1
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Yang X, Guan Y, Bayliss G, Zhao TC, Zhuang S. SET8 inhibition preserves PTEN to attenuate kidney cell apoptosis in cisplatin nephrotoxicity. RESEARCH SQUARE 2024:rs.3.rs-4603170. [PMID: 39184108 PMCID: PMC11343278 DOI: 10.21203/rs.3.rs-4603170/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
The aberrant expression of SET8, a histone methyltransferase that mediates H4 lysine 20 mono-methylation (H4K20me1), is implicated in the pathogenesis of various tumors, however, its role in acute kidney injury (AKI) is unknown. Here we showed that SET8 and H4K20me1 were upregulated in the murine kidney with AKI induced by cisplatin, along with increased renal tubular cell injury and apoptosis and decreased expression of E-cadherin and Phosphatase and Tensin Homolog (PTEN). Suppression of SET8 by UNC0379 improved renal function, attenuated tubule damage, and restored expression of PTEN, but not E-cadherin. UNC0379 was also effective in lessening cisplatin-induced DNA damage response (DDR) as indicated by reduced expression of γ-H2AX, p53, p21, and alleviating cisplatin-impaired autophagy as shown by retained expression of Atg5, Beclin-1, and CHMP2A and enhanced levels of LC3-II in the kidney. Consistently, inhibition of SET8 with either UNC0379 or siRNA mitigated apoptosis and DDR, and restored autophagy, along with PTEN preservation in cultured renal proximal tubular epithelial cell (TKPTs) exposed to cisplatin. Further studies showed that inhibition of PTEN with Bpv or siRNA potentiated cisplatin-induced apoptosis, DDR, and hindered autophagy, and conversely, alleviated by overexpression of PTEN in TKPTs. Finally, blocking PTEN largely abolished the inhibitory effect of UNC0379 on apoptosis. Taken together, these results suggest that SET8 inhibition protects against cisplatin-induced AKI and renal cell apoptosis through a mechanism associated with the preservation of PTEN, which in turn inhibits DDR and restores autophagy.
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Affiliation(s)
- Xu Yang
- Rhode Island Hospital and Alpert Medical School, Brown University
| | - Yingjie Guan
- Rhode Island Hospital and Alpert Medical School, Brown University
| | - George Bayliss
- Rhode Island Hospital and Alpert Medical School, Brown University
| | - Ting C Zhao
- Brown University School of Medicine-Rhode Island Hospital
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2
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Xiao CL, Lai HT, Zhou JJ, Liu WY, Zhao M, Zhao K. Nrf2 Signaling Pathway: Focus on Oxidative Stress in Spinal Cord Injury. Mol Neurobiol 2024:10.1007/s12035-024-04394-z. [PMID: 39093381 DOI: 10.1007/s12035-024-04394-z] [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: 12/11/2023] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Spinal cord injury (SCI) is a serious, disabling injury to the central nervous system that can lead to motor, sensory, and autonomic dysfunction below the injury plane. SCI can be divided into primary injury and secondary injury according to its pathophysiological process. Primary injury is irreversible in most cases, while secondary injury is a dynamic regulatory process. Secondary injury involves a series of pathological events, such as ischemia, oxidative stress, inflammatory events, apoptotic pathways, and motor dysfunction. Among them, oxidative stress is an important pathological event of secondary injury. Oxidative stress causes a series of destructive events such as lipid peroxidation, DNA damage, inflammation, and cell death, which further worsens the microenvironment of the injured site and leads to neurological dysfunction. The nuclear factor erythrocyte 2-associated factor 2 (Nrf2) is considered to be a key pathway of antioxidative stress and is closely related to the pathological process of SCI. Activation of this pathway can effectively inhibit the oxidative stress process and promote the recovery of nerve function after SCI. Therefore, the Nrf2 pathway may be a potential therapeutic target for SCI. This review deeply analyzed the generation of oxidative stress in SCI, the role and mechanism of Nrf2 as the main regulator of antioxidant stress in SCI, and the influence of cross-talk between Nrf2 and related pathways that may be involved in the pathological regulation of SCI on oxidative stress, and summarized the drugs and other treatment methods based on Nrf2 pathway regulation. The objective of this paper is to provide evidence for the role of Nrf2 activation in SCI and to highlight the important role of Nrf2 in alleviating SCI by elucidating the mechanism, so as to provide a theoretical basis for targeting Nrf2 pathway as a therapy for SCI.
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Affiliation(s)
- Chun-Lin Xiao
- Gannan Medical University, 1 Harmony Avenue, Rongjiang New District, Ganzhou, Jiangxi Province, 341000, People's Republic of China
- Department of Orthopaedics, Frist Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, 341000, People's Republic of China
| | - Hong-Tong Lai
- Gannan Medical University, 1 Harmony Avenue, Rongjiang New District, Ganzhou, Jiangxi Province, 341000, People's Republic of China
- Department of Orthopaedics, Frist Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, 341000, People's Republic of China
| | - Jiang-Jun Zhou
- Hospital 908, Joint Logistics Support Force, 1028 Jinggangshan Avenue, Qingyunpu District, Nanchang City, Jiangxi Province, 330001, People's Republic of China
| | - Wu-Yang Liu
- Gannan Medical University, 1 Harmony Avenue, Rongjiang New District, Ganzhou, Jiangxi Province, 341000, People's Republic of China
- Department of Orthopaedics, Frist Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, 341000, People's Republic of China
| | - Min Zhao
- Department of Spine Surgery, Yingtan People's Hospital, 116 Shengli West Road, Yuehu District, Yingtan City, Jiangxi Province, 335000, People's Republic of China.
| | - Kai Zhao
- Gannan Medical University, 1 Harmony Avenue, Rongjiang New District, Ganzhou, Jiangxi Province, 341000, People's Republic of China.
- Department of Orthopaedics, Frist Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, 341000, People's Republic of China.
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3
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Gil J, Navarrete E, Rosin L, Chowdhury N, Abraham S, Cornilleau G, Lei E, Mozziconacci J, Mirny L, Muller H, Drinnenberg I. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. RESEARCH SQUARE 2024:rs.3.rs-4732646. [PMID: 39149482 PMCID: PMC11326380 DOI: 10.21203/rs.3.rs-4732646/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and insulated domains, including topologically associated domains (TADs). Yet, most of these elements of chromosome organization are derived from analyses of a limited set of model organisms, while large eukaryotic groups, including insects, remain mostly unexplored. Here we combine Hi-C, biophysical modeling, and microscopy to characterize the 3D genome architecture of the silkmoth, Bombyx mori. In contrast to other eukaryotes, B. mori chromosomes form highly separated territories. Similar to other eukaryotes, B. mori chromosomes segregate into active A and inactive B compartments, yet unlike in vertebrate systems, contacts between euchromatic A regions appear to be a strong driver of compartmentalization. Remarkably, we also identify a third compartment, called secluded "S," with a unique contact pattern. Each S region shows prominent short-range self-contacts and is remarkably devoid of contacts with the rest of the chromosome, including other S regions. Compartment S hosts a unique combination of genetic and epigenetic features, localizes towards the periphery of CTs, and shows developmental plasticity. Biophysical modeling reveals that the formation of such secluded domains requires highly localized loop extrusion within them, along with a low level of extrusion in A and B. Our Hi-C data supports predicted genome-wide and localized extrusion. Such a broad, non-uniform distribution of extruders has not been seen in other organisms. Overall, our analyses support loop extrusion in insects and highlight the evolutionary plasticity of 3D genome organization, driven by a new combination of known processes.
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Affiliation(s)
- J. Gil
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - E. Navarrete
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - L.F. Rosin
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - N. Chowdhury
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - S. Abraham
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - G. Cornilleau
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - E.P. Lei
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - J. Mozziconacci
- StrInG Lab, Museum National d’Histoire Naturelle, Paris, France
| | - L.A. Mirny
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - H. Muller
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - I.A. Drinnenberg
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
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4
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Dai Y, Itai T, Pei G, Yan F, Chu Y, Jiang X, Weinberg SM, Mukhopadhyay N, Marazita ML, Simon LM, Jia P, Zhao Z. DeepFace: Deep-learning-based framework to contextualize orofacial-cleft-related variants during human embryonic craniofacial development. HGG ADVANCES 2024; 5:100312. [PMID: 38796699 PMCID: PMC11193024 DOI: 10.1016/j.xhgg.2024.100312] [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: 02/08/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 05/28/2024] Open
Abstract
Orofacial clefts (OFCs) are among the most common human congenital birth defects. Previous multiethnic studies have identified dozens of associated loci for both cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP). Although several nearby genes have been highlighted, the "casual" variants are largely unknown. Here, we developed DeepFace, a convolutional neural network model, to assess the functional impact of variants by SNP activity difference (SAD) scores. The DeepFace model is trained with 204 epigenomic assays from crucial human embryonic craniofacial developmental stages of post-conception week (pcw) 4 to pcw 10. The Pearson correlation coefficient between the predicted and actual values for 12 epigenetic features achieved a median range of 0.50-0.83. Specifically, our model revealed that SNPs significantly associated with OFCs tended to exhibit higher SAD scores across various variant categories compared to less related groups, indicating a context-specific impact of OFC-related SNPs. Notably, we identified six SNPs with a significant linear relationship to SAD scores throughout developmental progression, suggesting that these SNPs could play a temporal regulatory role. Furthermore, our cell-type specificity analysis pinpointed the trophoblast cell as having the highest enrichment of risk signals associated with OFCs. Overall, DeepFace can harness distal regulatory signals from extensive epigenomic assays, offering new perspectives for prioritizing OFC variants using contextualized functional genomic features. We expect DeepFace to be instrumental in accessing and predicting the regulatory roles of variants associated with OFCs, and the model can be extended to study other complex diseases or traits.
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Affiliation(s)
- Yulin Dai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Toshiyuki Itai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Guangsheng Pei
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Fangfang Yan
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yan Chu
- Center for Secure Artificial Intelligence for Healthcare, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaoqian Jiang
- Center for Secure Artificial Intelligence for Healthcare, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Seth M Weinberg
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Nandita Mukhopadhyay
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Mary L Marazita
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA; Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Lukas M Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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5
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Galanopoulou O, Tachmatzidi EC, Deligianni E, Botskaris D, Nikolaou KC, Gargani S, Dalezios Y, Chalepakis G, Talianidis I. Endonucleosis mediates internalization of cytoplasm into the nucleus. Nat Commun 2024; 15:5843. [PMID: 38992049 PMCID: PMC11239883 DOI: 10.1038/s41467-024-50259-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 07/03/2024] [Indexed: 07/13/2024] Open
Abstract
Setd8 regulates transcription elongation, mitotic DNA condensation, DNA damage response and replication licensing. Here we show that, in mitogen-stimulated liver-specific Setd8-KO mice, most of the hepatocytes are eliminated by necrosis but a significant number of them survive via entering a stage exhibiting several senescence-related features. Setd8-deficient hepatocytes had enlarged nuclei, chromosomal hyperploidy and nuclear engulfments progressing to the formation of intranuclear vesicles surrounded by nuclear lamina. These vesicles contain glycogen, cytoplasmic proteins and even entire organelles. We term this process "endonucleosis". Intranuclear vesicles are absent in hepatocytes of Setd8/Atg5 knockout mice, suggesting that the process requires the function of the canonical autophagy machinery. Endonucleosis and hyperploidization are temporary, early events in the surviving Setd8-deficient cells. Larger vesicles break down into microvesicles over time and are eventually eliminated. The results reveal sequential events in cells with extensive DNA damage, which function as part of survival mechanisms to prevent necrotic death.
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Affiliation(s)
- Ourania Galanopoulou
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Dept. of Biology University of Crete, Heraklion, Crete, Greece
| | - Evangelia C Tachmatzidi
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Dept. of Biology University of Crete, Heraklion, Crete, Greece
| | - Elena Deligianni
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Dimitris Botskaris
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Dept. of Biology University of Crete, Heraklion, Crete, Greece
| | | | - Sofia Gargani
- Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | - Yannis Dalezios
- School of Medicine University of Crete, Heraklion, Crete, Greece
| | | | - Iannis Talianidis
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece.
