1
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Liao Y, Zhang W, Liu Y, Zhu C, Zou Z. The role of ubiquitination in health and disease. MedComm (Beijing) 2024; 5:e736. [PMID: 39329019 PMCID: PMC11424685 DOI: 10.1002/mco2.736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
Ubiquitination is an enzymatic process characterized by the covalent attachment of ubiquitin to target proteins, thereby modulating their degradation, transportation, and signal transduction. By precisely regulating protein quality and quantity, ubiquitination is essential for maintaining protein homeostasis, DNA repair, cell cycle regulation, and immune responses. Nevertheless, the diversity of ubiquitin enzymes and their extensive involvement in numerous biological processes contribute to the complexity and variety of diseases resulting from their dysregulation. The ubiquitination process relies on a sophisticated enzymatic system, ubiquitin domains, and ubiquitin receptors, which collectively impart versatility to the ubiquitination pathway. The widespread presence of ubiquitin highlights its potential to induce pathological conditions. Ubiquitinated proteins are predominantly degraded through the proteasomal system, which also plays a key role in regulating protein localization and transport, as well as involvement in inflammatory pathways. This review systematically delineates the roles of ubiquitination in maintaining protein homeostasis, DNA repair, genomic stability, cell cycle regulation, cellular proliferation, and immune and inflammatory responses. Furthermore, the mechanisms by which ubiquitination is implicated in various pathologies, alongside current modulators of ubiquitination are discussed. Enhancing our comprehension of ubiquitination aims to provide novel insights into diseases involving ubiquitination and to propose innovative therapeutic strategies for clinical conditions.
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Affiliation(s)
- Yan Liao
- Faculty of Anesthesiology Changhai Hospital Naval Medical University Shanghai China
- School of Anesthesiology Naval Medical University Shanghai China
| | - Wangzheqi Zhang
- Faculty of Anesthesiology Changhai Hospital Naval Medical University Shanghai China
- School of Anesthesiology Naval Medical University Shanghai China
| | - Yang Liu
- Faculty of Anesthesiology Changhai Hospital Naval Medical University Shanghai China
- School of Anesthesiology Naval Medical University Shanghai China
| | - Chenglong Zhu
- Faculty of Anesthesiology Changhai Hospital Naval Medical University Shanghai China
- School of Anesthesiology Naval Medical University Shanghai China
| | - Zui Zou
- Faculty of Anesthesiology Changhai Hospital Naval Medical University Shanghai China
- School of Anesthesiology Naval Medical University Shanghai China
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2
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Okada R, Takenobu H, Satoh S, Sugino RP, Onuki R, Haruta M, Mukae K, Nakazawa A, Akter J, Ohira M, Kamijo T. L3MBTL2 maintains MYCN-amplified neuroblastoma cell proliferation through silencing NRIP3 and BRME1 genes. Genes Cells 2024; 29:838-853. [PMID: 39189159 DOI: 10.1111/gtc.13148] [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: 09/19/2023] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 08/28/2024]
Abstract
Epigenetic alterations critically affect tumor development. Polycomb-group complexes constitute an evolutionarily conserved epigenetic machinery that regulates stem cell fate and development. They are implicated in tumorigenesis, primarily via histone modification. Polycomb repressive complex 1 (PRC1) complexes 1-6 (PRC1.1-6) mediate the ubiquitination of histone H2A on lysine 119 (H2AK119ub). Here, we studied the functional roles of a PRC1.6 molecule, L3MBTL2, in neuroblastoma (NB) cells. L3MBTL2-knockout and knockdown revealed that L3MBTL2 depletion suppressed NB cell proliferation via cell-cycle arrest and gamma-H2A.X upregulation. L3MBTL2-knockout profoundly suppressed xenograft tumor formation. Transcriptome analysis revealed suppressed cell-cycle-related and activated differentiation-related pathways. Break repair meiotic recombinase recruitment factor 1 (BRME1) and nuclear receptor interacting protein 3 (NRIP3) were notably de-repressed by L3MBTL2-knockout. The deletion of L3MBTL2 reduced enrichment of H2AK119ub and PCGF6 at transcriptional start site proximal regions of the targets. Add-back studies unveiled the importance of L3MBTL2-BRME1 and -NRIP3 axes for NB cell proliferation. We further manifested the association of MYCN with de-repression of NRIP3 in an L3MBTL2-deficient context. Therefore, this study first revealed the significance of L3MBTL2-mediated gene silencing in MYCN-amplified NB cells.
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Affiliation(s)
- Ryu Okada
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
- Laboratory of Tumor Molecular Biology, Department of Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Hisanori Takenobu
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Shunpei Satoh
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Ryuichi P Sugino
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Ritsuko Onuki
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Masayuki Haruta
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Kyosuke Mukae
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Atsuko Nakazawa
- Department of Clinical Research, Saitama Children's Medical Center, Saitama, Japan
| | - Jesmin Akter
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Miki Ohira
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Takehiko Kamijo
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
- Laboratory of Tumor Molecular Biology, Department of Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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3
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Modafferi S, Esposito F, Tavella S, Gioia U, Francia S. Traffic light at DSB-transit regulation between gene transcription and DNA repair. FEBS Lett 2024. [PMID: 39333024 DOI: 10.1002/1873-3468.15024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 08/12/2024] [Accepted: 08/15/2024] [Indexed: 09/29/2024]
Abstract
Transcription of actively expressed genes is dampened for kilobases around DNA lesions via chromatin modifications. This is believed to favour repair and prevent genome instability. Nonetheless, mounting evidence suggests that transcription may be induced by DNA breakage, resulting in the local de novo synthesis of non-coding RNAs (ncRNAs). Such transcripts have been proposed to play important functions in both DNA damage signalling and repair. Here, we review the recently identified mechanistic details of transcriptional silencing at damaged chromatin, highlighting how post-translational histone modifications can also be modulated by the local synthesis of DNA damage-induced ncRNAs. Finally, we envision that these entangled transcriptional events at DNA breakages can be targeted to modulate DNA repair, with potential implications for locus-specific therapeutic strategies.
