosomes of eukaryotic chromatin. Chromatin assembly factor 1 (CAF-1) complex and histone regulatory protein A (HIRA) complex mediate replication-couple (RC) and replication-independent (RI) nucleosome assembly, respectively. CHAF1B and HIRA share a similar domain but play different roles in nucleosome assembly by binding to the different interactors. At present, there is limited understanding for the similarities and differences in their respective functions. Tetrahymena thermophila contains transcriptionally active polyploid macronuclei (MAC) and transcriptionally silent diploid micronuclei (MIC). Here, the distribution patterns of Caf1b and Hir1 exhibited both similarities and distinctions. Both proteins localized to the MAC and MIC during growth, and to the MIC during conjugation. However, Hir1 exhibited additional signaling on parental MAC and new MAC during sexual reproduction and displayed a punctate signal on developing anlagen. Caf1b and Hir1 only co-localized in the MIC with Pcna1 during conjugation. Knockdown of CAF1B impeded cellular growth and arrested sexual reproductive development. Loss of HIR1 led to MIC chromosome defects and aborted sexual development. Co-interference of CAF1B and HIR1 led to a more severe phenotype. Moreover, CAF1B knockdown led to the up-regulation of HIR1 expression, while knockdown of HIR1 also led to an increase in CAF1B expression. Furthermore, Caf1b and Hir1 interacted with different interactors. These results showed that CAF-1 and Hir1 have independent and complementary functions for chromatin assembly in T. thermophila.
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Affiliation(s)
- Huijuan Hao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Chenhui Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Yinjie Lian
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Min Zhao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
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6
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Horvath S, Haghani A, Zoller JA, Lu AT, Ernst J, Pellegrini M, Jasinska AJ, Mattison JA, Salmon AB, Raj K, Horvath M, Paul KC, Ritz BR, Robeck TR, Spriggs M, Ehmke EE, Jenkins S, Li C, Nathanielsz PW. Pan-primate studies of age and sex. GeroScience 2023; 45:3187-3209. [PMID: 37493860 PMCID: PMC10643767 DOI: 10.1007/s11357-023-00878-3] [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: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/27/2023] Open
Abstract
Age and sex have a profound effect on cytosine methylation levels in humans and many other species. Here we analyzed DNA methylation profiles of 2400 tissues derived from 37 primate species including 11 haplorhine species (baboons, marmosets, vervets, rhesus macaque, chimpanzees, gorillas, orangutan, humans) and 26 strepsirrhine species (suborders Lemuriformes and Lorisiformes). From these we present here, pan-primate epigenetic clocks which are highly accurate for all primates including humans (age correlation R = 0.98). We also carried out in-depth analysis of baboon DNA methylation profiles and generated five epigenetic clocks for baboons (Olive-yellow baboon hybrid), one of which, the pan-tissue epigenetic clock, was trained on seven tissue types (fetal cerebral cortex, adult cerebral cortex, cerebellum, adipose, heart, liver, and skeletal muscle) with ages ranging from late fetal life to 22.8 years of age. Using the primate data, we characterize the effect of age and sex on individual cytosines in highly conserved regions. We identify 11 sex-related CpGs on autosomes near genes (POU3F2, CDYL, MYCL, FBXL4, ZC3H10, ZXDC, RRAS, FAM217A, RBM39, GRIA2, UHRF2). Low overlap can be observed between age- and sex-related CpGs. Overall, this study advances our understanding of conserved age- and sex-related epigenetic changes in primates, and provides biomarkers of aging for all primates.
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Affiliation(s)
- Steve Horvath
- Altos Labs, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
| | | | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Jason Ernst
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and BiobehavioralSciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julie A Mattison
- Translational Gerontology Branch, National Institute On Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Adam B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies, and Department of Molecular Medicine, UT Health San Antonio, and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | | | - Kimberly C Paul
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Beate R Ritz
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Todd R Robeck
- Corporate Zoological Operations, SeaWorld Parks, Orlando, FL, USA
| | - Maria Spriggs
- Busch Gardens Tampa, SeaWorld Parks, Tampa, FL, 33612, USA
| | | | - Susan Jenkins
- Texas Pregnancy & Life-Course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources Department, Laramie, WY, USA
| | - Cun Li
- Texas Pregnancy & Life-Course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources Department, Laramie, WY, USA
| | - Peter W Nathanielsz
- Texas Pregnancy & Life-Course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources Department, Laramie, WY, USA
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7
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Liu Y, Peng Y, Du W, Yu C, Peng Z, Qin L, Ma Y, Wu X, Peng Y, Cheng X, Xia L, Fa H, Wu Y, Sun L, Liu J, Liu Z, Shang Y, Wang S, Liang J. PD-L1-mediated immune evasion in triple-negative breast cancer is linked to the loss of ZNF652. Cell Rep 2023; 42:113343. [PMID: 37906592 DOI: 10.1016/j.celrep.2023.113343] [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: 12/29/2022] [Revised: 08/01/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023] Open
Abstract
The intrinsic regulation of programmed death ligand-1 (PD-L1) expression remains unclear. Here, we report that zinc-finger protein 652 (ZNF652) is a potent transcription repressor of PD-L1. ZNF652 frequently experiences loss of heterozygosity (LOH) in various cancers. Higher LOH rate and lack of estrogen-inducible transcription lead to suppressed expression of ZNF652 in triple-negative breast cancer (TNBC). Mechanistically, ZNF652 is physically associated with the NuRD transcription co-repressor complex to repress a cohort of genes, including PD-L1. Overexpression of ZNF652 inhibits PD-L1 transcription, whereas depletion of ZNF652 upregulates PD-L1. Loss of ZNF652 in TNBC unleashes PD-L1-mediated immune evasion both in vitro and in vivo. Significantly, ZNF652 expression is progressively lost during breast cancer progression, and a low ZNF652 level is correlated with elevated PD-L1 expression, less infiltrated CD8+ T cells, and poor prognosis in TNBC. Our study provides insights into PD-L1 regulation and supports the pursuit of ZNF652 as a potential biomarker and drug target for breast cancer immunotherapy.