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6
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Gil J, Rosin LF, Navarrete E, Chowdhury N, Abraham S, Cornilleau G, Lei EP, Mozziconacci J, Mirny LA, Muller H, Drinnenberg IA. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557757. [PMID: 37745315 PMCID: PMC10515926 DOI: 10.1101/2023.09.14.557757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and insulated domains, including topologically associated domains (TADs). Yet, most of these elements of chromosome organization are derived from analyses of a limited set of model organisms, while large eukaryotic groups, including insects, remain mostly unexplored. Here we combine Hi-C, biophysical modeling, and microscopy to characterize the 3D genome architecture of the silkworm, Bombyx mori. In contrast to other eukaryotes, B. mori chromosomes form highly separated territories. Similar to other eukaryotes, B. mori chromosomes segregate into active A and inactive B compartments, yet unlike in vertebrate systems, contacts between euchromatic A regions appear to be a strong driver of compartmentalization. Remarkably, we also identify a third compartment, called secluded S, with a unique contact pattern. Each S region shows prominent short-range self-contacts and is remarkably devoid of contacts with the rest of the chromosome, including other S regions. Compartment S hosts a unique combination of genetic and epigenetic features, localizes towards the periphery of CTs, and shows developmental plasticity. Biophysical modeling reveals that the formation of such secluded domains requires highly localized loop extrusion within them, along with a low level of extrusion in A and B. Our Hi-C data supports predicted genome-wide and localized extrusion. Such a broad, non-uniform distribution of extruders has not been seen in other organisms. Overall, our analyses support loop extrusion in insects and highlight the evolutionary plasticity of 3D genome organization, driven by a new combination of known processes.
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7
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Mannervik M. Beyond histones: the elusive substrates of chromatin regulators. Genes Dev 2024; 38:357-359. [PMID: 38866554 PMCID: PMC11216167 DOI: 10.1101/gad.351969.124] [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] [Indexed: 06/14/2024]
Abstract
Gene transcription is intimately linked to chromatin state and histone modifications. However, the enzymes mediating these post-translational modifications have many additional, nonhistone substrates, making it difficult to ascribe the most relevant modification. In this issue of Genes & Development, Crain and colleagues (doi:10.1101/gad.351698.124) have combined a powerful histone replacement system with mutational analysis of a chromatin regulator and a chromatin reader in Drosophila melanogaster Importantly, they discovered that genes controlled by the histone 4 lysine 20 (H4K20) methyltransferase Set8 and the protein recognizing H4K20 monomethylation, L(3)mbt, differ substantially from those affected by mutation of H4K20 itself. This demonstrates that H4K20 is not the key substrate for Set8 but that methylation of other, unidentified proteins mediates its effects on transcription.
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Affiliation(s)
- Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm 10691, Sweden
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8
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Crain AT, Butler MB, Hill CA, Huynh M, McGinty RK, Duronio RJ. Drosophila melanogaster Set8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation. Genes Dev 2024; 38:455-472. [PMID: 38866557 PMCID: PMC11216177 DOI: 10.1101/gad.351698.124] [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: 03/12/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024]
Abstract
Monomethylation of lysine 20 of histone H4 (H4K20me1) is catalyzed by Set8 and thought to play important roles in many aspects of genome function that are mediated by H4K20me binding proteins. We interrogated this model in a developing animal by comparing in parallel the transcriptomes of Set8 null , H4 K20R/A , and l(3)mbt mutant Drosophila melanogaster We found that the gene expression profiles of H4 K20A and H4 K20R larvae are markedly different than Set8 null larvae despite similar reductions in H4K20me1. Set8 null mutant cells have a severely disrupted transcriptome and fail to proliferate in vivo, but these phenotypes are not recapitulated by mutation of H4 K20 , indicating that the developmental defects of Set8 null animals are largely due to H4K20me1-independent effects on gene expression. Furthermore, the H4K20me1 binding protein L(3)mbt is recruited to the transcription start sites of most genes independently of H4K20me even though genes bound by L(3)mbt have high levels of H4K20me1. Moreover, both Set8 and L(3)mbt bind to purified H4K20R nucleosomes in vitro. We conclude that gene expression changes in Set8 null and H4 K20 mutants cannot be explained by loss of H4K20me1 or L(3)mbt binding to chromatin and therefore that H4K20me1 does not play a large role in gene expression.
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Affiliation(s)
- Aaron T Crain
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Megan B Butler
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Christina A Hill
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Mai Huynh
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Robert K McGinty
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599 USA;
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 USA
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9
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Bao H, Sun Y, Deng N, Zhang L, Jia Y, Li G, Gao Y, Li X, Tang Y, Cai H, Lu J, Wang H, Deng W, Kong S. PR-SET7 epigenetically restrains uterine interferon response and cell death governing proper postnatal stromal development. Nat Commun 2024; 15:4920. [PMID: 38858353 PMCID: PMC11164956 DOI: 10.1038/s41467-024-49342-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/31/2024] [Indexed: 06/12/2024] Open
Abstract
The differentiation of the stroma is a hallmark event during postnatal uterine development. However, the spatiotemporal changes that occur during this process and the underlying regulatory mechanisms remain elusive. Here, we comprehensively delineated the dynamic development of the neonatal uterus at single-cell resolution and characterized two distinct stromal subpopulations, inner and outer stroma. Furthermore, single-cell RNA sequencing revealed that uterine ablation of Pr-set7, the sole methyltransferase catalyzing H4K20me1, led to a reduced proportion of the inner stroma due to massive cell death, thus impeding uterine development. By combining RNA sequencing and epigenetic profiling of H4K20me1, we demonstrated that PR-SET7-H4K20me1 either directly repressed the transcription of interferon stimulated genes or indirectly restricted the interferon response via silencing endogenous retroviruses. Declined H4K20me1 level caused viral mimicry responses and ZBP1-mediated apoptosis and necroptosis in stromal cells. Collectively, our study provides insight into the epigenetic machinery governing postnatal uterine stromal development mediated by PR-SET7.
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Affiliation(s)
- Haili Bao
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yang Sun
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Na Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Leilei Zhang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yuanyuan Jia
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Gaizhen Li
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yun Gao
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xinyi Li
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yedong Tang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Han Cai
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jinhua Lu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Wenbo Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Shuangbo Kong
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
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10
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Kelliher JL, Folkerts ML, Shen KV, Song W, Tengler K, Stiefel CM, Lee SO, Dray E, Zhao W, Koss B, Pannunzio NR, Leung JW. Evolved histone tail regulates 53BP1 recruitment at damaged chromatin. Nat Commun 2024; 15:4634. [PMID: 38821984 PMCID: PMC11143218 DOI: 10.1038/s41467-024-49071-w] [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: 11/02/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
The master DNA damage repair histone protein, H2AX, is essential for orchestrating the recruitment of downstream mediator and effector proteins at damaged chromatin. The phosphorylation of H2AX at S139, γH2AX, is well-studied for its DNA repair function. However, the extended C-terminal tail is not characterized. Here, we define the minimal motif on H2AX for the canonical function in activating the MDC1-RNF8-RNF168 phosphorylation-ubiquitination pathway that is important for recruiting repair proteins, such as 53BP1 and BRCA1. Interestingly, H2AX recruits 53BP1 independently from the MDC1-RNF8-RNF168 pathway through its evolved C-terminal linker region with S139 phosphorylation. Mechanistically, 53BP1 recruitment to damaged chromatin is mediated by the interaction between the H2AX C-terminal tail and the 53BP1 Oligomerization-Tudor domains. Moreover, γH2AX-linker mediated 53BP1 recruitment leads to camptothecin resistance in H2AX knockout cells. Overall, our study uncovers an evolved mechanism within the H2AX C-terminal tail for regulating DNA repair proteins at damaged chromatin.
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Affiliation(s)
- Jessica L Kelliher
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Melissa L Folkerts
- Department of Medicine, Division of Hematology/Oncology, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92626, USA
| | - Kaiyuan V Shen
- Department of Medicine, Division of Hematology/Oncology, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92626, USA
| | - Wan Song
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Kyle Tengler
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Clara M Stiefel
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Seong-Ok Lee
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Brian Koss
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Nicholas R Pannunzio
- Department of Medicine, Division of Hematology/Oncology, University of California, Irvine, Irvine, CA, 92697, USA.
| | - Justin W Leung
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA.
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11
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Aharonoff A, Kim J, Washington A, Ercan S. SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595224. [PMID: 38826443 PMCID: PMC11142195 DOI: 10.1101/2024.05.21.595224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Mechanisms of X chromosome dosage compensation have been studied extensively in a few model species representing clades of shared sex chromosome ancestry. However, the diversity within each clade as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, for which a well-studied mechanism of dosage compensation occurs through a specialized structural maintenance of chromosomes (SMC) complex, and explore the diversity of dosage compensation in the surrounding phylogeny of nematodes. Through phylogenetic analysis of the C. elegans dosage compensation complex and a survey of its epigenetic signatures, including X-specific topologically associating domains (TADs) and X-enrichment of H4K20me1, we found that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis through an SMC-4 duplication. Intriguingly, an independent duplication of SMC-4 and the presence of X-specific TADs in Pristionchus pacificus suggest that condensin-mediated dosage compensation arose more than once. mRNA-seq analyses of gene expression in several nematode species indicate that dosage compensation itself is ancestral, as expected from the ancient XO sex determination system. Indicative of the ancestral mechanism, H4K20me1 is enriched on the X chromosomes in Oscheius tipulae, which does not contain X-specific TADs or SMC-4 paralogs. Together, our results indicate that the dosage compensation system in C. elegans is surprisingly new, and condensin may have been co-opted repeatedly in nematodes, suggesting that the process of evolving a chromosome-wide gene regulatory mechanism for dosage compensation is constrained. Significance statement X chromosome dosage compensation mechanisms evolved in response to Y chromosome degeneration during sex chromosome evolution. However, establishment of dosage compensation is not an endpoint. As sex chromosomes change, dosage compensation strategies may have also changed. In this study, we performed phylogenetic and epigenomic analyses surrounding Caenorhabditis elegans and found that the condensin-mediated dosage compensation mechanism in C. elegans is surprisingly new, and has evolved in the presence of an ancestral mechanism. Intriguingly, condensin-based dosage compensation may have evolved more than once in the nematode lineage, the other time in Pristionchus. Together, our work highlights a previously unappreciated diversity of dosage compensation mechanisms within a clade, and suggests constraints in evolving new mechanisms in the presence of an existing one.
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Affiliation(s)
- Avrami Aharonoff
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Aaliyah Washington
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
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12
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Salzler HR, Vandadi V, Matera AG. Set2 and H3K36 regulate the Drosophila male X chromosome in a context-specific manner, independent from MSL complex spreading. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592390. [PMID: 38766267 PMCID: PMC11100620 DOI: 10.1101/2024.05.03.592390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Dosage compensation in Drosophila involves upregulating male X-genes two-fold. This process is carried out by the MSL (male-specific lethal) complex, which binds high-affinity sites and spreads to surrounding genes. Current models of MSL spreading focus on interactions of MSL3 (male-specific lethal 3) with histone marks; in particular, Set2-dependent H3 lysine-36 trimethylation (H3K36me3). However, Set2 might affect DC via another target, or there could be redundancy between canonical H3.2 and variant H3.3 histones. Further, it is difficult to parse male-specific effects from those that are simply X-specific. To discriminate among these possibilities, we employed genomic approaches in H3K36 (residue) and Set2 (writer) mutants. The results confirm a role for Set2 in X-gene regulation, but show that expression trends in males are often mirrored in females. Instead of global male-specific reduction of X-genes in Set2/H3K36 mutants, the effects were heterogeneous. We identified cohorts of genes whose expression was significantly altered following loss of H3K36 or Set2, but the changes were in opposite directions, suggesting that H3K36me states have reciprocal functions. In contrast to H4K16R controls, analysis of combined H3.2K36R/H3.3K36R mutants neither showed consistent reduction in X-gene expression, nor any correlation with MSL3 binding. Examination of other developmental stages/tissues revealed additional layers of context-dependence. Our studies implicate BEAF-32 and other insulator proteins in Set2/H3K36-dependent regulation. Overall, the data are inconsistent with the prevailing model wherein H3K36me3 directly recruits the MSL complex. We propose that Set2 and H3K36 support DC indirectly, via processes that are utilized by MSL but common to both sexes.