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Affiliation(s)
- Stefania Modafferi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli Sforza"- Consiglio Nazionale delle Ricerche, Pavia, Italy
- PhD Program in Biomolecular Sciences and Biotechnology (SBB), Istituto Universitario di Studi Superiori (IUSS), Pavia, Italy
| | - Francesca Esposito
- Istituto di Genetica Molecolare "Luigi Luca Cavalli Sforza"- Consiglio Nazionale delle Ricerche, Pavia, Italy
- PhD Program in Genetics, Molecular and Cellular Biology (GMCB), University of Pavia, Pavia, Italy
| | - Sara Tavella
- Istituto di Genetica Molecolare "Luigi Luca Cavalli Sforza"- Consiglio Nazionale delle Ricerche, Pavia, Italy
- IFOM-ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Ubaldo Gioia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli Sforza"- Consiglio Nazionale delle Ricerche, Pavia, Italy
- IFOM-ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Sofia Francia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli Sforza"- Consiglio Nazionale delle Ricerche, Pavia, Italy
- IFOM-ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
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4
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Chauhan AS, Jhujh SS, Stewart GS. E3 ligases: a ubiquitous link between DNA repair, DNA replication and human disease. Biochem J 2024; 481:923-944. [PMID: 38985307 PMCID: PMC11346458 DOI: 10.1042/bcj20240124] [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: 03/20/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.
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Affiliation(s)
- Anoop S. Chauhan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Satpal S. Jhujh
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Grant S. Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
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5
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Rodríguez TC, Yurkovetskiy L, Nagalekshmi K, Lam CHO, Jazbec E, Maitland SA, Wolfe SA, Sontheimer EJ, Luban J. PRC1.6 localizes on chromatin with the human silencing hub (HUSH) complex for promoter-specific silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603173. [PMID: 39026796 PMCID: PMC11257501 DOI: 10.1101/2024.07.12.603173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
An obligate step in the life cycle of HIV-1 and other retroviruses is the establishment of the provirus in target cell chromosomes. Transcriptional regulation of proviruses is complex, and understanding the mechanisms underlying this regulation has ramifications for fundamental biology, human health, and gene therapy implementation. The three core components of the Human Silencing Hub (HUSH) complex, TASOR, MPHOSPH8 (MPP8), and PPHLN1 (Periphilin 1), were identified in forward genetic screens for host genes that repress provirus expression. Subsequent loss-of-function screens revealed accessory proteins that collaborate with the HUSH complex to silence proviruses in particular contexts. To identify proteins associated with a HUSH complex-repressed provirus in human cells, we developed a technique, Provirus Proximal Proteomics, based on proximity labeling with C-BERST (dCas9-APEX2 biotinylation at genomic elements by restricted spatial tagging). Our screen exploited a lentiviral reporter that is silenced by the HUSH complex in a manner that is independent of the integration site in chromatin. Our data reveal that proviruses silenced by the HUSH complex are associated with DNA repair, mRNA processing, and transcriptional silencing proteins, including L3MBTL2, a member of the non-canonical polycomb repressive complex 1.6 (PRC1.6). A forward genetic screen confirmed that PRC1.6 components L3MBTL2 and MGA contribute to HUSH complex-mediated silencing. PRC1.6 was then shown to silence HUSH-sensitive proviruses in a promoter-specific manner. Genome wide profiling showed striking colocalization of the PRC1.6 and HUSH complexes on chromatin, primarily at sites of active promoters. Finally, PRC1.6 binding at a subset of genes that are silenced by the HUSH complex was dependent on the core HUSH complex component MPP8. These studies offer new tools with great potential for studying the transcriptional regulation of proviruses and reveal crosstalk between the HUSH complex and PRC1.6.
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Affiliation(s)
- Tomás C. Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Karthika Nagalekshmi
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Chin Hung Oscar Lam
- Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Eva Jazbec
- Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Stacy A. Maitland
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Erik J. Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jeremy Luban
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
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6
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Chen K, Dong Y, He G, He X, Pan M, Huang X, Yu X, Xia J. UBTF mediates activation of L3MBTL2 to suppress NISCH expression through histone H2AK119 monoubiquitination modification in breast cancer. Clin Exp Metastasis 2024:10.1007/s10585-024-10299-x. [PMID: 38935187 DOI: 10.1007/s10585-024-10299-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2) has been related to transcriptional inhibition and chromatin compaction. Nevertheless, the biological functions and mechanisms of L3MBTL2 are undefined in breast cancer (BRCA). Here, we revealed that L3MBTL2 is responsible for the decline of Nischarin (NISCH), a well-known tumor suppressor, in BRCA, and explored the detailed mechanism. Knockdown of L3MBTL2 reduced monoubiquitination of histone H2A at lysine-119 (H2AK119ub), leading to reduced binding to the NISCH promoter and increased expression of NISCH. Meanwhile, the knockdown of L3MBTL2 decreased proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) of BRCA cells, and increased apoptosis, which were abated by NISCH knockdown. Nucleolar transcription factor 1 (UBTF) induced the transcription of L3MBTL2 in BRCA, and the suppressing effects of UBTF silencing on EMT in BRCA cells were also reversed by NISCH knockdown. Knockdown of UBTF slowed tumor progression and attenuated lung tumor infiltration, whereas simultaneous knockdown of NISCH accelerated EMT and increased tumor lung metastasis. Taken together, our results show that L3MBTL2, transcriptionally activated by UBTF, exerts oncogenic functions in BRCA, by catalyzing H2AK119Ub and reducing expression of NISCH.
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Affiliation(s)
- Kun Chen
- Department of Technology and Social Services, Dazhou Vocational College of Chinese Medicine, Tongchuan District, Vocational Education Park, Dazhou, Sichuan, 635000, P.R. China
| | - Yun Dong
- Department of Traditional Chinese Medicine, Dazhou Vocational College of Chinese Medicine, Dazhou, Sichuan, 635000, P.R. China
| | - Gaojian He
- Dean's office, Dazhou Vocational College of Chinese Medicine, Dazhou, Sichuan, 635000, P.R. China
| | - Xuefeng He
- Department of Technology and Social Services, Dazhou Vocational College of Chinese Medicine, Tongchuan District, Vocational Education Park, Dazhou, Sichuan, 635000, P.R. China
| | - Meitong Pan
- Department of Technology and Social Services, Dazhou Vocational College of Chinese Medicine, Tongchuan District, Vocational Education Park, Dazhou, Sichuan, 635000, P.R. China
| | - Xuemei Huang
- Department of Oncology and Hematology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, 646099, P.R. China
| | - Xiaolan Yu
- Department of Obstetrics and Gynecology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, 646099, P.R. China.
| | - Jiyi Xia
- Department of Technology and Social Services, Dazhou Vocational College of Chinese Medicine, Tongchuan District, Vocational Education Park, Dazhou, Sichuan, 635000, P.R. China.