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Affiliation(s)
- Yuncheng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yuan Peng
- Breast Disease Center, Peking University People's Hospital, Beijing 100044, China
| | - Wei Du
- Breast Disease Center, Peking University People's Hospital, Beijing 100044, China
| | - Chunyu Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Zijun Peng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Leyi Qin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yilei Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Xin Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yani Peng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Xiao Cheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Lu Xia
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Hangwei Fa
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yuqing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jianying Liu
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Shu Wang
- Breast Disease Center, Peking University People's Hospital, Beijing 100044, China.
| | - Jing Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China.
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8
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Fu Y, Yu J, Li F, Ge S. Oncometabolites drive tumorigenesis by enhancing protein acylation: from chromosomal remodelling to nonhistone modification. J Exp Clin Cancer Res 2022; 41:144. [PMID: 35428309 PMCID: PMC9013066 DOI: 10.1186/s13046-022-02338-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/21/2022] [Indexed: 02/02/2023] Open
Abstract
AbstractMetabolites are intermediate products of cellular metabolism catalysed by various enzymes. Metabolic remodelling, as a biochemical fingerprint of cancer cells, causes abnormal metabolite accumulation. These metabolites mainly generate energy or serve as signal transduction mediators via noncovalent interactions. After the development of highly sensitive mass spectrometry technology, various metabolites were shown to covalently modify proteins via forms of lysine acylation, including lysine acetylation, crotonylation, lactylation, succinylation, propionylation, butyrylation, malonylation, glutarylation, 2-hydroxyisobutyrylation and β-hydroxybutyrylation. These modifications can regulate gene expression and intracellular signalling pathways, highlighting the extensive roles of metabolites. Lysine acetylation is not discussed in detail in this review since it has been broadly investigated. We focus on the nine aforementioned novel lysine acylations beyond acetylation, which can be classified into two categories: histone acylations and nonhistone acylations. We summarize the characteristics and common functions of these acylation types and, most importantly, provide a glimpse into their fine-tuned control of tumorigenesis and potential value in tumour diagnosis, monitoring and therapy.
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9
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Ang GCK, Gupta A, Surana U, Yap SXL, Taneja R. Potential Therapeutics Targeting Upstream Regulators and Interactors of EHMT1/2. Cancers (Basel) 2022; 14:2855. [PMID: 35740522 PMCID: PMC9221123 DOI: 10.3390/cancers14122855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
Euchromatin histone lysine methyltransferases (EHMTs) are epigenetic regulators responsible for silencing gene transcription by catalyzing H3K9 dimethylation. Dysregulation of EHMT1/2 has been reported in multiple cancers and is associated with poor clinical outcomes. Although substantial insights have been gleaned into the downstream targets and pathways regulated by EHMT1/2, few studies have uncovered mechanisms responsible for their dysregulated expression. Moreover, EHMT1/2 interacting partners, which can influence their function and, therefore, the expression of target genes, have not been extensively explored. As none of the currently available EHMT inhibitors have made it past clinical trials, understanding upstream regulators and EHMT protein complexes may provide unique insights into novel therapeutic avenues in EHMT-overexpressing cancers. Here, we review our current understanding of the regulators and interacting partners of EHMTs. We also discuss available therapeutic drugs that target the upstream regulators and binding partners of EHMTs and could potentially modulate EHMT function in cancer progression.
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Affiliation(s)
- Gareth Chin Khye Ang
- Healthy Longevity Translational Research Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; (G.C.K.A.); (A.G.)
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore;
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Amogh Gupta
- Healthy Longevity Translational Research Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; (G.C.K.A.); (A.G.)
| | - Uttam Surana
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore;
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Shirlyn Xue Ling Yap
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Reshma Taneja
- Healthy Longevity Translational Research Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; (G.C.K.A.); (A.G.)
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10
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Stow EC, Simmons JR, An R, Schoborg TA, Davenport NM, Labrador M. A Drosophila insulator interacting protein suppresses enhancer-blocking function and modulates replication timing. Gene 2022; 819:146208. [PMID: 35092858 DOI: 10.1016/j.gene.2022.146208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/17/2021] [Accepted: 01/13/2022] [Indexed: 01/02/2023]
Abstract
Insulators play important roles in genome structure and function in eukaryotes. Interactions between a DNA binding insulator protein and its interacting partner proteins define the properties of each insulator site. The different roles of insulator protein partners in the Drosophila genome and how they confer functional specificity remain poorly understood. The Suppressor of Hairy wing [Su(Hw)] insulator is targeted to the nuclear lamina, preferentially localizes at euchromatin/heterochromatin boundaries, and is associated with the gypsy retrotransposon. Insulator activity relies on the ability of the Su(Hw) protein to bind the DNA at specific sites and interact with Mod(mdg4)67.2 and CP190 partner proteins. HP1 and insulator partner protein 1 (HIPP1) is a partner of Su(Hw), but how HIPP1 contributes to the function of Su(Hw) insulator complexes is unclear. Here, we demonstrate that HIPP1 colocalizes with the Su(Hw) insulator complex in polytene chromatin and in stress-induced insulator bodies. We find that the overexpression of either HIPP1 or Su(Hw) or mutation of the HIPP1 crotonase-like domain (CLD) causes defects in cell proliferation by limiting the progression of DNA replication. We also show that HIPP1 overexpression suppresses the Su(Hw) insulator enhancer-blocking function, while mutation of the HIPP1 CLD does not affect Su(Hw) enhancer blocking. These findings demonstrate a functional relationship between HIPP1 and the Su(Hw) insulator complex and suggest that the CLD, while not involved in enhancer blocking, influences cell cycle progression.