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Affiliation(s)
- Harmony R. Salzler
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Vasudha Vandadi
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - A. Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- RNA Discovery and Lineberger Comprehensive Cancer Centers, University of North Carolina, Chapel Hill, NC, USA
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13
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Bamgbose G, Bordet G, Lodhi N, Tulin A. Mono-methylated histones control PARP-1 in chromatin and transcription. eLife 2024; 13:RP91482. [PMID: 38690995 PMCID: PMC11062633 DOI: 10.7554/elife.91482] [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] [Indexed: 05/03/2024] Open
Abstract
PARP-1 is central to transcriptional regulation under both normal and stress conditions, with the governing mechanisms yet to be fully understood. Our biochemical and ChIP-seq-based analyses showed that PARP-1 binds specifically to active histone marks, particularly H4K20me1. We found that H4K20me1 plays a critical role in facilitating PARP-1 binding and the regulation of PARP-1-dependent loci during both development and heat shock stress. Here, we report that the sole H4K20 mono-methylase, pr-set7, and parp-1 Drosophila mutants undergo developmental arrest. RNA-seq analysis showed an absolute correlation between PR-SET7- and PARP-1-dependent loci expression, confirming co-regulation during developmental phases. PARP-1 and PR-SET7 are both essential for activating hsp70 and other heat shock genes during heat stress, with a notable increase of H4K20me1 at their gene body. Mutating pr-set7 disrupts monomethylation of H4K20 along heat shock loci and abolish PARP-1 binding there. These data strongly suggest that H4 monomethylation is a key triggering point in PARP-1 dependent processes in chromatin.
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Affiliation(s)
- Gbolahan Bamgbose
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North DakotaGrand ForksUnited States
| | - Guillaume Bordet
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North DakotaGrand ForksUnited States
| | - Niraj Lodhi
- Fox Chase Cancer CenterPhiladelphiaUnited States
| | - Alexei Tulin
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North DakotaGrand ForksUnited States
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14
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Li J, Song H, Chen T, Zhang S, Zhang C, Ma C, Zhang L, Wang T, Qian Y, Deng X. Lysine Methyltransferase 5A Promotes the Progression of Growth Hormone Pituitary Neuroendocrine Tumors through the Wnt/β-Catenin Signaling Pathway. Neuroendocrinology 2024; 114:589-601. [PMID: 38565081 PMCID: PMC11152009 DOI: 10.1159/000538560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
INTRODUCTION Growth hormone (GH) secreting pituitary adenoma is considered one of the most harmful types of Pituitary Neuroendocrine Tumors (PitNETs). Our previous research has found that high expression of Lysine methyltransferase 5A (KMT5A) is closely related to the proliferation of PitNETs. The aim of this study was to investigate the role and molecular mechanism of KMT5A in the progression of GH PitNETs. METHODS Immunohistochemistry, qRT-PCR, and Western blot (WB) were used to assess the expression levels of KMT5A in human normal pituitary and GH PitNETs, as well as in rat normal pituitary and GH3 cells. Additionally, we utilized RNA interference technology and treatment with a selective KMT5A inhibitor to decrease the expression of KMT5A in GH3 cells. CCK-8, EdU, flow cytometry (FCM), clone formation, and WB assay were further employed to evaluate the impact of KMT5A on the proliferation of GH3 cells in vitro. A xenograft model was established to evaluate the role of KMT5A in GH PitNETs progression in vivo. RESULTS KMT5A was highly expressed in GH PitNETs and GH3 cells. Moreover, the reduction of KMT5A expression led to inhibited growth of GH PitNETs and increased apoptosis of tumor cells, as indicated by the findings from CCK-8, EdU, clone formation, and FCM assays. Additionally, WB analysis identified the Wnt/β-catenin signaling pathway as a potential mechanism through which KMT5A promotes GH PitNETs progression. CONCLUSION Our research suggests that KMT5A may facilitate the progression of GH PitNETs via the Wnt/β-catenin signaling pathway. Therefore, KMT5A may serve as a potential therapeutic target and molecular biomarker for GH PitNETs.
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Affiliation(s)
- Junjun Li
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Hao Song
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- Guangyuan Central Hospital, Guangyuan, China
| | - Ting Chen
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Sixi Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chao Zhang
- Xiangyang First People’s Hospital, Xiangyang, China
| | - Chen Ma
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lingye Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Tengfei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yuan Qian
- The Clinical Medical Research Center for Obstetrics and Gynecology (Yunnan Joint Key Laboratory), Kunming City of Maternal and Child Health Hospital, Kunming City of Women and Children Hospital, Kunming, China
| | - Xingli Deng
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- Puer People’s Hospital, Puer, China
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15
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Crain AT, Butler MB, Hill CA, Huynh M, McGinty RK, Duronio RJ. Drosophila melanogaster Set8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584710. [PMID: 38559189 PMCID: PMC10980064 DOI: 10.1101/2024.03.12.584710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mono-methylation of Lysine 20 of histone H4 (H4K20me1) is catalyzed by Set8 and thought to play important roles in many aspects of genome function that are mediated by H4K20me-binding proteins. We interrogated this model in a developing animal by comparing in parallel the transcriptomes of Set8 null , H4 K20R/A , and l(3)mbt mutant Drosophila melanogaster . We found that the gene expression profiles of H4 K20A and H4 K20R larvae are markedly different than Set8 null larvae despite similar reductions in H4K20me1. Set8 null mutant cells have a severely disrupted transcriptome and fail to proliferate in vivo , but these phenotypes are not recapitulated by mutation of H4 K20 indicating that the developmental defects of Set8 null animals are largely due to H4K20me1-independent effects on gene expression. Further, the H4K20me1 binding protein L(3)mbt is recruited to the transcription start sites of most genes independently of H4K20me even though genes bound by L(3)mbt have high levels of H4K20me1. Moreover, both Set8 and L(3)mbt bind to purified H4K20R nucleosomes in vitro. We conclude that gene expression changes in Set8 null and H4 K20 mutants cannot be explained by loss of H4K20me1 or L(3)mbt binding to chromatin, and therefore that H4K20me1 does not play a large role in gene expression.
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16
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Yue B, Chen J, Bao T, Zhang Y, Yang L, Zhang Z, Wang Z, Zhu C. Chromosomal copy number amplification-driven Linc01711 contributes to gastric cancer progression through histone modification-mediated reprogramming of cholesterol metabolism. Gastric Cancer 2024; 27:308-323. [PMID: 38270815 DOI: 10.1007/s10120-023-01464-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND Chromosome gains or localized amplifications are frequently observed in human gastric cancer (GC) and are major causes of aberrant oncogene activation. However, the significance of long non-coding RNAs (LncRNAs) in the above process is largely unknown. METHODS The copy number aberrations (CNAs) data of GC samples were downloaded and analyzed from the TCGA database. qRT-PCR and fluorescence in situ hybridization were used to evaluate the expression of Linc01711 in GC. The effects of Linc01711 on GC progression were investigated through in vitro and in vivo assays. The mechanism of Linc01711 action was explored through transcriptome sequencing, chromatin immunoprecipitation sequencing, RNA immunoprecipitation, RNA pull-down and chromatin isolation by RNA purification (ChIRP) assays. RESULTS We report for the first time a novel DNA copy number amplification-driven LncRNA on chromosome 20q13, designated Linc01711 in human GC, which is highly associated with malignant features. Functionally, Linc01711 significantly accelerates the proliferation and metastasis of GC. Mechanistically, Linc01711 acts as a modular scaffold to promote the binding of histone acetyltransferase HBO1 and histone demethylase KDM9. By coordinating the localization of the HBO1/KDM9 complex, Linc01711 specifies the histone modification pattern on the target genes, such as LPCAT1, and consequently facilitates the cholesterol synthesis, thereby contributing to tumor progression. CONCLUSIONS Our findings suggest that copy number amplification-driven Linc01711 may serve as a promising prognostic predictor for GC patients and targeting Linc01711-related cholesterol metabolism pathway may be meaningful in anticancer strategies.
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Affiliation(s)
- Ben Yue
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Jianjun Chen
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Tianshang Bao
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Yuanruohan Zhang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Linxi Yang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Zizhen Zhang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Zheng Wang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Chunchao Zhu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
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17
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Ahmad H, Chetlangia N, Prasanth SG. Chromatin's Influence on Pre-Replication Complex Assembly and Function. BIOLOGY 2024; 13:152. [PMID: 38534422 DOI: 10.3390/biology13030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
In all eukaryotes, the initiation of DNA replication requires a stepwise assembly of factors onto the origins of DNA replication. This is pioneered by the Origin Recognition Complex, which recruits Cdc6. Together, they bring Cdt1, which shepherds MCM2-7 to form the OCCM complex. Sequentially, a second Cdt1-bound hexamer of MCM2-7 is recruited by ORC-Cdc6 to form an MCM double hexamer, which forms a part of the pre-RC. Although the mechanism of ORC binding to DNA varies across eukaryotes, how ORC is recruited to replication origins in human cells remains an area of intense investigation. This review discusses how the chromatin environment influences pre-RC assembly, function, and, eventually, origin activity.
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Affiliation(s)
- Hina Ahmad
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Neha Chetlangia
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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18
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Li Y, Cheng M, Jin J, Zhang D, Zhang S, Bai Y, Xu J. Interaction of Sp1 and Setd8 promotes vascular smooth muscle cells apoptosis by activating Mark4 in vascular calcification. Aging (Albany NY) 2024; 16:2438-2456. [PMID: 38301049 PMCID: PMC10911351 DOI: 10.18632/aging.205492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/29/2023] [Indexed: 02/03/2024]
Abstract
Vascular calcification (VC) is directly related to high mortality in chronic kidney disease (CKD), and cellular apoptosis of vascular smooth muscle cells (VSMCs) is a crucial process in the initiation of VC. Microtubule affinity-regulating kinase 4 (Mark4), known as a serine/threonine protein kinase, can induce cell apoptosis and autophagy by modulating Akt phosphorylation. However, the potential functions and molecular mechanisms of Mark4 in VSMCs apoptosis and calcification need to be further explored. Initially, our data indicated that the mRNA expression of Mark4 was prominently elevated in high phosphorus-stimulated human VSMCs compared with the other members in Marks. Consistently, Mark4 expression was found to be significantly increased in the calcified arteries of both CKD patients and rats. In vitro, silencing Mark4 suppressed apoptosis-specific marker expression by promoting Akt phosphorylation, finally attenuating VSMCs calcification induced by high phosphate. Mechanically, the transcription factor Sp1 was enriched in the Mark4 promoter region and modulated Mark4 transcription. Moreover, SET domain-containing protein 8 (Setd8) was proved to interact with Sp1 and jointly participated in the transcriptional regulation of Mark4. Finally, rescue experiments revealed that Setd8 contributed to VSMCs apoptosis and calcification by modulating Mark4 expression. In conclusion, these findings reveal that Mark4 is transcriptionally activated by Sp1, which is interacted with Setd8, to promote VSMCs calcification through Akt-mediated antiapoptotic effects, suggesting that Mark4 represents a potent and promising therapeutic target for VC in CKD.