- Dazhou Chinese medicine research and development center, Dazhou, Sichuan, 635000, P.R. China.
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7
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Yue T, Guo Y, Qi X, Zheng W, Zhang H, Wang B, Liu K, Zhou B, Zeng X, Ouzhuluobu, He Y, Su B. Sex-biased regulatory changes in the placenta of native highlanders contribute to adaptive fetal development. eLife 2024; 12:RP89004. [PMID: 38869160 PMCID: PMC11175615 DOI: 10.7554/elife.89004] [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] Open
Abstract
Compared with lowlander migrants, native Tibetans have a higher reproductive success at high altitude though the underlying mechanism remains unclear. Here, we compared the transcriptome and histology of full-term placentas between native Tibetans and Han migrants. We found that the placental trophoblast shows the largest expression divergence between Tibetans and Han, and Tibetans show decreased immune response and endoplasmic reticulum stress. Remarkably, we detected a sex-biased expression divergence, where the male-infant placentas show a greater between-population difference than the female-infant placentas. The umbilical cord plays a key role in the sex-biased expression divergence, which is associated with the higher birth weight of the male newborns of Tibetans. We also identified adaptive histological changes in the male-infant placentas of Tibetans, including larger umbilical artery wall and umbilical artery intima and media, and fewer syncytial knots. These findings provide valuable insights into the sex-biased adaptation of human populations, with significant implications for medical and genetic studies of human reproduction.
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Affiliation(s)
- Tian Yue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life Science, University of Chinese Academy of SciencesBeijingChina
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life Science, University of Chinese Academy of SciencesBeijingChina
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang HospitalKunmingChina
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
| | - Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
| | - Bin Wang
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang HospitalKunmingChina
| | - Kai Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Bin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life Science, University of Chinese Academy of SciencesBeijingChina
| | - Xuerui Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life Science, University of Chinese Academy of SciencesBeijingChina
| | - Ouzhuluobu
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang HospitalKunmingChina
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of SciencesKunmingChina
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8
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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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9
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Franz P, Fierz B. Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective. J Mol Biol 2024; 436:168442. [PMID: 38211893 DOI: 10.1016/j.jmb.2024.168442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene transcription, the regulation of deposition and removal of histone post-translational modifications (PTMs), such as acetylation, methylation, and phosphorylation, have been implicated in many chromatin regulation pathways. However, large PTMs such as ubiquitylation challenge research on many levels due to their chemical complexity. In recent years, chemical tools have been developed to generate chromatin in defined ubiquitylation states in vitro. Chemical biology approaches are now used to link specific histone ubiquitylation marks with downstream chromatin regulation events on the molecular level. Here, we want to highlight how chemical biology approaches have empowered the mechanistic study of chromatin ubiquitylation in the context of gene regulation and DNA repair with attention to future challenges.
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Affiliation(s)
- Pauline Franz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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10
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Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G. Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol Cell 2024; 84:839-853.e12. [PMID: 38242129 PMCID: PMC10939898 DOI: 10.1016/j.molcel.2023.12.036] [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: 09/12/2023] [Revised: 12/06/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for cell-cycle-dependent DNA double-strand break (DSB) repair pathway selection. The mechanism by which RNF168 catalyzes the targeted accumulation of H2A ubiquitin conjugates to form repair foci around DSBs remains unclear. Here, using cryoelectron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and functional assays, we provide a molecular description of the reaction cycle and dynamics of RNF168 as it modifies the nucleosome and recognizes its ubiquitylation products. We demonstrate an interaction of a canonical ubiquitin-binding domain within full-length RNF168, which not only engages ubiquitin but also the nucleosome surface, clarifying how such site-specific ubiquitin recognition propels a signal amplification loop. Beyond offering mechanistic insights into a key DDR protein, our study aids in understanding site specificity in both generating and interpreting chromatin ubiquitylation.
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Affiliation(s)
- Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Debiao Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | | | | | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; Department of Cancer Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
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11
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Sheng X, Xia Z, Yang H, Hu R. The ubiquitin codes in cellular stress responses. Protein Cell 2024; 15:157-190. [PMID: 37470788 PMCID: PMC10903993 DOI: 10.1093/procel/pwad045] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Ubiquitination/ubiquitylation, one of the most fundamental post-translational modifications, regulates almost every critical cellular process in eukaryotes. Emerging evidence has shown that essential components of numerous biological processes undergo ubiquitination in mammalian cells upon exposure to diverse stresses, from exogenous factors to cellular reactions, causing a dazzling variety of functional consequences. Various forms of ubiquitin signals generated by ubiquitylation events in specific milieus, known as ubiquitin codes, constitute an intrinsic part of myriad cellular stress responses. These ubiquitination events, leading to proteolytic turnover of the substrates or just switch in functionality, initiate, regulate, or supervise multiple cellular stress-associated responses, supporting adaptation, homeostasis recovery, and survival of the stressed cells. In this review, we attempted to summarize the crucial roles of ubiquitination in response to different environmental and intracellular stresses, while discussing how stresses modulate the ubiquitin system. This review also updates the most recent advances in understanding ubiquitination machinery as well as different stress responses and discusses some important questions that may warrant future investigation.