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Affiliation(s)
- Emily C Stow
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - James R Simmons
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Ran An
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Todd A Schoborg
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Nastasya M Davenport
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Mariano Labrador
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA.
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11
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Abu-Zhayia ER, Bishara LA, Machour FE, Barisaac AS, Ben-Oz BM, Ayoub N. CDYL1-dependent decrease in lysine crotonylation at DNA double-strand break sites functionally uncouples transcriptional silencing and repair. Mol Cell 2022; 82:1940-1955.e7. [PMID: 35447080 DOI: 10.1016/j.molcel.2022.03.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 01/17/2022] [Accepted: 03/23/2022] [Indexed: 11/16/2022]
Abstract
Previously, we showed that CDYL1 is recruited to DNA double-strand breaks (DSBs) to promote homologous recombination (HR) repair and foster transcriptional silencing. However, how CDYL1 elicits DSB-induced silencing is not fully understood. Here, we identify a CDYL1-dependent local decrease in the transcriptionally active marks histone lysine crotonylation (Kcr) and crotonylated lysine 9 of H3 (H3K9cr) at AsiSI-induced DSBs, which correlates with transcriptional silencing. Mechanistically, we reveal that CDYL1 crotonyl-CoA hydratase activity counteracts Kcr and H3K9cr at DSB sites, which triggers the eviction of the transcription elongation factor ENL and fosters transcriptional silencing. Furthermore, genetic inhibition of CDYL1 hydratase activity blocks the reduction in H3K9cr and alleviates DSB-induced silencing, whereas HR efficiency unexpectedly remains intact. Therefore, our results functionally uncouple the repair and silencing activity of CDYL1 at DSBs. In a broader context, we address a long-standing question concerning the functional relationship between HR repair and DSB-induced silencing, suggesting that they may occur independently.
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Affiliation(s)
- Enas R Abu-Zhayia
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Laila A Bishara
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Feras E Machour
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Alma Sophia Barisaac
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Bella M Ben-Oz
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel.
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12
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Sun Z, Waybright JM, Beldar S, Chen L, Foley CA, Norris‐Drouin JL, Lyu T, Dong A, Min J, Wang Y, James LI, Wang Y. Cdyl Deficiency Brakes Neuronal Excitability and Nociception through Promoting Kcnb1 Transcription in Peripheral Sensory Neurons. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104317. [PMID: 35119221 PMCID: PMC8981457 DOI: 10.1002/advs.202104317] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/28/2021] [Indexed: 05/24/2023]
Abstract
Epigenetic modifications are involved in the onset, development, and maintenance of pain; however, the precise epigenetic mechanism underlying pain regulation remains elusive. Here it is reported that the epigenetic factor chromodomain Y-like (CDYL) is crucial for pain processing. Selective knockout of CDYL in sensory neurons results in decreased neuronal excitability and nociception. Moreover, CDYL facilitates histone 3 lysine 27 trimethylation (H3K27me3) deposition at the Kcnb1 intron region thus silencing voltage-gated potassium channel (Kv ) subfamily member Kv 2.1 transcription. Loss function of CDYL enhances total Kv and Kv 2.1 current density in dorsal root ganglia and knockdown of Kv 2.1 reverses the pain-related phenotypes of Cdyl deficiency mice. Furthermore, focal administration of a novel potent CDYL antagonist blunts nociception and attenuates neuropathic pain. These findings reveal that CDYL is a critical regulator of pain sensation and shed light on the development of novel analgesics targeting epigenetic mechanisms.