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Affiliation(s)
- Yun Li
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Meijuan Cheng
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Jingjing Jin
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Dongxue Zhang
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Shenglei Zhang
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Yaling Bai
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Jinsheng Xu
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
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19
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Nagasaka M, Inoue Y, Nagao Y, Miyajima C, Morishita D, Aoki H, Aoyama M, Imamura T, Hayashi H. SET8 is a novel negative regulator of TGF-β signaling in a methylation-independent manner. Sci Rep 2023; 13:22877. [PMID: 38129484 PMCID: PMC10739863 DOI: 10.1038/s41598-023-49961-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Transforming growth factor β (TGF-β) is a multifunctional cytokine that induces a diverse set of cellular processes principally through Smad-dependent transcription. Transcriptional responses induced by Smads are tightly regulated by Smad cofactors and histone modifications; however, the underlying mechanisms have not yet been elucidated in detail. We herein report lysine methyltransferase SET8 as a negative regulator of TGF-β signaling. SET8 physically associates with Smad2/3 and negatively affects transcriptional activation by TGF-β in a catalytic activity-independent manner. The depletion of SET8 results in an increase in TGF-β-induced plasminogen activator inhibitor-1 (PAI-1) and p21 expression and enhances the antiproliferative effects of TGF-β. Mechanistically, SET8 occupies the PAI-1 and p21 promoters, and a treatment with TGF-β triggers the replacement of the suppressive binding of SET8 with p300 on these promoters, possibly to promote gene transcription. Collectively, the present results reveal a novel role for SET8 in the negative regulation of TGF-β signaling.
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Affiliation(s)
- Mai Nagasaka
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Yasumichi Inoue
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
| | - Yuji Nagao
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Chiharu Miyajima
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Daisuke Morishita
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Hiromasa Aoki
- Department of Pathobiology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Mineyoshi Aoyama
- Department of Pathobiology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Takeshi Imamura
- Department of Molecular Medicine for Pathogenesis, Graduate School of Medicine, Ehime University, Ehime, 791-0295, Japan
| | - Hidetoshi Hayashi
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
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20
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Zhang T, Li L, Sun H, Xu D, Wang G. DeepICSH: a complex deep learning framework for identifying cell-specific silencers and their strength from the human genome. Brief Bioinform 2023; 24:bbad316. [PMID: 37643374 DOI: 10.1093/bib/bbad316] [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: 07/01/2023] [Revised: 07/25/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
Silencers are noncoding DNA sequence fragments located on the genome that suppress gene expression. The variation of silencers in specific cells is closely related to gene expression and cancer development. Computational approaches that exclusively rely on DNA sequence information for silencer identification fail to account for the cell specificity of silencers, resulting in diminished accuracy. Despite the discovery of several transcription factors and epigenetic modifications associated with silencers on the genome, there is still no definitive biological signal or combination thereof to fully characterize silencers, posing challenges in selecting suitable biological signals for their identification. Therefore, we propose a sophisticated deep learning framework called DeepICSH, which is based on multiple biological data sources. Specifically, DeepICSH leverages a deep convolutional neural network to automatically capture biologically relevant signal combinations strongly associated with silencers, originating from a diverse array of biological signals. Furthermore, the utilization of attention mechanisms facilitates the scoring and visualization of these signal combinations, whereas the employment of skip connections facilitates the fusion of multilevel sequence features and signal combinations, thereby empowering the accurate identification of silencers within specific cells. Extensive experiments on HepG2 and K562 cell line data sets demonstrate that DeepICSH outperforms state-of-the-art methods in silencer identification. Notably, we introduce for the first time a deep learning framework based on multi-omics data for classifying strong and weak silencers, achieving favorable performance. In conclusion, DeepICSH shows great promise for advancing the study and analysis of silencers in complex diseases. The source code is available at https://github.com/lyli1013/DeepICSH.
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Affiliation(s)
- Tianjiao Zhang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Liangyu Li
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Hailong Sun
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Dali Xu
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Guohua Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
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21
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Abstract
H4K20me1 (histone H4 monomethylated at lysine 20) generally has a broad distribution along genes and has been reported to be associated with expressed and repressed genes. In contrast, H3K4me3 (histone H3 trimethylated at lysine 4) is positioned as a narrow peak at the 5' end of most expressed genes in vertebrate cells. A small population of genes involved in cell identity has H3K4me3 distributed throughout the gene body. In this report, we show that H4K20me1 is associated with expressed genes in estrogen receptor-positive breast cancer MCF7 cells and erythroleukemic K562 cells. Further, we identified the genes with the broadest H4K20me1 domains in these two cell types. The broad H4K20me1 domain marked gene bodies of expressed genes, but not the promoter or enhancer regions. The most significant GO term (biological processes) of these genes was cytoplasmic translation. There was little overlap between the genes marked with the broad H4K20me1 domain and those marked with H3K4me3. H4K20me1 and H3K79me2 distributions along expressed gene bodies were similar, suggesting a relationship between the enzymes catalyzing these histone modifications.
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Affiliation(s)
- Narges Fatemiyan
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
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22
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Rahimian N, Sheida A, Rajabi M, Heidari MM, Tobeiha M, Esfahani PV, Ahmadi Asouri S, Hamblin MR, Mohamadzadeh O, Motamedzadeh A, Khaksary Mahabady M. Non-coding RNAs and exosomal non-coding RNAs in pituitary adenoma. Pathol Res Pract 2023; 248:154649. [PMID: 37453360 DOI: 10.1016/j.prp.2023.154649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/25/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023]
Abstract
Pituitary adenoma (PA) is the third most common primary intracranial tumor in terms of overall disease incidence. Although they are benign tumors, they can have a variety of clinical symptoms, but are mostly asymptomatic, which often leads to diagnosis at an advanced stage when surgical intervention is ineffective. Earlier identification of PA could reduce morbidity and allow better clinical management of the affected patients. Non-coding RNAs (ncRNAs) do not generally code for proteins, but can modulate biological processes at the post-transcriptional level through a variety of molecular mechanisms. An increased number of ncRNA expression profiles have been found in PAs. Therefore, understanding the expression patterns of different ncRNAs could be a promising method for developing non-invasive biomarkers. This review summarizes the expression patterns of dysregulated ncRNAs (microRNAs, long non-coding RNAs, and circular RNAs) involved in PA, which could one day serve as innovative biomarkers or therapeutic targets for the treatment of this neoplasia. We also discuss the potential molecular pathways by which the dysregulated ncRNAs could cause PA and affect its progression.
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Affiliation(s)
- Neda Rahimian
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran; Department of Internal Medicine, School of Medicine, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Amirhossein Sheida
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran; School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammadreza Rajabi
- Department of Pathology, Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Mahdi Heidari
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Department of Pediatric, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammad Tobeiha
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran; School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Pegah Veradi Esfahani
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran; School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Sahar Ahmadi Asouri
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Omid Mohamadzadeh
- Department of Neurological Surgery, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran.
| | - Alireza Motamedzadeh
- Department of Internal Medicine, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
| | - Mahmood Khaksary Mahabady
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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23
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Angerilli A, Tait J, Berges J, Shcherbakova I, Pokrovsky D, Schauer T, Smialowski P, Hsam O, Mentele E, Nicetto D, Rupp RA. The histone H4K20 methyltransferase SUV4-20H1/KMT5B is required for multiciliated cell differentiation in Xenopus. Life Sci Alliance 2023; 6:e202302023. [PMID: 37116939 PMCID: PMC10147948 DOI: 10.26508/lsa.202302023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023] Open
Abstract
H4 lysine 20 dimethylation (H4K20me2) is the most abundant histone modification in vertebrate chromatin. It arises from sequential methylation of unmodified histone H4 proteins by the mono-methylating enzyme PR-SET7/KMT5A, followed by conversion to the dimethylated state by SUV4-20H (KMT5B/C) enzymes. We have blocked the deposition of this mark by depleting Xenopus embryos of SUV4-20H1/H2 methyltransferases. In the larval epidermis, this results in a severe loss of cilia in multiciliated cells (MCC), a key component of mucociliary epithelia. MCC precursor cells are correctly specified, amplify centrioles, but ultimately fail in ciliogenesis because of the perturbation of cytoplasmic processes. Genome-wide transcriptome profiling reveals that SUV4-20H1/H2-depleted ectodermal explants preferentially down-regulate the expression of several hundred ciliogenic genes. Further analysis demonstrated that knockdown of SUV4-20H1 alone is sufficient to generate the MCC phenotype and that its catalytic activity is needed for axoneme formation. Overexpression of the H4K20me1-specific histone demethylase PHF8/KDM7B also rescues the ciliogenic defect in a significant manner. Taken together, this indicates that the conversion of H4K20me1 to H4K20me2 by SUV4-20H1 is critical for the formation of cilia tufts.
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Affiliation(s)
- Alessandro Angerilli
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Janet Tait
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Julian Berges
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Sektion Pädiatrische Pneumologie und Allergologie und Mukoviszidose-Zentrum, Universitäts-Klinikum Heidelberg, Heidelberg, Germany
| | - Irina Shcherbakova
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Daniil Pokrovsky
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tamas Schauer
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Pawel Smialowski
- Institute for Stem Cell Research, Helmholtz Centre Munich, Neuherberg, Germany
- Department of Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ohnmar Hsam
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Klinik und Poliklinik für Neurologie der Universität Regensburg, Regensburg, Germany
| | - Edith Mentele
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Dario Nicetto
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Ambys Medicines, South San Francisco, CA, USA
| | - Ralph Aw Rupp
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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24
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Wang X, Cao C, Tan X, Liao X, Du X, Wang X, Liu T, Gong D, Hu Z, Tian X. SETD8, a frequently mutated gene in cervical cancer, enhances cisplatin sensitivity by impairing DNA repair. Cell Biosci 2023; 13:107. [PMID: 37308924 DOI: 10.1186/s13578-023-01054-y] [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: 10/31/2022] [Accepted: 05/17/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Cisplatin is commonly used to treat cervical cancer while drug resistance limits its effectiveness. There is an urgent need to identify strategies that increase cisplatin sensitivity and improve the outcomes of chemotherapy. RESULTS We performed whole exome sequencing (WES) of 156 cervical cancer tissues to assess genomic features related to platinum-based chemoresistance. By using WES, we identified a frequently mutated locus SETD8 (7%), which was associated with drug sensitivity. Cell functional assays, in vivo xenografts tumor growth experiments, and survival analysis were used to investigate the functional significance and mechanism of chemosensitization after SETD8 downregulation. Knockdown of SETD8 increased the responsiveness of cervical cancer cells to cisplatin treatment. The mechanism is exerted by reduced binding of 53BP1 to DNA breaks and inhibition of the non-homologous end joining (NHEJ) repair pathway. In addition, SETD8 expression was positively correlated with resistance to cisplatin and negatively associated with the prognosis of cervical cancer patients. Further, UNC0379 as a small molecule inhibitor of SETD8 was found to enhance cisplatin sensitivity both in vitro and in vivo. CONCLUSIONS SETD8 was a promising therapeutic target to ameliorate cisplatin resistance and improve the efficacy of chemotherapy.
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Affiliation(s)
- Xin Wang
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Chen Cao
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Xiangyu Tan
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Xueyao Liao
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Xiaofang Du
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Xueqian Wang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Ting Liu
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Danni Gong
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Zheng Hu
- Department of Gynecologic Oncology, Women and Children's Hospital Affiliated to Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.
- Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.
| | - Xun Tian
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China.