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Affiliation(s)
- Xiangpeng Sheng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhixiong Xia
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hanting Yang
- Department of Neurology, State Key Laboratory of Medical Neurobiology, Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ronggui Hu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
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12
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Zhong L, Wang J, Chen W, Lv D, Zhang R, Wang X, Zeng C, He X, Zheng L, Gao Y, Wang S, Li M, Wu Y, Yin J, Kang T, Liao D. Augmenting L3MBTL2-induced condensates suppresses tumor growth in osteosarcoma. SCIENCE ADVANCES 2023; 9:eadi0889. [PMID: 37992172 PMCID: PMC10664996 DOI: 10.1126/sciadv.adi0889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/24/2023] [Indexed: 11/24/2023]
Abstract
Osteosarcoma is a highly aggressive cancer and lacks effective therapeutic targets. We found that L3MBTL2 acts as a tumor suppressor by transcriptionally repressing IFIT2 in osteosarcoma. L3MBTL2 recruits the components of Polycomb repressive complex 1.6 to form condensates via both Pho-binding pockets and polybasic regions within carboxyl-terminal intrinsically disordered regions; the L3MBTL2-induced condensates are required for its tumor suppression. Multi-monoubiquitination of L3MBTL2 by UBE2O results in its proteasomal degradation, and the UBE2O/L3MBTL2 axis was crucial for osteosarcoma growth. There is a reverse correlation between L3MBTL2 and UBE2O in osteosarcoma tissues, and higher UBE2O and lower L3MBTL2 are associated with poorer prognosis in osteosarcoma. Pharmacological blockage of UBE2O by arsenic trioxide can enhance L3MBTL2-induced condensates and consequently suppress osteosarcoma growth. Our findings unveil a crucial biological function of L3MBTL2-induced condensates in mediating tumor suppression, proposing the UBE2O-L3MBTL2 axis as a potential cancer therapeutic target in osteosarcoma.
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Affiliation(s)
- Li Zhong
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
- Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jingxuan Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wanqi Chen
- Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Dongming Lv
- Department of Musculoskeletal Oncology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xin Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Cuiling Zeng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaobo He
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lisi Zheng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Gao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shang Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Miao Li
- Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yuanzhong Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Junqiang Yin
- Department of Musculoskeletal Oncology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
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13
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Qin C, Wang YL, Zhou JY, Shi J, Zhao WW, Zhu YX, Bai SM, Feng LL, Bie SY, Zeng B, Zheng J, Zeng GD, Feng WX, Wan XB, Fan XJ. RAP80 phase separation at DNA double-strand break promotes BRCA1 recruitment. Nucleic Acids Res 2023; 51:9733-9747. [PMID: 37638744 PMCID: PMC10570032 DOI: 10.1093/nar/gkad686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 07/29/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023] Open
Abstract
RAP80 has been characterized as a component of the BRCA1-A complex and is responsible for the recruitment of BRCA1 to DNA double-strand breaks (DSBs). However, we and others found that the recruitment of RAP80 and BRCA1 were not absolutely temporally synchronized, indicating that other mechanisms, apart from physical interaction, might be implicated. Recently, liquid-liquid phase separation (LLPS) has been characterized as a novel mechanism for the organization of key signaling molecules to drive their particular cellular functions. Here, we characterized that RAP80 LLPS at DSB was required for RAP80-mediated BRCA1 recruitment. Both cellular and in vitro experiments showed that RAP80 phase separated at DSB, which was ascribed to a highly disordered region (IDR) at its N-terminal. Meanwhile, the Lys63-linked poly-ubiquitin chains that quickly formed after DSBs occur, strongly enhanced RAP80 phase separation and were responsible for the induction of RAP80 condensation at the DSB site. Most importantly, abolishing the condensation of RAP80 significantly suppressed the formation of BRCA1 foci, encovering a pivotal role of RAP80 condensates in BRCA1 recruitment and radiosensitivity. Together, our study disclosed a new mechanism underlying RAP80-mediated BRCA1 recruitment, which provided new insight into the role of phase separation in DSB repair.
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Affiliation(s)
- Caolitao Qin
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Yun-Long Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Jin-Ying Zhou
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Wan-Wen Zhao
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Ya-Xi Zhu
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Shao-Mei Bai
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Li-Li Feng
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510655, P.R. China
| | - Shu-Ying Bie
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Bing Zeng
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Gastroenterology, Hernia and Abdominal Wall Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Guang-Dong Zeng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Wei-Xing Feng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
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14
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Qiu L, Xu W, Lu X, Chen F, Chen Y, Tian Y, Zhu Q, Liu X, Wang Y, Pei XH, Xu X, Zhang J, Zhu WG. The HDAC6-RNF168 axis regulates H2A/H2A.X ubiquitination to enable double-strand break repair. Nucleic Acids Res 2023; 51:9166-9182. [PMID: 37503842 PMCID: PMC10516627 DOI: 10.1093/nar/gkad631] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/24/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
Histone deacetylase 6 (HDAC6) mediates DNA damage signaling by regulating the mismatch repair and nucleotide excision repair pathways. Whether HDAC6 also mediates DNA double-strand break (DSB) repair is unclear. Here, we report that HDAC6 negatively regulates DSB repair in an enzyme activity-independent manner. In unstressed cells, HDAC6 interacts with H2A/H2A.X to prevent its interaction with the E3 ligase RNF168. Upon sensing DSBs, RNF168 rapidly ubiquitinates HDAC6 at lysine 116, leading to HDAC6 proteasomal degradation and a restored interaction between RNF168 and H2A/H2A.X. H2A/H2A.X is ubiquitinated by RNF168, precipitating the recruitment of DSB repair factors (including 53BP1 and BRCA1) to chromatin and subsequent DNA repair. These findings reveal novel regulatory machinery based on an HDAC6-RNF168 axis that regulates the H2A/H2A.X ubiquitination status. Interfering with this axis might be leveraged to disrupt a key mechanism of cancer cell resistance to genotoxic damage and form a potential therapeutic strategy for cancer.
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Affiliation(s)
- Lingyu Qiu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yongcan Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiangyu Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yongqing Wang
- Division of Rheumatology and Immunology, University of Toledo Medical Center, 3120 Glendale Avenue, Toledo 43614, OH, USA
| | - Xin-Hai Pei
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Anatomy and Histology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xingzhi Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
- School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, China
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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15
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Lee SO, Kelliher JL, Song W, Tengler K, Sarkar A, Dray E, Leung JWC. UBA80 and UBA52 fine-tune RNF168-dependent histone ubiquitination and DNA repair. J Biol Chem 2023; 299:105043. [PMID: 37451480 PMCID: PMC10413357 DOI: 10.1016/j.jbc.2023.105043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 06/29/2023] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
The ubiquitin signaling pathway is crucial for the DNA damage response pathway. More specifically, RNF168 is integral in regulating DNA repair proteins at damaged chromatin. However, the detailed mechanism by which RNF168 is regulated in cells is not fully understood. Here, we identify the ubiquitin-ribosomal fusion proteins UBA80 (also known as RPS27A) and UBA52 (also known as RPL40) as interacting proteins for H2A/H2AX histones and RNF168. Both UBA80 and UBA52 are recruited to laser-induced micro-irradiation DNA damage sites and are required for DNA repair. Ectopic expression of UBA80 and UBA52 inhibits RNF168-mediated H2A/H2AX ubiquitination at K13/15 and impairs 53BP1 recruitment to DNA lesions. Mechanistically, the C-terminal ribosomal fragments of UBA80 and UBA52, S27A and L40, respectively, limit RNF168-nucleosome engagement by masking the regulatory acidic residues at E143/E144 and the nucleosome acidic patch. Together, our results reveal that UBA80 and UBA52 antagonize the ubiquitination signaling pathway and fine-tune the spatiotemporal regulation of DNA repair proteins at DNA damage sites.