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Affiliation(s)
- Zhao‐Wei Sun
- Neuroscience Research Institute and Department of NeurobiologySchool of Basic Medical SciencesKey Laboratory for NeuroscienceMinistry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing100083China
- Institute of Military Cognitive and Brain SciencesAcademy of Military Medical SciencesBeijing100039China
| | - Jarod M. Waybright
- Center for Integrative Chemical Biology and Drug DiscoveryDivision of Chemical Biology and Medicinal ChemistryUNC Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillNC27599USA
| | - Serap Beldar
- Structural Genomics ConsortiumUniversity of Toronto101 College StreetTorontoOntarioM5G 1L7Canada
| | - Lu Chen
- Neuroscience Research Institute and Department of NeurobiologySchool of Basic Medical SciencesKey Laboratory for NeuroscienceMinistry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing100083China
| | - Caroline A. Foley
- Center for Integrative Chemical Biology and Drug DiscoveryDivision of Chemical Biology and Medicinal ChemistryUNC Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillNC27599USA
| | - Jacqueline L. Norris‐Drouin
- Center for Integrative Chemical Biology and Drug DiscoveryDivision of Chemical Biology and Medicinal ChemistryUNC Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillNC27599USA
| | - Tian‐Jie Lyu
- Neuroscience Research Institute and Department of NeurobiologySchool of Basic Medical SciencesKey Laboratory for NeuroscienceMinistry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing100083China
| | - Aiping Dong
- Structural Genomics ConsortiumUniversity of Toronto101 College StreetTorontoOntarioM5G 1L7Canada
| | - Jinrong Min
- Structural Genomics ConsortiumUniversity of Toronto101 College StreetTorontoOntarioM5G 1L7Canada
- Hubei Key Laboratory of Genetic Regulation and Integrative BiologySchool of Life SciencesCentral China Normal UniversityWuhanHubei430079China
- Department of PhysiologyUniversity of TorontoTorontoOntarioM5S 1A8Canada
| | - Yu‐Pu Wang
- Neuroscience Research Institute and Department of NeurobiologySchool of Basic Medical SciencesKey Laboratory for NeuroscienceMinistry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing100083China
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug DiscoveryDivision of Chemical Biology and Medicinal ChemistryUNC Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillNC27599USA
| | - Yun Wang
- Neuroscience Research Institute and Department of NeurobiologySchool of Basic Medical SciencesKey Laboratory for NeuroscienceMinistry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing100083China
- PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
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13
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Zhang Z, Liu X, Li L, Yang Y, Yang J, Wang Y, Wu J, Wu X, Shan L, Pei F, Liu J, Wang S, Li W, Sun L, Liang J, Shang Y. SNP rs4971059 predisposes to breast carcinogenesis and chemoresistance via TRIM46-mediated HDAC1 degradation. EMBO J 2021; 40:e107974. [PMID: 34459501 DOI: 10.15252/embj.2021107974] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/28/2021] [Accepted: 08/16/2021] [Indexed: 12/19/2022] Open
Abstract
Identification of the driving force behind malignant transformation holds the promise to combat the relapse and therapeutic resistance of cancer. We report here that the single nucleotide polymorphism (SNP) rs4971059, one of 65 new breast cancer risk loci identified in a recent genome-wide association study (GWAS), functions as an active enhancer of TRIM46 expression. Recreating the G-to-A polymorphic switch caused by the SNP via CRISPR/Cas9-mediated homologous recombination leads to an overt upregulation of TRIM46. We find that TRIM46 is a ubiquitin ligase that targets histone deacetylase HDAC1 for ubiquitination and degradation and that the TRIM46-HDAC1 axis regulates a panel of genes, including ones critically involved in DNA replication and repair. Consequently, TRIM46 promotes breast cancer cell proliferation and chemoresistance in vitro and accelerates tumor growth in vivo. Moreover, TRIM46 is frequently overexpressed in breast carcinomas, and its expression is correlated with lower HDAC1 expression, higher histological grades, and worse prognosis of the patients. Together, our study links SNP rs4971059 to replication and to breast carcinogenesis and chemoresistance and support the pursuit of TRIM46 as a potential target for breast cancer intervention.
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Affiliation(s)
- Zihan Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China
| | - Xiaoping Liu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Lei Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yang Yang
- Breast Disease Center, Peking University People's Hospital, Beijing, China
| | - Jianguo Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jiajing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xiaodi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Fei Pei
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jianying Liu
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shu Wang
- Breast Disease Center, Peking University People's Hospital, Beijing, China
| | - Wei Li
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Luyang Sun
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China
| | - Jing Liang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China
| | - Yongfeng Shang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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14
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Wang X, Zhang L, Song Y, Jiang Y, Zhang D, Wang R, Hu T, Han S. MCM8 is regulated by EGFR signaling and promotes the growth of glioma stem cells through its interaction with DNA-replication-initiating factors. Oncogene 2021; 40:4615-4624. [PMID: 34131285 DOI: 10.1038/s41388-021-01888-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 02/05/2023]
Abstract
Mini-chromosome maintenance (MCM) proteins are critical components of DNA-replication-licensing factors. MCM8 is an MCM protein that exhibits oncogenic functions in several human malignancies. However, the role of MCM8 in glioblastomas (GBMs) has remained unclear. In the present study, we investigated the biological functions and mechanisms of MCM8 in glioma stem cells (GSCs). The clinical relevance of MCM8 mRNA expression was explored via TCGA and REMBRANDT datasets. The effects of MCM8 on the self-renewal and tumorigenicity of GSCs were examined both in vitro and in vivo. The regulation of MCM8 expression and its interacting proteins were also evaluated. We found that the expression of MCM8 was elevated in high-grade gliomas and classical molecular subtypes and was inversely correlated with patient prognosis. GSCs had a significantly higher expression of MCM8 compared with that in normal glioma cells. Silencing of MCM8 induced G0/G1 arrest and apoptosis, as well as inhibited the proliferation and self-renewal of GSCs. Forced expression of MCM8 enhanced clonogenicity of GSCs both in vitro and in vivo. MCM8 expression was regulated by EGFR signaling, which was mediated by NF-κB (p65). MCM8 interacted with DNA-replication-initiating factors-including EZH2, CDC6, and CDCA2-and influenced these factors to associate with chromatin. In addition, MCM8 knockdown increased the sensitivity of GSCs to radiation and TMZ treatments. Our findings suggest that MCM8, regulated by the EGFR pathway, maintains the clonogenic and tumorigenic potential of GSCs through interaction with DNA-replication-initiating factors; hence, MCM8 may represent a novel therapeutic target in GBMs.