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
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25
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Narwanti I, Yu ZY, Sethy B, Lai MJ, Lee HY, Olena P, Lee SB, Liou JP. 6-Regioisomeric 5,8-quinolinediones as potent CDC25 inhibitors against colorectal cancers. Eur J Med Chem 2023; 258:115505. [PMID: 37302341 DOI: 10.1016/j.ejmech.2023.115505] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 06/13/2023]
Abstract
Precise and accurate control of cell cycle progression is required to maintain cell identity and proliferation. Failing to keep it will lead to genome instability and tumorigenesis. Cell Division Cycle 25 (CDC25) phosphatases are the key to regulating the activity of the master cell cycle controller, cyclin-dependent kinases (CDKs). Dysregulation of CDC25 has been shown to associate with several human malignancies. Here, we reported a series of derivatives of the CDC25 inhibitor, NSC663284, bearing quinones as core scaffolds and morpholin alkylamino side chains. Among these derivatives, the cytotoxic activity of the 6-isomer of 5,8-quinolinedione derivatives (6b, 16b, 17b, and 18b) displayed higher potency against colorectal cancer (CRC) cells. Compound 6b possessed the most antiproliferative activity, with IC50 values of 0.59 μM (DLD1) and 0.44 μM (HCT116). The treatment of compound 6b resulted in a remarkable effect on cell cycle progression, blocking S-phase progression in DLD1 cells straight away while slowing S-phase progression and accumulated cells in the G2/M phase in HCT116 cells. Furthermore, we showed that compound 6b inhibited CDK1 dephosphorylation and H4K20 methylation in cells. The treatment with compound 6b induced DNA damage and triggered apoptosis. Our study identifies compound 6b as a potent CDC25 inhibitor that induces genome instability and kills cancer cells through an apoptotic pathway, deserving further investigation to fulfill its candidacy as an anti-CRC agent.
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Affiliation(s)
- Iin Narwanti
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta, Indonesia
| | - Zih-Yao Yu
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Bidyadhar Sethy
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Mei-Jung Lai
- TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, Taiwan
| | - Hsueh-Yun Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, Taiwan
| | | | - Sung-Bau Lee
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
| | - Jing-Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, Taiwan.
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26
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Discovery of cysteine-targeting covalent histone methyltransferase inhibitors. Eur J Med Chem 2023; 246:115028. [PMID: 36528996 DOI: 10.1016/j.ejmech.2022.115028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/02/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Post-translational methylation of histone lysine or arginine residues by histone methyltransferases (HMTs) plays crucial roles in gene regulation and diverse physiological processes and is implicated in a plethora of human diseases, especially cancer. Therefore, histone methyltransferases have been increasingly recognized as potential therapeutic targets. Consequently, the discovery and development of histone methyltransferase inhibitors have been pursued with steadily increasing interest over the past decade. However, the disadvantages of limited clinical efficacy, moderate selectivity, and propensity for acquired resistance have hindered the development of HMTs inhibitors. Targeted covalent modification represents a proven strategy for kinase drug development and has gained increasing attention in HMTs drug discovery. In this review, we focus on the discovery, characterization, and biological applications of covalent inhibitors for HMTs with emphasis on advancements in the field. In addition, we identify the challenges and future directions in this fast-growing research area of drug discovery.
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27
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Shao P, Liu Q, Qi HH. KDM7 Demethylases: Regulation, Function and Therapeutic Targeting. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:167-184. [PMID: 37751140 DOI: 10.1007/978-3-031-38176-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
It was more than a decade ago that PHF8, KDM7A/JHDM1D and PHF2 were first proposed to be a histone demethylase family and were named as KDM7 (lysine demethylase) family. Since then, knowledge of their demethylation activities, roles as co-regulators of transcription and roles in development and diseases such as cancer has been steadily growing. The demethylation activities of PHF8 and KDM7A toward various methylated histones including H3K9me2/1, H3K27me2 and H4K20me1 have been identified and proven in various cell types. In contrast, PHF2, due to a mutation of a key residue in an iron-binding domain, demethylates H3K9me2 upon PKA-mediated phosphorylation. Interestingly, it was reported that PHF2 possesses an unusual H4K20me3 demethylation activity, which was not observed for PHF8 and KDM7A. PHF8 has been most extensively studied with respect to its roles in development and oncogenesis, revealing that it contributes to regulation of the cell cycle, cell viability and cell migration. Moreover, accumulating lines of evidence demonstrated that the KDM7 family members are subjected to post-transcriptional and post-translational regulations, leading to a higher horizon for evaluating their actual protein expression and functions in development and cancer. This chapter provides a general view of the current understanding of the regulation and functions of the KDM7 family and discusses their potential as therapeutic targets in cancer as well as perspectives for further studies.
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Affiliation(s)
- Peng Shao
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA, 52242, USA
| | - Qi Liu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA, 52242, USA
| | - Hank Heng Qi
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA, 52242, USA.
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28
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Li X, Qian Y, Shen W, Zhang S, Han H, Zhang Y, Liu S, Lv S, Zhang X. Mechanism of SET8 Activates the Nrf2-KEAP1-ARE Signaling Pathway to Promote the Recovery of Motor Function after Spinal Cord Injury. Mediators Inflamm 2023; 2023:4420592. [PMID: 36936537 PMCID: PMC10023234 DOI: 10.1155/2023/4420592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/10/2022] [Accepted: 11/24/2022] [Indexed: 03/12/2023] Open
Abstract
Background Spinal cord injury (SCI) is a common injury of the central nervous system (CNS), and astrocytes are relatively abundant glial cells in the CNS that impairs the recovery of motor function after SCI. It was confirmed that the oxidative stress of mitochondria leads to the accumulation of reactive oxygen species (ROS) in cells, which plays a key role in the motor function of astrocytes. However, the mechanism by which oxidative stress affects astrocyte motility after SCI is still unexplained. Therefore, this study investigated the influence of SET8-regulated oxidative stress on astrocyte autophagy levels after SCI in rats and the potential mechanisms of action. Methods We used real-time quantitative PCR, western blotting, and immunohistochemical staining to analyze SET8, Keap1, and Nrf2 expression at the cellular level and in SCI tissues. ChIP to detect H4K20me1 enrichment in the Keap1 promoter region under OE-SET8 (overexpression of SET8) conditions. Western blotting was used to assess the expression of signature proteins of astrocytes, proteins associated with autophagy, proteins associated with glial scar formation, reactive oxygen species (ROS) levels in cells using DHE staining, and astrocyte number, morphological alterations, and induction of glial scar formation processes using immunofluorescence. In addition, the survival rate of neurons after SCI in rats was examined by using NiSSl staining. Results OE-SET8 upregulates the enrichment of H4K20me1 in Keap1, inhibits Keap1 expression, activates the Nrf2-ARE signaling pathway to suppress ROS accumulation, inhibits oxidative stress-induced autophagy and glial scar formation in astrocytes, and leads to reduced neuronal loss, which promoted the recovery and improvement of motor function after SCI in rats. Conclusion Overexpression of SET8 alleviated oxidative stress by regulating Keap1/Nrf2/ARE, inhibited astrocyte autophagy levels, and reduced glial scar formation as well as neuronal loss, thereby promoting improved recovery of motor function after SCI. Thus, the SET8/H4K20me1 regulatory function may be a promising cellular therapeutic intervention point after SCI.
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Affiliation(s)
- Xin Li
- Rehabilitation Medicine of Qujing No. 1 Hospital, Qujing, 655000 Yunnan, China
| | - Yan Qian
- Rehabilitation Medicine of Qujing No. 1 Hospital, Qujing, 655000 Yunnan, China
| | - Wanling Shen
- Rehabilitation Medicine of Qujing No. 1 Hospital, Qujing, 655000 Yunnan, China
| | - Shiying Zhang
- Rehabilitation Medicine of Qujing No. 1 Hospital, Qujing, 655000 Yunnan, China
| | - Hui Han
- Rehabilitation Medicine of Qujing No. 1 Hospital, Qujing, 655000 Yunnan, China
| | - Yu Zhang
- Rehabilitation Medicine of Qujing No. 1 Hospital, Qujing, 655000 Yunnan, China
| | - Shuangmei Liu
- Rehabilitation Medicine of Qujing No. 1 Hospital, Qujing, 655000 Yunnan, China
| | - Shaokun Lv
- Rehabilitation Medicine of Qujing No. 1 Hospital, Qujing, 655000 Yunnan, China
| | - Xiuying Zhang
- Rehabilitation Medicine of Qujing No. 1 Hospital, Qujing, 655000 Yunnan, China
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29
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Martín-Rufo R, de la Vega-Barranco G, Lecona E. Ubiquitin and SUMO as timers during DNA replication. Semin Cell Dev Biol 2022; 132:62-73. [PMID: 35210137 DOI: 10.1016/j.semcdb.2022.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 12/14/2022]
Abstract
Every time a cell copies its DNA the genetic material is exposed to the acquisition of mutations and genomic alterations that corrupt the information passed on to daughter cells. A tight temporal regulation of DNA replication is necessary to ensure the full copy of the DNA while preventing the appearance of genomic instability. Protein modification by ubiquitin and SUMO constitutes a very complex and versatile system that allows the coordinated control of protein stability, activity and interactome. In chromatin, their action is complemented by the AAA+ ATPase VCP/p97 that recognizes and removes ubiquitylated and SUMOylated factors from specific cellular compartments. The concerted action of the ubiquitin/SUMO system and VCP/p97 determines every step of DNA replication enforcing the ordered activation/inactivation, loading/unloading and stabilization/destabilization of replication factors. Here we analyze the mechanisms used by ubiquitin/SUMO and VCP/p97 to establish molecular timers throughout DNA replication and their relevance in maintaining genome stability. We propose that these PTMs are the main molecular watch of DNA replication from origin recognition to replisome disassembly.
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Affiliation(s)
- Rodrigo Martín-Rufo
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain
| | - Guillermo de la Vega-Barranco
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain
| | - Emilio Lecona
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain.
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30
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Jackson LM, Moldovan GL. Mechanisms of PARP1 inhibitor resistance and their implications for cancer treatment. NAR Cancer 2022; 4:zcac042. [PMID: 36568963 PMCID: PMC9773381 DOI: 10.1093/narcan/zcac042] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The discovery of synthetic lethality as a result of the combined loss of PARP1 and BRCA has revolutionized the treatment of DNA repair-deficient cancers. With the development of PARP inhibitors, patients displaying germline or somatic mutations in BRCA1 or BRCA2 were presented with a novel therapeutic strategy. However, a large subset of patients do not respond to PARP inhibitors. Furthermore, many of those who do respond eventually acquire resistance. As such, combating de novo and acquired resistance to PARP inhibitors remains an obstacle in achieving durable responses in patients. In this review, we touch on some of the key mechanisms of PARP inhibitor resistance, including restoration of homologous recombination, replication fork stabilization and suppression of single-stranded DNA gap accumulation, as well as address novel approaches for overcoming PARP inhibitor resistance.
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Affiliation(s)
- Lindsey M Jackson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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di Meo NA, Lasorsa F, Rutigliano M, Loizzo D, Ferro M, Stella A, Bizzoca C, Vincenti L, Pandolfo SD, Autorino R, Crocetto F, Montanari E, Spilotros M, Battaglia M, Ditonno P, Lucarelli G. Renal Cell Carcinoma as a Metabolic Disease: An Update on Main Pathways, Potential Biomarkers, and Therapeutic Targets. Int J Mol Sci 2022; 23:ijms232214360. [PMID: 36430837 PMCID: PMC9698586 DOI: 10.3390/ijms232214360] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most frequent histological kidney cancer subtype. Over the last decade, significant progress has been made in identifying the genetic and metabolic alterations driving ccRCC development. In particular, an integrated approach using transcriptomics, metabolomics, and lipidomics has led to a better understanding of ccRCC as a metabolic disease. The metabolic profiling of this cancer could help define and predict its behavior in terms of aggressiveness, prognosis, and therapeutic responsiveness, and would be an innovative strategy for choosing the optimal therapy for a specific patient. This review article describes the current state-of-the-art in research on ccRCC metabolic pathways and potential therapeutic applications. In addition, the clinical implication of pharmacometabolomic intervention is analyzed, which represents a new field for novel stage-related and patient-tailored strategies according to the specific susceptibility to new classes of drugs.