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Affiliation(s)
- Seong-Ok Lee
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Jessica L Kelliher
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Wan Song
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Kyle Tengler
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Aradhan Sarkar
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Justin W C Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.
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16
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Guo Y, Shen R, Yang K, Wang Y, Song H, Liu X, Cheng X, Wu R, Song Y, Wang D. RNF8 enhances the sensitivity of PD-L1 inhibitor against melanoma through ubiquitination of galectin-3 in stroma. Cell Death Discov 2023; 9:205. [PMID: 37391451 DOI: 10.1038/s41420-023-01500-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 05/19/2023] [Accepted: 06/19/2023] [Indexed: 07/02/2023] Open
Abstract
The failure of melanoma immunotherapy can be mediated by immunosuppression in the tumor microenvironment (TME), and insufficient activation of effector T cells against the tumor. Here, we show that inhibition of galectin-3 (gal-3) enhances the infiltration of T cells in TME and improves the sensitivity of anti-PD-L1 therapy. We identify that RNF8 downregulated the expression of gal-3 by K48-polyubiquitination and promoted gal-3 degradation via the ubiquitin-proteasome system. RNF8 deficiency in the host but sufficiency in implanted melanoma results in immune exclusion and tumor progression due to the upregulation of gal-3. Upregulation of gal-3 decreased the immune cell infiltration by restricting IL-12 and IFN-γ. Inhibition of gal-3 reverses immunosuppression and induces immune cell infiltration in the tumor microenvironment. Moreover, gal-3 inhibitor treatment can increase the sensitivity of PD-L1 inhibitors via increasing immune cell infiltration and enhancing immune response in tumors. This study reveals a previously unrecognized immunoregulation function of RNF8 and provides a promising strategy for the therapy of "cold" tumors. Tremendous effects of melanoma treatment can be achieved by facilitating immune cell infiltration combined with anti-PD-L1 treatment.
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Affiliation(s)
- Yanan Guo
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China
| | - Rong Shen
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China
| | - Keren Yang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China
| | - Yutong Wang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China
| | - Haoyun Song
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China
| | - Xiangwen Liu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China
| | - Xin Cheng
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China
| | - Rile Wu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China
| | - Yanfeng Song
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China
| | - Degui Wang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China.
- NHC Key Laboratory of diagnosis and therapy of Gastrointestinal Tumor, Lanzhou, 730000, China.
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17
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Koo SY, Park EJ, Noh HJ, Jo SM, Ko BK, Shin HJ, Lee CW. Ubiquitination Links DNA Damage and Repair Signaling to Cancer Metabolism. Int J Mol Sci 2023; 24:ijms24098441. [PMID: 37176148 PMCID: PMC10179089 DOI: 10.3390/ijms24098441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Changes in the DNA damage response (DDR) and cellular metabolism are two important factors that allow cancer cells to proliferate. DDR is a set of events in which DNA damage is recognized, DNA repair factors are recruited to the site of damage, the lesion is repaired, and cellular responses associated with the damage are processed. In cancer, DDR is commonly dysregulated, and the enzymes associated with DDR are prone to changes in ubiquitination. Additionally, cellular metabolism, especially glycolysis, is upregulated in cancer cells, and enzymes in this metabolic pathway are modulated by ubiquitination. The ubiquitin-proteasome system (UPS), particularly E3 ligases, act as a bridge between cellular metabolism and DDR since they regulate the enzymes associated with the two processes. Hence, the E3 ligases with high substrate specificity are considered potential therapeutic targets for treating cancer. A number of small molecule inhibitors designed to target different components of the UPS have been developed, and several have been tested in clinical trials for human use. In this review, we discuss the role of ubiquitination on overall cellular metabolism and DDR and confirm the link between them through the E3 ligases NEDD4, APC/CCDH1, FBXW7, and Pellino1. In addition, we present an overview of the clinically important small molecule inhibitors and implications for their practical use.
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Affiliation(s)
- Seo-Young Koo
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Eun-Ji Park
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyun-Ji Noh
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Su-Mi Jo
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Bo-Kyoung Ko
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyun-Jin Shin
- Team of Radiation Convergence Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Republic of Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
- SKKU Institute for Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
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18
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Xie T, Qin H, Yuan Z, Zhang Y, Li X, Zheng L. Emerging Roles of RNF168 in Tumor Progression. Molecules 2023; 28:molecules28031417. [PMID: 36771081 PMCID: PMC9920519 DOI: 10.3390/molecules28031417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/23/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
RING finger protein 168 (RNF168) is an E3 ubiquitin ligase with the RING finger domain. It is an important protein contributing to the DNA double-strand damage repair pathway. Recent studies have found that RNF168 is significantly implicated in the occurrence and development of various cancers. Additionally, RNF168 contributes to the drug resistance of tumor cells by enhancing their DNA repair ability or regulating the degradation of target proteins. This paper summarizes and prospects the research progress of the structure and main functions of RNF168, especially its roles and the underlying mechanisms in tumorigenesis.
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Affiliation(s)
- Tianyuan Xie
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
| | - Hai Qin
- Department of Clinical Laboratory, Guizhou Provincial Orthopedic Hospital, No. 206, Sixian Street, Baiyun District, Guiyang 550007, China
| | - Zhengdong Yuan
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
| | - Yiwen Zhang
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Correspondence: (X.L.); (L.Z.)
| | - Lufeng Zheng
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
- Correspondence: (X.L.); (L.Z.)