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Affiliation(s)
- Xiaoliang Wang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Li Zhang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Yifu Song
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Yang Jiang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
- Department of Neurosurgery, Shanghai First People's Hospital of Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Di Zhang
- Department of Pathology, China Medical University, Shenyang, China
| | - Run Wang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Tianhao Hu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Sheng Han
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China.
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15
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Hou JY, Zhou L, Li JL, Wang DP, Cao JM. Emerging roles of non-histone protein crotonylation in biomedicine. Cell Biosci 2021; 11:101. [PMID: 34059135 PMCID: PMC8166067 DOI: 10.1186/s13578-021-00616-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 05/22/2021] [Indexed: 12/25/2022] Open
Abstract
Crotonylation of proteins is a newly found type of post-translational modifications (PTMs) which occurs leadingly on the lysine residue, namely, lysine crotonylation (Kcr). Kcr is conserved and is regulated by a series of enzymes and co-enzymes including lysine crotonyltransferase (writer), lysine decrotonylase (eraser), certain YEATS proteins (reader), and crotonyl-coenzyme A (donor). Histone Kcr has been substantially studied since 2011, but the Kcr of non-histone proteins is just an emerging field since its finding in 2017. Recent advances in the identification and quantification of non-histone protein Kcr by mass spectrometry have increased our understanding of Kcr. In this review, we summarized the main proteomic characteristics of non-histone protein Kcr and discussed its biological functions, including gene transcription, DNA damage response, enzymes regulation, metabolic pathways, cell cycle, and localization of heterochromatin in cells. We further proposed the performance of non-histone protein Kcr in diseases and the prospect of Kcr manipulators as potential therapeutic candidates in the diseases.
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Affiliation(s)
- Jia-Yi Hou
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.,Department of Clinical Laboratory, Shanxi Provincial Academy of Traditional Chinese Medicine, Taiyuan, China
| | - Lan Zhou
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Jia-Lei Li
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - De-Ping Wang
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Ji-Min Cao
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.
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16
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Ntorla A, Burgoyne JR. The Regulation and Function of Histone Crotonylation. Front Cell Dev Biol 2021; 9:624914. [PMID: 33889571 PMCID: PMC8055951 DOI: 10.3389/fcell.2021.624914] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 03/10/2021] [Indexed: 12/14/2022] Open
Abstract
Histone crotonylation is a newly identified epigenetic modification that has a pronounced ability to regulate gene expression. It belongs to an expanding group of short chain lysine acylations that also includes the extensively studied mark histone acetylation. Emerging evidence suggests that histone crotonylation is functionally distinct from histone acetylation and that competition for sites of modification, which reflects the cellular metabolic status, could be an important epigenetic mechanism that regulates diverse processes. Here, we discuss the enzymatic and metabolic regulation of histone crotonylation, the “reader” proteins that selectively recognise this modification and translate it into diverse functional outcomes within the cell, as well as the identified physiological roles of histone crotonylation, which range from signal-dependent gene activation to spermatogenesis and tissue injury.
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Affiliation(s)
- Angeliki Ntorla
- The Rayne Institute, School of Cardiovascular Medicine and Sciences, The British Heart Foundation Centre of Research Excellence, King's College London, St. Thomas' Hospital, London, United Kingdom
| | - Joseph Robert Burgoyne
- The Rayne Institute, School of Cardiovascular Medicine and Sciences, The British Heart Foundation Centre of Research Excellence, King's College London, St. Thomas' Hospital, London, United Kingdom
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17
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Mognato M, Burdak-Rothkamm S, Rothkamm K. Interplay between DNA replication stress, chromatin dynamics and DNA-damage response for the maintenance of genome stability. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108346. [PMID: 34083038 DOI: 10.1016/j.mrrev.2020.108346] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
DNA replication stress is a major source of DNA damage, including double-stranded breaks that promote DNA damage response (DDR) signaling. Inefficient repair of such lesions can affect genome integrity. During DNA replication different factors act on chromatin remodeling in a coordinated way. While recent studies have highlighted individual molecular mechanisms of interaction, less is known about the orchestration of chromatin changes under replication stress. In this review we attempt to explore the complex relationship between DNA replication stress, DDR and genome integrity in mammalian cells, taking into account the role of chromatin disposition as an important modulator of DNA repair. Recent data on chromatin restoration and epigenetic re-establishment after DNA replication stress are reviewed.