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Affiliation(s)
- Nicola Antonio di Meo
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Francesco Lasorsa
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Monica Rutigliano
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Davide Loizzo
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Alessandro Stella
- Laboratory of Human Genetics, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Cinzia Bizzoca
- Division of General Surgery, Polyclinic Hospital, 70124 Bari, Italy
| | | | | | | | - Felice Crocetto
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy
| | - Emanuele Montanari
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Marco Spilotros
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Michele Battaglia
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Pasquale Ditonno
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Giuseppe Lucarelli
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
- Correspondence: or
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Pang B, van Weerd JH, Hamoen FL, Snyder MP. Identification of non-coding silencer elements and their regulation of gene expression. Nat Rev Mol Cell Biol 2022; 24:383-395. [DOI: 10.1038/s41580-022-00549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
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Kukita A, Sone K, Kaneko S, Kawakami E, Oki S, Kojima M, Wada M, Toyohara Y, Takahashi Y, Inoue F, Tanimoto S, Taguchi A, Fukuda T, Miyamoto Y, Tanikawa M, Mori-Uchino M, Tsuruga T, Iriyama T, Matsumoto Y, Nagasaka K, Wada-Hiraike O, Oda K, Hamamoto R, Osuga Y. The Histone Methyltransferase SETD8 Regulates the Expression of Tumor Suppressor Genes via H4K20 Methylation and the p53 Signaling Pathway in Endometrial Cancer Cells. Cancers (Basel) 2022; 14:5367. [PMID: 36358786 PMCID: PMC9655767 DOI: 10.3390/cancers14215367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 08/01/2023] Open
Abstract
The histone methyltransferase SET domain-containing protein 8 (SETD8), which methylates histone H4 lysine 20 (H4K20) and non-histone proteins such as p53, plays key roles in human carcinogenesis. Our aim was to determine the involvement of SETD8 in endometrial cancer and its therapeutic potential and identify the downstream genes regulated by SETD8 via H4K20 methylation and the p53 signaling pathway. We examined the expression profile of SETD8 and evaluated whether SETD8 plays a critical role in the proliferation of endometrial cancer cells using small interfering RNAs (siRNAs). We identified the prognostically important genes regulated by SETD8 via H4K20 methylation and p53 signaling using chromatin immunoprecipitation sequencing, RNA sequencing, and machine learning. We confirmed that SETD8 expression was elevated in endometrial cancer tissues. Our in vitro results suggest that the suppression of SETD8 using siRNA or a selective inhibitor attenuated cell proliferation and promoted the apoptosis of endometrial cancer cells. In these cells, SETD8 regulates genes via H4K20 methylation and the p53 signaling pathway. We also identified the prognostically important genes related to apoptosis, such as those encoding KIAA1324 and TP73, in endometrial cancer. SETD8 is an important gene for carcinogenesis and progression of endometrial cancer via H4K20 methylation.
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Affiliation(s)
- Asako Kukita
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Kenbun Sone
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Syuzo Kaneko
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Eiryo Kawakami
- Graduate School of Medicine, Chiba University, Chiba 263-8522, Japan
| | - Shinya Oki
- National Hospital Organization Tokyo Medical Center, Tokyo 152-8902, Japan
| | - Machiko Kojima
- Tazuke Kofukai, Medical Research Institute, Kitano Hospital, Osaka 530-8480, Japan
| | - Miku Wada
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yusuke Toyohara
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yu Takahashi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Futaba Inoue
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Saki Tanimoto
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ayumi Taguchi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Tomohiko Fukuda
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yuichiro Miyamoto
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Michihiro Tanikawa
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Mayuyo Mori-Uchino
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Tetsushi Tsuruga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Takayuki Iriyama
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yoko Matsumoto
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Kazunori Nagasaka
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Tokyo 173-0003, Japan
| | - Osamu Wada-Hiraike
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Katsutoshi Oda
- Division of Integrated Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
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Signaling pathways and targeted therapies in lung squamous cell carcinoma: mechanisms and clinical trials. Signal Transduct Target Ther 2022; 7:353. [PMID: 36198685 PMCID: PMC9535022 DOI: 10.1038/s41392-022-01200-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/03/2022] [Accepted: 09/18/2022] [Indexed: 11/08/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related death across the world. Unlike lung adenocarcinoma, patients with lung squamous cell carcinoma (LSCC) have not benefitted from targeted therapies. Although immunotherapy has significantly improved cancer patients' outcomes, the relatively low response rate and severe adverse events hinder the clinical application of this promising treatment in LSCC. Therefore, it is of vital importance to have a better understanding of the mechanisms underlying the pathogenesis of LSCC as well as the inner connection among different signaling pathways, which will surely provide opportunities for more effective therapeutic interventions for LSCC. In this review, new insights were given about classical signaling pathways which have been proved in other cancer types but not in LSCC, including PI3K signaling pathway, VEGF/VEGFR signaling, and CDK4/6 pathway. Other signaling pathways which may have therapeutic potentials in LSCC were also discussed, including the FGFR1 pathway, EGFR pathway, and KEAP1/NRF2 pathway. Next, chromosome 3q, which harbors two key squamous differentiation markers SOX2 and TP63 is discussed as well as its related potential therapeutic targets. We also provided some progress of LSCC in epigenetic therapies and immune checkpoints blockade (ICB) therapies. Subsequently, we outlined some combination strategies of ICB therapies and other targeted therapies. Finally, prospects and challenges were given related to the exploration and application of novel therapeutic strategies for LSCC.
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Hickenlooper SM, Davis K, Szulik MW, Sheikh H, Miller M, Valdez S, Bia R, Franklin S. Histone H4K20 Trimethylation Is Decreased in Murine Models of Heart Disease. ACS OMEGA 2022; 7:30710-30719. [PMID: 36092581 PMCID: PMC9453978 DOI: 10.1021/acsomega.2c00984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Heart disease is the leading cause of death in the developed world, and its comorbidities such as hypertension, diabetes, and heart failure are accompanied by major transcriptomic changes in the heart. During cardiac dysfunction, which leads to heart failure, there are global epigenetic alterations to chromatin that occur concomitantly with morphological changes in the heart in response to acute and chronic stress. These epigenetic alterations include the reversible methylation of lysine residues on histone proteins. Lysine methylations on histones H3K4 and H3K9 were among the first methylated lysine residues identified and have been linked to gene activation and silencing, respectively. However, much less is known regarding other methylated histone residues, including histone H4K20. Trimethylation of histone H4K20 has been shown to repress gene expression; however, this modification has never been examined in the heart. Here, we utilized immunoblotting and mass spectrometry to quantify histone H4K20 trimethylation in three models of cardiac dysfunction. Our results show that lysine methylation at this site is differentially regulated in the cardiomyocyte, leading to increased H4K20 trimethylation during acute hypertrophic stress in cell models and decreased H4K20 trimethylation during sustained ischemic injury and cardiac dysfunction in animal models. In addition, we examined publicly available data sets to analyze enzymes that regulate H4K20 methylation and identified two demethylases (KDM7B and KDM7C) and two methyltransferases (KMT5A and SMYD5) that were all differentially expressed in heart failure patients. This is the first study to examine histone H4K20 trimethylation in the heart and to determine how this post-translational modification is differentially regulated in multiple models of cardiac disease.
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Affiliation(s)
- Samuel M. Hickenlooper
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Kathryn Davis
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Marta W. Szulik
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Hanin Sheikh
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Mickey Miller
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Steven Valdez
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan Bia
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Sarah Franklin
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
- Division
of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
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36
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Hernández-Reyes Y, Paz-Cabrera MC, Freire R, Smits VAJ. USP29 Deubiquitinates SETD8 and Regulates DNA Damage-Induced H4K20 Monomethylation and 53BP1 Focus Formation. Cells 2022; 11:cells11162492. [PMID: 36010569 PMCID: PMC9406528 DOI: 10.3390/cells11162492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
SETD8 is a histone methyltransferase that plays pivotal roles in several cellular functions, including transcriptional regulation, cell cycle progression, and genome maintenance. SETD8 regulates the recruitment of 53BP1 to sites of DNA damage by controlling histone H4K20 methylation. Moreover, SETD8 levels are tightly regulated in a cell cycle-dependent manner by ubiquitin-dependent proteasomal degradation. Here, we identified ubiquitin-specific peptidase 29, USP29, as a novel regulator of SETD8. Depletion of USP29 leads to decreased SETD8 protein levels, an effect that is independent of the cell cycle. We demonstrate that SETD8 binds to USP29 in vivo, and this interaction is dependent on the catalytic activity of USP29. Wildtype USP29 can deubiquitinate SETD8 in vivo, indicating that USP29 directly regulates SETD8 protein levels. Importantly, USP29 knockdown inhibits the irradiation-induced increase in H4K20 monomethylation, thereby preventing focus formation of 53BP1 in response to DNA damage. Lastly, depletion of USP29 increases the cellular sensitivity to irradiation. These results demonstrate that USP29 is critical for the DNA damage response and cell survival, likely by controlling protein levels of SETD8.
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Affiliation(s)
- Yeray Hernández-Reyes
- Unidad de Investigación, Hospital Universitario de Canarias, 38320 Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain
- Escuela de Doctorado y Estudio de Postgrado, Universidad de la Laguna, 38200 Santa Cruz de Tenerife, Spain
| | | | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, 38320 Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
| | - Veronique A. J. Smits
- Unidad de Investigación, Hospital Universitario de Canarias, 38320 Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
- Correspondence: ; Tel.: +34-922-678107
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The Roles of Histone Post-Translational Modifications in the Formation and Function of a Mitotic Chromosome. Int J Mol Sci 2022; 23:ijms23158704. [PMID: 35955838 PMCID: PMC9368973 DOI: 10.3390/ijms23158704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/25/2022] Open
Abstract
During mitosis, many cellular structures are organized to segregate the replicated genome to the daughter cells. Chromatin is condensed to shape a mitotic chromosome. A multiprotein complex known as kinetochore is organized on a specific region of each chromosome, the centromere, which is defined by the presence of a histone H3 variant called CENP-A. The cytoskeleton is re-arranged to give rise to the mitotic spindle that binds to kinetochores and leads to the movement of chromosomes. How chromatin regulates different activities during mitosis is not well known. The role of histone post-translational modifications (HPTMs) in mitosis has been recently revealed. Specific HPTMs participate in local compaction during chromosome condensation. On the other hand, HPTMs are involved in CENP-A incorporation in the centromere region, an essential activity to maintain centromere identity. HPTMs also participate in the formation of regulatory protein complexes, such as the chromosomal passenger complex (CPC) and the spindle assembly checkpoint (SAC). Finally, we discuss how HPTMs can be modified by environmental factors and the possible consequences on chromosome segregation and genome stability.
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Wang Y, Wu L, Yuen KWY. The roles of transcription, chromatin organisation and chromosomal processes in holocentromere establishment and maintenance. Semin Cell Dev Biol 2022; 127:79-89. [PMID: 35042676 DOI: 10.1016/j.semcdb.2022.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/09/2022] [Accepted: 01/09/2022] [Indexed: 12/15/2022]
Abstract
The centromere is a unique functional region on each eukaryotic chromosome where the kinetochore assembles and orchestrates microtubule attachment and chromosome segregation. Unlike monocentromeres that occupy a specific region on the chromosome, holocentromeres are diffused along the length of the chromosome. Despite being less common, holocentromeres have been verified in almost 800 nematode, insect, and plant species. Understanding of the molecular and epigenetic regulation of holocentromeres is lagging that of monocentromeres. Here we review how permissive locations for holocentromeres are determined across the genome, potentially by chromatin organisation, transcription, and non-coding RNAs, specifically in the nematode C. elegans. In addition, we discuss how holocentric CENP-A or CENP-T-containing nucleosomes are recruited and deposited, through the help of histone chaperones, licensing factors, and condensin complexes, both during de novo holocentromere establishment, and in each mitotic cell cycle. The process of resolving sister centromeres after DNA replication in holocentric organisms is also mentioned. Conservation and diversity between holocentric and monocentric organisms are highlighted, and outstanding questions are proposed.