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19
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Ming H, Li B, Jiang J, Qin S, Nice EC, He W, Lang T, Huang C. Protein degradation: expanding the toolbox to restrain cancer drug resistance. J Hematol Oncol 2023; 16:6. [PMID: 36694209 PMCID: PMC9872387 DOI: 10.1186/s13045-023-01398-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/01/2023] [Indexed: 01/25/2023] Open
Abstract
Despite significant progress in clinical management, drug resistance remains a major obstacle. Recent research based on protein degradation to restrain drug resistance has attracted wide attention, and several therapeutic strategies such as inhibition of proteasome with bortezomib and proteolysis-targeting chimeric have been developed. Compared with intervention at the transcriptional level, targeting the degradation process seems to be a more rapid and direct strategy. Proteasomal proteolysis and lysosomal proteolysis are the most critical quality control systems responsible for the degradation of proteins or organelles. Although proteasomal and lysosomal inhibitors (e.g., bortezomib and chloroquine) have achieved certain improvements in some clinical application scenarios, their routine application in practice is still a long way off, which is due to the lack of precise targeting capabilities and inevitable side effects. In-depth studies on the regulatory mechanism of critical protein degradation regulators, including E3 ubiquitin ligases, deubiquitylating enzymes (DUBs), and chaperones, are expected to provide precise clues for developing targeting strategies and reducing side effects. Here, we discuss the underlying mechanisms of protein degradation in regulating drug efflux, drug metabolism, DNA repair, drug target alteration, downstream bypass signaling, sustaining of stemness, and tumor microenvironment remodeling to delineate the functional roles of protein degradation in drug resistance. We also highlight specific E3 ligases, DUBs, and chaperones, discussing possible strategies modulating protein degradation to target cancer drug resistance. A systematic summary of the molecular basis by which protein degradation regulates tumor drug resistance will help facilitate the development of appropriate clinical strategies.
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Affiliation(s)
- Hui Ming
- West China School of Basic Medical Sciences and Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China
| | - Jingwen Jiang
- West China School of Basic Medical Sciences and Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Weifeng He
- Institute of Burn Research, Southwest Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Army Military Medical University, Chongqing, 400038, China.
| | - Tingyuan Lang
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, 400030, People's Republic of China. .,Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, People's Republic of China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China.
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20
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Oda T, Gotoh N, Kasamatsu T, Handa H, Saitoh T, Sasaki N. DNA damage-induced cellular senescence is regulated by 53BP1 accumulation in the nuclear foci and phase separation. Cell Prolif 2023:e13398. [PMID: 36642815 DOI: 10.1111/cpr.13398] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/14/2022] [Accepted: 12/28/2022] [Indexed: 01/17/2023] Open
Abstract
Cellular senescence is linked to a wide range of age-related diseases and can be triggered by a variety of stresses, including DNA damage. A variety of genotoxic stressors, such as anti-cancer drugs, cause DNA double-strand breaks (DSBs), which trigger the accumulation of the tumour suppressor protein p53 in the nucleus. Cellular stresses stabilize and activate the p53 signalling pathway, which regulates various cellular processes, such as apoptosis, DNA repair, and senescence. Although p53 signalling is a well-known tumour suppressor pathway, it remains unclear how it is regulated during cellular senescence. Here, we show that p53-binding protein 1 (53BP1) accumulation in the nuclear foci is required for DNA damage-induced cellular senescence via p53 activation. In human immortalized fibroblast, shRNA-mediated 53BP1 depletion decreased not only the expression of p53-target genes but also the cellular senescence induced by adriamycin treatment. Furthermore, we confirmed that DSBs trigger the hyperaccumulation of 53BP1 in the nuclear foci, which plays a key role in the regulation of cellular senescence. To prevent the accumulation of 53BP1 in the nuclear foci, we used phase separation inhibitors, and siRNA against RNF168, which accumulates at DSB loci and forms complexes with 53BP1. This blocks the formation of 53BP1 nuclear foci and DNA damage-induced cellular senescence by activating the p53 signaling pathway. In conclusion, we demonstrated that increased accumulation of 53BP1 in the nuclear foci following DNA damage activates p53 and governs cellular senescence via a liquid-liquid phase separation mechanism.
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Affiliation(s)
- Tsukasa Oda
- Laboratory of Mucosal Ecosystem Design, The Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Nanami Gotoh
- Graduate School of Health Sciences, Gunma University, Maebashi, Gunma, Japan
| | - Tetsuhiro Kasamatsu
- Graduate School of Health Sciences, Gunma University, Maebashi, Gunma, Japan
| | - Hiroshi Handa
- Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
| | - Takayuki Saitoh
- Graduate School of Health Sciences, Gunma University, Maebashi, Gunma, Japan
| | - Nobuo Sasaki
- Laboratory of Mucosal Ecosystem Design, The Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
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21
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TRIP13 Participates in Immediate-Early Sensing of DNA Strand Breaks and ATM Signaling Amplification through MRE11. Cells 2022; 11:cells11244095. [PMID: 36552858 PMCID: PMC9776959 DOI: 10.3390/cells11244095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Thyroid hormone receptor-interacting protein 13 (TRIP13) participates in various regulatory steps related to the cell cycle, such as the mitotic spindle assembly checkpoint and meiotic recombination, possibly by interacting with members of the HORMA domain protein family. Recently, it was reported that TRIP13 could regulate the choice of the DNA repair pathway, i.e., homologous recombination (HR) or nonhomologous end-joining (NHEJ). However, TRIP13 is recruited to DNA damage sites within a few seconds after damage and may therefore have another function in DNA repair other than regulation of the pathway choice. Furthermore, the depletion of TRIP13 inhibited both HR and NHEJ, suggesting that TRIP13 plays other roles besides regulation of choice between HR and NHEJ. To explore the unidentified functions of TRIP13 in the DNA damage response, we investigated its genome-wide interaction partners in the context of DNA damage using quantitative proteomics with proximity labeling. We identified MRE11 as a novel interacting partner of TRIP13. TRIP13 controlled the recruitment of MDC1 to DNA damage sites by regulating the interaction between MDC1 and the MRN complex. Consistently, TRIP13 was involved in ATM signaling amplification. Our study provides new insight into the function of TRIP13 in immediate-early DNA damage sensing and ATM signaling activation.