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Affiliation(s)
| | - Susanne Burdak-Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
| | - Kai Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
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18
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Dong C, Liu Y, Lyu TJ, Beldar S, Lamb KN, Tempel W, Li Y, Li Z, James LI, Qin S, Wang Y, Min J. Structural Basis for the Binding Selectivity of Human CDY Chromodomains. Cell Chem Biol 2020; 27:827-838.e7. [DOI: 10.1016/j.chembiol.2020.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/21/2020] [Accepted: 05/11/2020] [Indexed: 01/22/2023]
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19
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Pham V, Pitti R, Tindell CA, Cheung TK, Masselot A, Stephan JP, Guler GD, Wilson C, Lill J, Arnott D, Classon M. Proteomic Analyses Identify a Novel Role for EZH2 in the Initiation of Cancer Cell Drug Tolerance. J Proteome Res 2020; 19:1533-1547. [DOI: 10.1021/acs.jproteome.9b00773] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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20
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Yu H, Bu C, Liu Y, Gong T, Liu X, Liu S, Peng X, Zhang W, Peng Y, Yang J, He L, Zhang Y, Yi X, Yang X, Sun L, Shang Y, Cheng Z, Liang J. Global crotonylome reveals CDYL-regulated RPA1 crotonylation in homologous recombination-mediated DNA repair. SCIENCE ADVANCES 2020; 6:eaay4697. [PMID: 32201722 PMCID: PMC7069697 DOI: 10.1126/sciadv.aay4697] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 12/17/2019] [Indexed: 05/15/2023]
Abstract
Previously, we reported that chromodomain Y-like (CDYL) acts as a crotonyl-coenzyme A hydratase and negatively regulates histone crotonylation (Kcr). However, the global CDYL-regulated crotonylome remains unclear. Here, we report a large-scale proteomics analysis for protein Kcr. We identify 14,311 Kcr sites across 3734 proteins in HeLa cells, providing by far the largest crotonylome dataset. We show that depletion of CDYL alters crotonylome landscape affecting diverse cellular pathways. Specifically, CDYL negatively regulated Kcr of RPA1, and mutation of the Kcr sites of RPA1 impaired its interaction with single-stranded DNA and/or with components of resection machinery, supporting a key role of RPA1 Kcr in homologous recombination DNA repair. Together, our study indicates that protein crotonylation has important implication in various pathophysiological processes.
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Affiliation(s)
- Huajing Yu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Yuncheng Liu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tianyu Gong
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaoping Liu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shumeng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaojun Peng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Wenting Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yani Peng
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xia Yi
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaohan Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yongfeng Shang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
- Corresponding author. (J.L.); (Z.C.)
| | - Jing Liang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Corresponding author. (J.L.); (Z.C.)
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Machour FE, Ayoub N. Transcriptional Regulation at DSBs: Mechanisms and Consequences. Trends Genet 2020; 36:981-997. [PMID: 32001024 DOI: 10.1016/j.tig.2020.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/31/2019] [Accepted: 01/03/2020] [Indexed: 12/11/2022]
Abstract
Defective double-strand break (DSB) repair leads to genomic instabilities that may augment carcinogenesis. DSBs trigger transient transcriptional silencing in the vicinity of transcriptionally active genes through multilayered processes instigated by Ataxia telangiectasia mutated (ATM), DNA-dependent protein kinase (DNA-PK), and poly-(ADP-ribose) polymerase 1 (PARP1). Novel factors have been identified that ensure DSB-induced silencing via two distinct pathways: direct inhibition of RNA Polymerase II (Pol II) mediated by negative elongation factor (NELF), and histone code editing by CDYL1 and histone deacetylases (HDACs) that catalyze H3K27me3 and erase lysine crotonylation, respectively. Here, we highlight major advances in understanding the mechanisms underlying transcriptional silencing at DSBs, and discuss its functional implications on repair. Furthermore, we discuss consequential links between DSB-silencing factors and carcinogenesis and discuss the potential of exploiting them for targeted cancer therapy.
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Affiliation(s)
- Feras E Machour
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
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22
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Melnikova L, Molodina V, Erokhin M, Georgiev P, Golovnin A. HIPP1 stabilizes the interaction between CP190 and Su(Hw) in the Drosophila insulator complex. Sci Rep 2019; 9:19102. [PMID: 31836797 PMCID: PMC6911044 DOI: 10.1038/s41598-019-55617-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/29/2019] [Indexed: 12/14/2022] Open
Abstract
Suppressor of Hairy-wing [Su(Hw)] is one of the best characterized architectural proteins in Drosophila and recruits the CP190 and Mod(mdg4)-67.2 proteins to chromatin, where they form a well-known insulator complex. Recently, HP1 and insulator partner protein 1 (HIPP1), a homolog of the human co-repressor Chromodomain Y-Like (CDYL), was identified as a new partner for Su(Hw). Here, we performed a detailed analysis of the domains involved in the HIPP1 interactions with Su(Hw)-dependent complexes. HIPP1 was found to directly interact with the Su(Hw) C-terminal region (aa 720–892) and with CP190, but not with Mod(mdg4)-67.2. We have generated Hipp1 null mutants (HippΔ1) and found that the loss of Hipp1 does not affect the enhancer-blocking or repression activities of the Su(Hw)-dependent complex. However, the simultaneous inactivation of both HIPP1 and Mod(mdg4)-67.2 proteins resulted in reduced CP190 binding with Su(Hw) sites and significantly altered gypsy insulator activity. Taken together, these results suggested that the HIPP1 protein stabilized the interaction between CP190 and the Su(Hw)-dependent complex.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Varvara Molodina
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Maksim Erokhin
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia.