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Affiliation(s)
- Yue Wang
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Lillian Wu
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong; Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong.
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39
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Deng W, Wang H. Efficient cell chatting between embryo and uterus ensures embryo implantation. Biol Reprod 2022; 107:339-348. [PMID: 35774025 PMCID: PMC9310511 DOI: 10.1093/biolre/ioac135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/12/2022] Open
Abstract
Embryo implantation is one of the hottest topics during female reproduction since it is the first dialogue between maternal uterus and developing embryo whose disruption will contribute to adverse pregnancy outcome. Numerous achievements have been made to decipher the underlying mechanism of embryo implantation by genetic and molecular approaches accompanied with emerging technological advances. In recent decades, raising concepts incite insightful understanding on the mechanism of reciprocal communication between implantation competent embryos and receptive uterus. Enlightened by these gratifying evolvements, we aim to summarize and revisit current progress on the critical determinants of mutual communication between maternal uterus and embryonic signaling on the perspective of embryo implantation to alleviate infertility, enhance fetal health, and improve contraceptive design.
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Affiliation(s)
- Wenbo Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
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40
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Chen Z, Tyler JK. The Chromatin Landscape Channels DNA Double-Strand Breaks to Distinct Repair Pathways. Front Cell Dev Biol 2022; 10:909696. [PMID: 35757003 PMCID: PMC9213757 DOI: 10.3389/fcell.2022.909696] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022] Open
Abstract
DNA double-strand breaks (DSBs), the most deleterious DNA lesions, are primarily repaired by two pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ), the choice of which is largely dependent on cell cycle phase and the local chromatin landscape. Recent studies have revealed that post-translational modifications on histones play pivotal roles in regulating DSB repair pathways including repair pathway choice. In this review, we present our current understanding of how these DSB repair pathways are employed in various chromatin landscapes to safeguard genomic integrity. We place an emphasis on the impact of different histone post-translational modifications, characteristic of euchromatin or heterochromatin regions, on DSB repair pathway choice. We discuss the potential roles of damage-induced chromatin modifications in the maintenance of genome and epigenome integrity. Finally, we discuss how RNA transcripts from the vicinity of DSBs at actively transcribed regions also regulate DSB repair pathway choice.
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Affiliation(s)
- Zulong Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, United States
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, United States
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41
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Cao YC, Shan SK, Guo B, Li CC, Li FXZ, Zheng MH, Xu QS, Wang Y, Lei LM, Tang KX, Ou-Yang WL, Duan JY, Wu YY, Ullah MHE, Zhou ZA, Xu F, Lin X, Wu F, Liao XB, Yuan LQ. Histone Lysine Methylation Modification and Its Role in Vascular Calcification. Front Endocrinol (Lausanne) 2022; 13:863708. [PMID: 35784574 PMCID: PMC9243330 DOI: 10.3389/fendo.2022.863708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/06/2022] [Indexed: 01/10/2023] Open
Abstract
Histone methylation is an epigenetic change mediated by histone methyltransferase, and has been connected to the beginning and progression of several diseases. The most common ailments that affect the elderly are cardiovascular and cerebrovascular disorders. They are the leading causes of death, and their incidence is linked to vascular calcification (VC). The key mechanism of VC is the transformation of vascular smooth muscle cells (VSMCs) into osteoblast-like phenotypes, which is a highly adjustable process involving a variety of complex pathophysiological processes, such as metabolic abnormalities, apoptosis, oxidative stress and signalling pathways. Many researchers have investigated the mechanism of VC and related targets for the prevention and treatment of cardiovascular and cerebrovascular diseases. Their findings revealed that histone lysine methylation modification may play a key role in the various stages of VC. As a result, a thorough examination of the role and mechanism of lysine methylation modification in physiological and pathological states is critical, not only for identifying specific molecular markers of VC and new therapeutic targets, but also for directing the development of new related drugs. Finally, we provide this review to discover the association between histone methylation modification and VC, as well as diverse approaches with which to investigate the pathophysiology of VC and prospective treatment possibilities.
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Affiliation(s)
- Ye-Chi Cao
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Su-Kang Shan
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Bei Guo
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Chang-Chun Li
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Fu-Xing-Zi Li
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ming-Hui Zheng
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qiu-Shuang Xu
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yi Wang
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Li-Min Lei
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ke-Xin Tang
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wen-Lu Ou-Yang
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jia-Yue Duan
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yun-Yun Wu
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Muhammad Hasnain Ehsan Ullah
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhi-Ang Zhou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Feng Xu
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiao Lin
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Feng Wu
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiao-Bo Liao
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ling-Qing Yuan
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
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Meyer BJ. The X chromosome in C. elegans sex determination and dosage compensation. Curr Opin Genet Dev 2022; 74:101912. [PMID: 35490475 DOI: 10.1016/j.gde.2022.101912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 11/16/2022]
Abstract
Abnormalities in chromosome dose can reduce organismal fitness and viability by disrupting the balance of gene expression. Unlike imbalances in chromosome dose that cause pathologies, differences in X-chromosome dose that determine sex are well tolerated. Dosage compensation mechanisms have evolved in diverse species to balance X-chromosome gene expression between sexes. Mechanisms underlying nematode X-chromosome counting to determine sex revealed how small quantitative differences in molecular signals are translated into dramatically different developmental fates. Mechanisms underlying X-chromosome dosage compensation revealed the interplay between chromatin modification and three-dimensional chromosome structure imposed by an X-specific condensin complex to regulate gene expression over vast chromosomal territories. In a surprising twist of evolution, this dosage-compensation condensin complex also regulates lifespan and tolerance to proteotoxic stress.
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Affiliation(s)
- Barbara J Meyer
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, 16 Barker Hall, Berkeley, CA 94720-3204, USA.
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43
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Crain AT, Klusza S, Armstrong RL, Santa Rosa P, Temple BRS, Strahl BD, McKay DJ, Matera AG, Duronio RJ. Distinct developmental phenotypes result from mutation of Set8/KMT5A and histone H4 lysine 20 in Drosophila melanogaster. Genetics 2022; 221:iyac054. [PMID: 35404465 PMCID: PMC9157153 DOI: 10.1093/genetics/iyac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023] Open
Abstract
Mono-methylation of histone H4 lysine 20 (H4K20me1) is catalyzed by Set8/KMT5A and regulates numerous aspects of genome organization and function. Loss-of-function mutations in Drosophila melanogaster Set8 or mammalian KMT5A prevent H4K20me1 and disrupt development. Set8/KMT5A also has non-histone substrates, making it difficult to determine which developmental functions of Set8/KMT5A are attributable to H4K20me1 and which to other substrates or to non-catalytic roles. Here, we show that human KMT5A can functionally substitute for Set8 during Drosophila development and that the catalytic SET domains of the two enzymes are fully interchangeable. We also uncovered a role in eye development for the N-terminal domain of Set8 that cannot be complemented by human KMT5A. Whereas Set820/20 null mutants are inviable, we found that an R634G mutation in Set8 predicted from in vitro experiments to ablate catalytic activity resulted in viable adults. Additionally, Set8(R634G) mutants retain significant, albeit reduced, H4K20me1, indicating that the R634G mutation does not eliminate catalytic activity in vivo and is functionally hypomorphic rather than null. Flies engineered to express only unmodifiable H4 histones (H4K20A) can also complete development, but are phenotypically distinct from H4K20R, Set820/20 null, and Set8R634G mutants. Taken together, our results demonstrate functional conservation of KMT5A and Set8 enzymes, as well as distinct roles for Set8 and H4K20me1 in Drosophila development.
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Affiliation(s)
- Aaron T Crain
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Stephen Klusza
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Robin L Armstrong
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
| | | | - Brenda R S Temple
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
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Gujar MR, Wang H. A fly's eye view of quiescent neural stem cells. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac001. [PMID: 38596705 PMCID: PMC10913722 DOI: 10.1093/oons/kvac001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 04/11/2024]
Abstract
The balance between proliferation and quiescence of stem cells is crucial in maintaining tissue homeostasis. Neural stem cells (NSCs) in the brain have the ability to be reactivated from a reversible quiescent state to generate new neurons. However, how NSCs transit between quiescence and reactivation remains largely elusive. Drosophila larval brain NSCs, also known as neuroblasts, have emerged as an excellent in vivo model to study molecular mechanisms underlying NSC quiescence and reactivation. Here, we discuss our current understanding of the molecular mechanisms underlying the reactivation of quiescent NSCs in Drosophila. We review the most recent advances on epigenetic regulations and microtubule cytoskeleton in Drosophila quiescent NSCs and their cross-talk with signaling pathways that are required in regulating NSC reactivation.
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Affiliation(s)
- Mahekta R Gujar
- Neuroscience & Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Hongyan Wang
- Neuroscience & Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, 169857, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, 117456, Singapore
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45
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Nicu AT, Medar C, Chifiriuc MC, Gradisteanu Pircalabioru G, Burlibasa L. Epigenetics and Testicular Cancer: Bridging the Gap Between Fundamental Biology and Patient Care. Front Cell Dev Biol 2022; 10:861995. [PMID: 35465311 PMCID: PMC9023878 DOI: 10.3389/fcell.2022.861995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/22/2022] [Indexed: 11/15/2022] Open
Abstract
Testicular cancer is the most common solid tumor affecting young males. Most testicular cancers are testicular germ cell tumors (TGCTs), which are divided into seminomas (SGCTs) and non-seminomatous testicular germ cell tumors (NSGCTs). During their development, primordial germ cells (PGCs) undergo epigenetic modifications and any disturbances in their pattern might lead to cancer development. The present study provides a comprehensive review of the epigenetic mechanisms–DNA methylation, histone post-translational modifications, bivalent marks, non-coding RNA–associated with TGCT susceptibility, initiation, progression and response to chemotherapy. Another important purpose of this review is to highlight the recent investigations regarding the identification and development of epigenetic biomarkers as powerful tools for the diagnostic, prognostic and especially for epigenetic-based therapy.