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22
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Gonzalez-Santamarta M, Bouvier C, Rodriguez MS, Xolalpa W. Ubiquitin-chains dynamics and its role regulating crucial cellular processes. Semin Cell Dev Biol 2022; 132:155-170. [PMID: 34895814 DOI: 10.1016/j.semcdb.2021.11.023] [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: 09/16/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
The proteome adapts to multiple situations occurring along the life of the cell. To face these continuous changes, the cell uses posttranslational modifications (PTMs) to control the localization, association with multiple partners, stability, and activity of protein targets. One of the most dynamic protein involved in PTMs is Ubiquitin (Ub). Together with other members of the same family, known as Ubiquitin-like (UbL) proteins, Ub rebuilds the architecture of a protein in a few minutes to change its properties in a very efficient way. This capacity of Ub and UbL is in part due to their potential to form complex architectures when attached to target proteins or when forming Ub chains. The highly dynamic formation and remodeling of Ub chains is regulated by the action of conjugating and deconjugating enzymes that determine, in due time, the correct chain architecture for a particular cellular function. Chain remodeling occurs in response to physiologic stimuli but also in pathologic situations. Here, we illustrate well-documented cases of chain remodeling during DNA repair, activation of the NF-κB pathway and autophagy, as examples of this dynamic regulation. The crucial role of enzymes and cofactors regulating chain remodeling is discussed.
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Affiliation(s)
- Maria Gonzalez-Santamarta
- Laboratoire de Chimie de Coordination (LCC) - UPR 8241 CNRS, and UMR 152 Pharma-Dev, Université de Toulouse, IRD, UPS, 31400 Toulouse, France.
| | - Corentin Bouvier
- Laboratoire de Chimie de Coordination (LCC) - UPR 8241 CNRS, and UMR 152 Pharma-Dev, Université de Toulouse, IRD, UPS, 31400 Toulouse, France.
| | - Manuel S Rodriguez
- Laboratoire de Chimie de Coordination (LCC) - UPR 8241 CNRS, and UMR 152 Pharma-Dev, Université de Toulouse, IRD, UPS, 31400 Toulouse, France.
| | - Wendy Xolalpa
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250 Cuernavaca, Morelos, Mexico.
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23
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Bader AS, Luessing J, Hawley BR, Skalka GL, Lu WT, Lowndes N, Bushell M. DDX17 is required for efficient DSB repair at DNA:RNA hybrid deficient loci. Nucleic Acids Res 2022; 50:10487-10502. [PMID: 36200807 PMCID: PMC9561282 DOI: 10.1093/nar/gkac843] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022] Open
Abstract
Proteins with RNA-binding activity are increasingly being implicated in DNA damage responses (DDR). Additionally, DNA:RNA-hybrids are rapidly generated around DNA double-strand breaks (DSBs), and are essential for effective repair. Here, using a meta-analysis of proteomic data, we identify novel DNA repair proteins and characterise a novel role for DDX17 in DNA repair. We found DDX17 to be required for both cell survival and DNA repair in response to numerous agents that induce DSBs. Analysis of DSB repair factor recruitment to damage sites suggested a role for DDX17 early in the DSB ubiquitin cascade. Genome-wide mapping of R-loops revealed that while DDX17 promotes the formation of DNA:RNA-hybrids around DSB sites, this role is specific to loci that have low levels of pre-existing hybrids. We propose that DDX17 facilitates DSB repair at loci that are inefficient at forming DNA:RNA-hybrids by catalysing the formation of DSB-induced hybrids, thereby allowing propagation of the damage response.
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Affiliation(s)
- Aldo S Bader
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Janna Luessing
- Centre for Chromosome Biology, Biomedical Sciences Biulding (BSB), School of Biological & Checmical Sciences, University of Galway, Galway, H91W2TY, Ireland
| | - Ben R Hawley
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | | | - Wei-Ting Lu
- The Francis Crick Institute, London NW1 1AT, UK
| | - Noel F Lowndes
- Centre for Chromosome Biology, Biomedical Sciences Biulding (BSB), School of Biological & Checmical Sciences, University of Galway, Galway, H91W2TY, Ireland
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
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24
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Kloeber JA, Lou Z. Critical DNA damaging pathways in tumorigenesis. Semin Cancer Biol 2022; 85:164-184. [PMID: 33905873 PMCID: PMC8542061 DOI: 10.1016/j.semcancer.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022]
Abstract
The acquisition of DNA damage is an early driving event in tumorigenesis. Premalignant lesions show activated DNA damage responses and inactivation of DNA damage checkpoints promotes malignant transformation. However, DNA damage is also a targetable vulnerability in cancer cells. This requires a detailed understanding of the cellular and molecular mechanisms governing DNA integrity. Here, we review current work on DNA damage in tumorigenesis. We discuss DNA double strand break repair, how repair pathways contribute to tumorigenesis, and how double strand breaks are linked to the tumor microenvironment. Next, we discuss the role of oncogenes in promoting DNA damage through replication stress. Finally, we discuss our current understanding on DNA damage in micronuclei and discuss therapies targeting these DNA damage pathways.
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Affiliation(s)
- Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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25
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N6-Methyladenosine (m6A)-Related lncRNAs Are Potential Signatures for Predicting Prognosis and Immune Response in Lung Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:5240611. [PMID: 36090906 PMCID: PMC9462982 DOI: 10.1155/2022/5240611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/21/2022] [Indexed: 12/16/2022]
Abstract
Background Despite increasing understanding of m6A-related lncRNAs in lung cancer, the role of m6A-related lncRNAs in the prognosis and treatment of lung squamous cell carcinoma is poorly understood to date. Thus, the current study aims to elucidate its role and build a model to predict the prognosis of LUSC patients. Materials and Methods The data of the current study were accessed from the TCGA database. Pearson correlation analysis was performed to identify lncRNAs correlated to m6A. Next, an m6A-related lncRNAs risk model was built using a single factor, least absolute association, selection operator, and multivariate Cox regression analysis. Results The relevance between 23 m6A genes and 14,056 lncRNAs is shown by Pearson correlation analysis by Sankey diagram. Multivariate Cox regression analysis determined that 11 m6A-lncRNAs show predictive potential in prognosis, which is confirmed by the consistency index, Kaplan–Meier analysis, principal component analysis, and ROC curve. Additionally, the immune analysis showed that the enrichment of immune cells, major histocompatibility complex molecules, and immune checkpoints in the high and low-risk subgroups were markedly disparate, with the high-risk group showing a stronger immune escape ability and a worse response to immunotherapy. Conclusion In conclusion, the risk model based on m6A-related lncRNAs showed great promise in predicting the prognosis and the efficacy of immunotherapy.