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23
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Yang L, Liu Y, Fan M, Zhu G, Jin H, Liang J, Liu Z, Huang Z, Zhang L. Identification and characterization of benzo[d]oxazol-2(3H)-one derivatives as the first potent and selective small-molecule inhibitors of chromodomain protein CDYL. Eur J Med Chem 2019; 182:111656. [DOI: 10.1016/j.ejmech.2019.111656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/24/2019] [Accepted: 08/28/2019] [Indexed: 12/17/2022]
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Qiu Z, Zhu W, Meng H, Tong L, Li X, Luo P, Yi L, Zhang X, Guo L, Wei T, Zhang J. CDYL promotes the chemoresistance of small cell lung cancer by regulating H3K27 trimethylation at the CDKN1C promoter. Am J Cancer Res 2019; 9:4717-4729. [PMID: 31367252 PMCID: PMC6643436 DOI: 10.7150/thno.33680] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/05/2019] [Indexed: 01/10/2023] Open
Abstract
Rationale: Chemoresistance frequently occurs in patients with small cell lung cancer (SCLC) and leads to a dismal prognosis. However, the mechanisms underlying this process remain largely unclear. Methods: The effects of chromodomain Y-like (CDYL) on chemoresistance in SCLC were determined using Western blotting, immunohistochemistry, cell counting kit-8 assays, flow cytometry, and tumorigenicity experiments, and the underlying mechanisms were investigated using mRNA sequencing, chromatin immunoprecipitation-qPCR, electrophoretic mobility shift assays, co-immunoprecipitation, GST pull down assays, bisulfite sequencing PCR, ELISA, and bioinformatics analyses. Results: CDYL is expressed at high levels in chemoresistant SCLC tissues from patients, and elevated CDYL levels correlate with an advanced clinical stage and a poor prognosis. Furthermore, CDYL expression is significantly upregulated in chemoresistant SCLC cells. Using gain- and loss-of-function methods, we show that CDYL promotes chemoresistance in SCLC in vitro and in vivo. Mechanistically, CDYL promotes SCLC chemoresistance by silencing its downstream mediator cyclin-dependent kinase inhibitor 1C (CDKN1C). Further mechanistic investigations showed that CDYL recruits the enhancer of zeste homolog 2 (EZH2) to regulate trimethylation of lysine 27 in histone 3 (H3K27me3) at the CDKN1C promoter region and promotes transcriptional silencing. Accordingly, the EZH2 inhibitor GSK126 de-represses CDKN1C and decreases CDYL-induced chemoresistance in SCLC. Principal conclusions: Based on these results, the CDYL/EZH2/CDKN1C axis promotes chemoresistance in SCLC, and these markers represent promising therapeutic targets for overcoming chemoresistance in patients with SCLC.
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Xia X, Zhou X, Quan Y, Hu Y, Xing F, Li Z, Xu B, Xu C, Zhang A. Germline deletion of Cdyl causes teratozoospermia and progressive infertility in male mice. Cell Death Dis 2019; 10:229. [PMID: 30850578 PMCID: PMC6408431 DOI: 10.1038/s41419-019-1455-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/25/2019] [Accepted: 02/01/2019] [Indexed: 12/02/2022]
Abstract
Chromodomain Y (CDY) is one of the candidate genes for male dyszoospermia related to Y chromosome microdeletion (YCM). However, the function of CDY in regulating spermatogenesis has not been completely determined. The mouse Cdyl (CDY-like) gene is the homolog of human CDY. In the present study, we generated a germline conditional knockout (cKO) model of mouse Cdyl. Significantly, the CdylcKO male mice suffered from the defects in spermatogonia maintenance and spermatozoon morphogenesis, demonstrating teratozoospermia and a progressive infertility phenotype in early adulthood. Importantly, patterns of specific histone methylation and acetylation were extensively changed, which disturbed the transcriptome in CdylcKO testis. Our findings indicated that Cdyl is crucial for spermatogenesis and male fertility, which provides novel insights into the function of CDY gene, as well as the pathogenesis of YCM-related reproductive failure.
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Affiliation(s)
- Xiaoyu Xia
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University, School of Medicine; Shanghai Key Laboratory of Reproductive Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Xiaowei Zhou
- Reproductive Medical Center of Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, China
| | - Yanmei Quan
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University, School of Medicine; Shanghai Key Laboratory of Reproductive Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Yanqin Hu
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University, School of Medicine; Shanghai Key Laboratory of Reproductive Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Fengying Xing
- Department of Laboratory Animal Science, Shanghai Jiao Tong University, School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Zhengzheng Li
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University, School of Medicine; Shanghai Key Laboratory of Reproductive Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Bufang Xu
- Reproductive Medical Center of Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, China.
| | - Chen Xu
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University, School of Medicine; Shanghai Key Laboratory of Reproductive Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
| | - Aijun Zhang
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University, School of Medicine; Shanghai Key Laboratory of Reproductive Medicine, 280 South Chongqing Road, Shanghai, 200025, China. .,Reproductive Medical Center of Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, China.
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Schoeler NE, Leu C, Balestrini S, Mudge JM, Steward CA, Frankish A, Leung M, Mackay M, Scheffer I, Williams R, Sander JW, Cross JH, Sisodiya SM. Genome-wide association study: Exploring the genetic basis for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy. Epilepsia 2018; 59:1557-1566. [PMID: 30009487 PMCID: PMC6099477 DOI: 10.1111/epi.14516] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 06/19/2018] [Indexed: 02/04/2023]
Abstract
OBJECTIVE With the exception of specific metabolic disorders, predictors of response to ketogenic dietary therapies (KDTs) are unknown. We aimed to determine whether common variation across the genome influences the response to KDT for epilepsy. METHODS We genotyped individuals who were negative for glucose transporter type 1 deficiency syndrome or other metabolic disorders, who received KDT for epilepsy. Genotyping was performed with the Infinium HumanOmniExpressExome Beadchip. Hospital records were used to obtain demographic and clinical data. KDT response (≥50% seizure reduction) at 3-month follow-up was used to dissect out nonresponders and responders. We then performed a genome-wide association study (GWAS) in nonresponders vs responders, using a linear mixed model and correcting for population stratification. Variants with minor allele frequency <0.05 and those that did not pass quality control filtering were excluded. RESULTS After quality control filtering, the GWAS of 112 nonresponders vs 123 responders revealed an association locus at 6p25.1, 61 kb upstream of CDYL (rs12204701, P = 3.83 × 10-8 , odds ratio [A] = 13.5, 95% confidence interval [CI] 4.07-44.8). Although analysis of regional linkage disequilibrium around rs12204701 did not strengthen the likelihood of CDYL being the candidate gene, additional bioinformatic analyses suggest it is the most likely candidate. SIGNIFICANCE CDYL deficiency has been shown to disrupt neuronal migration and to influence susceptibility to epilepsy in mice. Further exploration with a larger replication cohort is warranted to clarify whether CDYL is the causal gene underlying the association signal.