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Affiliation(s)
- Alina-Teodora Nicu
- Faculty of Biology, University of Bucharest, Bucharest, Romania
- Department of Genetics, University of Bucharest, Bucharest, Romania
| | - Cosmin Medar
- University of Medicine and Pharmacy “Carol Davila”, Clinical Hospital “Prof. dr Theodor Burghele”, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of University of Bucharest (ICUB), Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- Romanian Academy, Bucharest, Romania
| | | | - Liliana Burlibasa
- Faculty of Biology, University of Bucharest, Bucharest, Romania
- Department of Genetics, University of Bucharest, Bucharest, Romania
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46
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Li X, Lu L, Hou W, Wang F, Huang T, Meng Z, Zhu M. The SETD8/ELK1/bach1 complex regulates hyperglycaemia-mediated EndMT in diabetic nephropathy. J Transl Med 2022; 20:147. [PMID: 35351142 PMCID: PMC8961497 DOI: 10.1186/s12967-022-03352-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/16/2022] [Indexed: 12/18/2022] Open
Abstract
Background Diabetic nephropathy (DN), the most common microvascular complication in patients with diabetes, induces kidney failure. Previous research showed that endothelial-to-mesenchymal transition (EndMT) of human glomerular endothelial cells (HGECs) is involved in the progression of DN. Moreover, SET domain-containing protein 8 (SETD8), ETS-domain containing protein (ELK1) and BTB and CNC homology 1 (bach1) all participate in endothelial injury. In this study, we hypothesize that the SETD8/ELK1/bach1 functional axis is involved in mediating EndMT in diabetic nephropathy. Methods Immunohistochemistry, Western blotting and qPCR were performed to determine the protein and mRNA levels of genes in HGECs and the kidney tissues of participants and rats. Immunofluorescence, Co-IP and GST pulldown assays were performed to verify the direct interaction between SETD8 and ELK1. ChIP and dual-luciferase assays were performed to determine the transcriptional regulation of bach1 and Snail. AVV-SETD8 injection in rat kidney was used to verify the potential protective effect of SETD8 on DN. Results Our current study showed that hyperglycaemia triggered EndMT by increasing Snail expression both in vitro and in vivo. Moreover, high glucose increased bach1 expression in HGECs, positively regulating Snail and EndMT. As a transcription factor, ELK1 was augmented and participated in hyperglycaemia-induced EndMT via modulation of bach1 expression. Moreover, ELK1 was found to associate with SETD8. Furthermore, SETD8 negatively regulated EndMT by cooperating with bach1 to regulate Snail transcription. Furthermore, histone H4-Lys-20 monomethylation (H4K20me1), which is downstream of SETD8, was accompanied by ELK1 localization at the same promoter region of bach1. ELK1 overexpression enhanced bach1 promoter activity, which disappeared after specific binding site deletion. Mutual inhibition between ELK1 and SETD8 was found in HGECs. In vivo, SETD8 overexpression decreased ELK1 and bach1 expression, as well as EndMT. Moreover, SETD8 overexpression improved the renal function of rats with DN. Conclusions SETD8 cooperates with ELK1 to regulate bach1 transcription, thus participating in the progression of DN. In addition, SETD8 interacts with bach1 to modulate Snail transcription, thus inducing EndMT in DN. SETD8 plays a core role in the SETD8/ELK1/bach1 functional axis, which participates in hyperglycaemia-mediated EndMT in DN, and SETD8 may be a potential therapeutic target for DN. Trial registration ChiCTR, ChiCTR2000029425. 2020/1/31, http://www.chictr.org.cn/showproj.aspx?proj=48548 Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03352-4.
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Affiliation(s)
- Xue Li
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lihong Lu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wenting Hou
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Fei Wang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ting Huang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhipeng Meng
- Department of Anaesthesiology, Huzhou Hospital Affiliated to Zhejiang University, Affiliated Central Hospital of HuZhou University, Huzhou, 313000, Zhejiang, China.
| | - Minmin Zhu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China. .,Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, People's Republic of China.
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Wang F, Hou W, Li X, Lu L, Huang T, Zhu M, Miao C. SETD8 cooperates with MZF1 to participate in hyperglycemia-induced endothelial inflammation via elevation of WNT5A levels in diabetic nephropathy. Cell Mol Biol Lett 2022; 27:30. [PMID: 35350980 PMCID: PMC8962284 DOI: 10.1186/s11658-022-00328-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 02/22/2023] Open
Abstract
Objective Diabetic nephropathy (DN) is regarded as the main vascular complication of diabetes mellitus, directly affecting the outcome of diabetic patients. Inflammatory factors were reported to participate in the progress of DN. Wingless-type family member 5 (WNT5A), myeloid zinc finger 1 (MZF1), and lysine methyltransferase 8 (SETD8) have also been reported to elevate inflammatory factor levels and activate the nuclear factor kappa B (NF-κB) pathway to induce endothelial dysfunction. In the current study, it was assumed that MZF1 associates with SETD8 to regulate WNT5A transcription, thus resulting in hyperglycemia-induced glomerular endothelial inflammation in DN. Methods The present study recruited 25 diagnosed DN patients (type 2 diabetes) and 25 control participants (nondiabetic renal cancer patients with normal renal function, stage I–II) consecutively. Moreover, a DN rat and cellular model was constructed in the present study. Immunohistochemistry, Western blot, and quantitative polymerase chain reaction (qPCR) were implemented to determine protein and messenger RNA (mRNA) levels. Coimmunoprecipitation (CoIP) and immunofluorescence were implemented in human glomerular endothelial cells (HGECs). Chromatin immunoprecipitation assays and dual luciferase assays were implemented to determine transcriptional activity. Results The results of this study indicated that levels of WNT5A expression, p65 phosphorylation (p-p65), and inflammatory factors were all elevated in DN patients and rats. In vitro, levels of p-p65 and inflammatory factors increased along with the increase of WNT5A expression in hyperglycemic HGECs. Moreover, high glucose increased MZF1 expression and decreased SETD8 expression. MZF1 and SETD8 inhibit each other under the stimulus of high glucose, but cooperate to regulate WNT5A expression, thus influencing p-p65 and endothelial inflammatory factors levels. Overexpression of MZF1 and silencing of SETD8 induced endothelial p-p65 and inflammatory factors levels, which can be reversed by si-WNT5A. Mechanistic research indicated that MZF1, SETD8, and its downstream target histone H4 lysine 20 methylation (H4K20me1) all occupied the WNT5A promoter region. sh-SETD8 expanded the enrichment of MZF1 on WNT5A promoter. Our in vivo study proved that SETD8 overexpression inhibited levels of WNT5A, p-p65 expression, and inflammatory factors in DN rats. Conclusions MZF1 links with SETD8 to regulate WNT5A expression in HGECs, thus elevating levels of hyperglycemia-mediated inflammatory factors in glomerular endothelium of DN patients and rats. Trial registration ChiCTR, ChiCTR2000029425. 2020/1/31, http://www.chictr.org.cn/showproj.aspx?proj=48548 Supplementary Information The online version contains supplementary material available at 10.1186/s11658-022-00328-6.
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Affiliation(s)
- Fei Wang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wenting Hou
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xue Li
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lihong Lu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ting Huang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Minmin Zhu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China. .,Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, People's Republic of China.
| | - Changhong Miao
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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48
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Meyer BJ. Mechanisms of sex determination and X-chromosome dosage compensation. Genetics 2022; 220:6498458. [PMID: 35100381 PMCID: PMC8825453 DOI: 10.1093/genetics/iyab197] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/25/2021] [Indexed: 12/03/2022] Open
Abstract
Abnormalities in chromosome number have the potential to disrupt the balance of gene expression and thereby decrease organismal fitness and viability. Such abnormalities occur in most solid tumors and also cause severe developmental defects and spontaneous abortions. In contrast to the imbalances in chromosome dose that cause pathologies, the difference in X-chromosome dose used to determine sexual fate across diverse species is well tolerated. Dosage compensation mechanisms have evolved in such species to balance X-chromosome gene expression between the sexes, allowing them to tolerate the difference in X-chromosome dose. This review analyzes the chromosome counting mechanism that tallies X-chromosome number to determine sex (XO male and XX hermaphrodite) in the nematode Caenorhabditis elegans and the associated dosage compensation mechanism that balances X-chromosome gene expression between the sexes. Dissecting the molecular mechanisms underlying X-chromosome counting has revealed how small quantitative differences in intracellular signals can be translated into dramatically different fates. Dissecting the process of X-chromosome dosage compensation has revealed the interplay between chromatin modification and chromosome structure in regulating gene expression over vast chromosomal territories.
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Affiliation(s)
- Barbara J Meyer
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720-3204, USA
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49
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Li X, Liu Z, Xia C, Yan K, Fang Z, Fan Y. SETD8 stabilized by USP17 epigenetically activates SREBP1 pathway to drive lipogenesis and oncogenesis of ccRCC. Cancer Lett 2021; 527:150-163. [PMID: 34942305 DOI: 10.1016/j.canlet.2021.12.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/01/2021] [Accepted: 12/13/2021] [Indexed: 02/06/2023]
Abstract
Recently, epigenetic modifications, including DNA methylation, histone modification and noncoding RNA (ncRNA)-associated gene silencing, have received increasing attention from the scientific community. Many studies have demonstrated that epigenetic regulation can render dynamic alterations in the transcriptional potential of a cell, which then affects the cell's biological function. The initiation and development of clear cell renal cell carcinoma (ccRCC), the most common subtype of renal cell cancer (RCC), is also closely related to genomic alterations by epigenetic modification. For ccRCC, lipid accumulation is one of the most typical characteristics. In other words, dysregulation of lipid uptake and synthesis occurs in ccRCC, which inversely promotes cancer proliferation and progression. However, the link among epigenetic alterations, lipid biosynthesis and renal cancer progression remains unclear. SETD8 is a histone methyltransferase and plays pivotal roles in cell cycle regulation and oncogenesis of various cancers, but its role in RCC is not well understood. In this study, we discovered that SETD8 was significantly overexpressed in RCC tumors, which was positively related to lipid storage and correlated with advanced tumor grade and stage and poor patient prognosis. Depletion of SETD8 by siRNAs or inhibitor UNC0379 diminished fatty acid (FA) de novo synthesis, cell proliferation and metastasis in ccRCC cells. Mechanistically, SETD8, which was posttranslationally stabilized by USP17, could transcriptionally modulate sterol regulatory element-binding protein 1 (SREBP1), a key transcription factor in fatty acid biosynthesis and lipogenesis, by monomethylating the 20th lysine of the H4 histone, elevating lipid biosynthesis and accumulation in RCC and further promoting cancer progression and metastasis. Taken together, the USP17/SETD8/SREBP1 signaling pathway plays a pivotal role in promoting RCC progression. SETD8 might be a novel biomarker and potential therapeutic target for treating RCC.
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Affiliation(s)
- Xiaofeng Li
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji Nan 250012, Shandong, China; Key Laboratory of Cardio-vascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health, China.
| | - Zhengfang Liu
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji Nan 250012, Shandong, China.
| | - Chuanyou Xia
- The First Affiliated Hospital of Shandong First Medical University/Shandong Provincial Qian-Fo-Shan Hospital, China.
| | - Keqiang Yan
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji Nan 250012, Shandong, China.
| | - Zhiqing Fang
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji Nan 250012, Shandong, China.
| | - Yidong Fan
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji Nan 250012, Shandong, China.
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50
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Lu L, Li X, Zhong Z, Zhou W, Zhou D, Zhu M, Miao C. KMT5A downregulation participated in High Glucose-mediated EndMT via Upregulation of ENO1 Expression in Diabetic Nephropathy. Int J Biol Sci 2021; 17:4093-4107. [PMID: 34803485 PMCID: PMC8579450 DOI: 10.7150/ijbs.62867] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/26/2021] [Indexed: 12/17/2022] Open
Abstract
Diabetic nephropathy (DN) has become the common and principal microvascular complication of diabetes that could lead to end-stage renal disease. It was reported endothelial-to-mesenchymal transition (EndMT) in glomeruli plays an important role in DN. Enolase1 (ENO1) and Lysine Methyltransferase 5A (KMT5A) were found to modulate epithelial-to-mesenchymal transition in some situations. In the present study, we speculated KMT5A regulates ENO1 transcript, thus participating in hyperglycemia-induced EndMT in glomeruli of DN. Our study represented vimentin, αSMA and ENO1 expression elevated, and CD31 expression decreased in glomeruli of DN participants and rats. In vitro, high glucose induced EndMT by increase of ENO1 levels. Moreover, high glucose downregulated KMT5A levels and increased regulatory factor X1 (RFX1) levels. KMT5A upregulation or si-RFX1 decreased high glucose-induced ENO1 expression and EndMT. RFX1 overexpression- or sh-KMT5A-induced EndMT was attenuated by si-ENO1. Further, the association between KMT5A and RFX1 was verified. Furthermore, histone H4 lysine20 methylation (the direct target of KMT5A) and RFX1 positioned on ENO1 promoter region. sh-KMT5A enhanced positive action of RFX1 on ENO1 promoter activity. KMT5A reduction and RFX1 upregulation were verified in glomeruli of DN patients and rats. KMT5A associated with RFX1 to modulate ENO1, thus involved in hyperglycemia-mediated EndMT in glomeruli of DN.
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Affiliation(s)
- Lihong Lu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xue Li
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ziwen Zhong
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Department of Anesthesiology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Wenchang Zhou
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Di Zhou
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Minmin Zhu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, People's Republic of China
| | - Changhong Miao
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
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