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Affiliation(s)
- Natasha E. Schoeler
- Department of Clinical and Experimental EpilepsyUCL Institute of NeurologyLondonUK
- UCL Great Ormond Street Institute of Child HealthLondonUK
| | - Costin Leu
- Department of Clinical and Experimental EpilepsyUCL Institute of NeurologyLondonUK
- NIHR University College London Hospitals Biomedical Research CentreUCL Institute of NeurologyLondonUK
| | - Simona Balestrini
- Department of Clinical and Experimental EpilepsyUCL Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyChalfont St PeterUK
| | - Jonathan M. Mudge
- European Molecular Biology LaboratoryWellcome Genome CampusEuropean Bioinformatics InstituteCambridgeUK
| | | | - Adam Frankish
- European Molecular Biology LaboratoryWellcome Genome CampusEuropean Bioinformatics InstituteCambridgeUK
| | - Mary‐Anne Leung
- Children's Neurosciences CentreGuy's and St Thomas’ NHS Foundation TrustLondonUK
| | - Mark Mackay
- Department of PaediatricsThe University of MelbourneRoyal Children's HospitalMelbourneVic.Australia
- Murdoch Children's Research InstituteMelbourneVic.Australia
| | - Ingrid Scheffer
- Department of PaediatricsThe University of MelbourneRoyal Children's HospitalMelbourneVic.Australia
- Epilepsy Research CentreDepartment of MedicineThe University of MelbourneAustin HealthMelbourneVic.Australia
- Austin HealthFlorey Institute of Neurosciences and Mental HealthMelbourneVic.Australia
| | - Ruth Williams
- Children's Neurosciences CentreGuy's and St Thomas’ NHS Foundation TrustLondonUK
| | - Josemir W. Sander
- NIHR University College London Hospitals Biomedical Research CentreUCL Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyChalfont St PeterUK
- Stichting Epilepsie Instellingen Nederland (SEIN)HeemstedeThe Netherlands
| | - J. Helen Cross
- UCL Great Ormond Street Institute of Child HealthLondonUK
- Great Ormond Street Hospital for ChildrenLondonUK
- Young EpilepsyLingfieldUK
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental EpilepsyUCL Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyChalfont St PeterUK
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27
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Liu S, Yu H, Liu Y, Liu X, Zhang Y, Bu C, Yuan S, Chen Z, Xie G, Li W, Xu B, Yang J, He L, Jin T, Xiong Y, Sun L, Liu X, Han C, Cheng Z, Liang J, Shang Y. Chromodomain Protein CDYL Acts as a Crotonyl-CoA Hydratase to Regulate Histone Crotonylation and Spermatogenesis. Mol Cell 2017; 67:853-866.e5. [PMID: 28803779 DOI: 10.1016/j.molcel.2017.07.011] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 06/02/2017] [Accepted: 07/07/2017] [Indexed: 11/25/2022]
Abstract
Lysine crotonylation (Kcr) is a newly identified histone modification that is associated with active transcription in mammalian cells. Here we report that the chromodomain Y-like transcription corepressor CDYL negatively regulates histone Kcr by acting as a crotonyl-CoA hydratase to convert crotonyl-CoA to β-hydroxybutyryl-CoA. We showed that the negative regulation of histone Kcr by CDYL is intrinsically linked to its transcription repression activity and functionally implemented in the reactivation of sex chromosome-linked genes in round spermatids and genome-wide histone replacement in elongating spermatids. Significantly, Cdyl transgenic mice manifest dysregulation of histone Kcr and reduction of male fertility with a decreased epididymal sperm count and sperm cell motility. Our study uncovers a biochemical pathway in the regulation of histone Kcr and implicates CDYL-regulated histone Kcr in spermatogenesis, adding to the understanding of the physiology of male reproduction and the mechanism of the spermatogenic failure in AZFc (Azoospermia Factor c)-deleted infertile men.
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Affiliation(s)
- Shumeng Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Huajing Yu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yongqing Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yu Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou), Co. Ltd., Hangzhou 310018, China
| | - Shuai Yuan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhe Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Guojia Xie
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Wanjin Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Bosen Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tong Jin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yundong Xiong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaohui Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chunsheng Han
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou), Co. Ltd., Hangzhou 310018, China
| | - Jing Liang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Yongfeng Shang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
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28
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Barnash KD, Lamb KN, James LI, Frye SV. Peptide Technologies in the Development of Chemical Tools for Chromatin-Associated Machinery. Drug Dev Res 2017. [DOI: 10.1002/ddr.21398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kimberly D. Barnash
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
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