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26
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Zeng X, Zhao F, Cui G, Zhang Y, Deshpande RA, Chen Y, Deng M, Kloeber JA, Shi Y, Zhou Q, Zhang C, Hou J, Kim W, Tu X, Yan Y, Xu Z, Chen L, Gao H, Guo G, Liu J, Zhu Q, Cao Y, Huang J, Wu Z, Zhu S, Yin P, Luo K, Mer G, Paull TT, Yuan J, Tao K, Lou Z. METTL16 antagonizes MRE11-mediated DNA end resection and confers synthetic lethality to PARP inhibition in pancreatic ductal adenocarcinoma. NATURE CANCER 2022; 3:1088-1104. [PMID: 36138131 DOI: 10.1038/s43018-022-00429-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/26/2022] [Indexed: 06/16/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers. Characterization of genetic alterations will improve our understanding and therapies for this disease. Here, we report that PDAC with elevated expression of METTL16, one of the 'writers' of RNA N6-methyladenosine modification, may benefit from poly-(ADP-ribose)-polymerase inhibitor (PARPi) treatment. Mechanistically, METTL16 interacts with MRE11 through RNA and this interaction inhibits MRE11's exonuclease activity in a methyltransferase-independent manner, thereby repressing DNA end resection. Upon DNA damage, ATM phosphorylates METTL16 resulting in a conformational change and autoinhibition of its RNA binding. This dissociates the METTL16-RNA-MRE11 complex and releases inhibition of MRE11. Concordantly, PDAC cells with high METTL16 expression show increased sensitivity to PARPi, especially when combined with gemcitabine. Thus, our findings reveal a role for METTL16 in homologous recombination repair and suggest that a combination of PARPi with gemcitabine could be an effective treatment strategy for PDAC with elevated METTL16 expression.
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Affiliation(s)
- Xiangyu Zeng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Yong Zhang
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Yuping Chen
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, USA
| | - Yu Shi
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Chao Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jing Hou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Wootae Kim
- Soonchunhyang Institute of Med-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Republic of Korea
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Yuanliang Yan
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Lifeng Chen
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Center for Reproductive Medicine, Department of Gynecology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaqi Liu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yueyu Cao
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Zheming Wu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Shouhai Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Jian Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China.
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA.
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27
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Averbeck NB, Barent C, Jakob B, Syzonenko T, Durante M, Taucher-Scholz G. The Ubiquitin Ligase RNF138 Cooperates with CtIP to Stimulate Resection of Complex DNA Double-Strand Breaks in Human G1-Phase Cells. Cells 2022; 11:cells11162561. [PMID: 36010636 PMCID: PMC9406464 DOI: 10.3390/cells11162561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Abstract
DNA double-strand breaks (DSBs) represent the molecular origin of ionizing-radiation inflicted biological effects. An increase in the ionization density causes more complex, clustered DSBs that can be processed by resection also in G1 phase, where repair of resected DSBs is considered erroneous and may contribute to the increased biological effectiveness of heavy ions in radiotherapy. To investigate the resection regulation of complex DSBs, we exposed G1 cells depleted for different candidate factors to heavy ions or α-particle radiation. Immunofluorescence microscopy was used to monitor the resection marker RPA, the DSB marker γH2AX and the cell-cycle markers CENP-F and geminin. The Fucci system allowed to select G1 cells, cell survival was measured by clonogenic assay. We show that in G1 phase the ubiquitin ligase RNF138 functions in resection regulation. RNF138 ubiquitinates the resection factor CtIP in a radiation-dependent manner to allow its DSB recruitment in G1 cells. At complex DSBs, RNF138′s participation becomes more relevant, consistent with the observation that also resection is more frequent at these DSBs. Furthermore, deficiency of RNF138 affects both DSB repair and cell survival upon induction of complex DSBs. We conclude that RNF138 is a regulator of resection that is influenced by DSB complexity and can affect the quality of DSB repair in G1 cells.
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Affiliation(s)
- Nicole B. Averbeck
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
- Correspondence:
| | - Carina Barent
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstr. 11, 64287 Darmstadt, Germany
| | - Tatyana Syzonenko
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
| | - Marco Durante
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
- Department of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6–8, 64289 Darmstadt, Germany
| | - Gisela Taucher-Scholz
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstr. 11, 64287 Darmstadt, Germany
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28
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Qin B, Yu J, Zhao F, Huang J, Zhou Q, Lou Z. Dynamic recruitment of UFM1-specific peptidase 2 to the DNA double-strand breaks regulated by WIP1. GENOME INSTABILITY & DISEASE 2022; 3:217-226. [PMID: 36042814 PMCID: PMC9418083 DOI: 10.1007/s42764-022-00076-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/17/2022] [Accepted: 07/24/2022] [Indexed: 10/29/2022]
Abstract
The ufmylation ligase-UFL1 promotes ATM activation by monoufmylating H4 at K31 in a positive-feedback loop after double-strand breaks (DSB) occur, whereas UFM1 Specific Peptidase 2 (UfSP2) suppresses ATM activation, but the mechanism of recruitment of UfSP2 to the DSB finetuning DNA damage response is still not clear. Here, we report that UfSP2 foci formation is delayed compared to UFL1 foci formation following the radiation insult. Mechanistically, UfSP2 binds to the MRN complex in absence of DSB. Irradiation-induced phosphorylation of UfSP2 by ATM leads to the dissociation of UfSP2 from the MRN complex. This phosphorylation can be removed by the phosphatase WIP1, thereby UfSP2 is recruited to the DSBs, deufmylating H4 and suppressing ATM activation. In summary, we identify a mechanism of delicately negative modulation of ATM activation by UfSP2 and rewires ATM activation pathways.
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Affiliation(s)
- Bo Qin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Jia Yu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
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Yin X, Liu Q, Liu F, Tian X, Yan T, Han J, Jiang S. Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis. Front Cell Dev Biol 2022; 10:944460. [PMID: 35874839 PMCID: PMC9298949 DOI: 10.3389/fcell.2022.944460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a critical type of protein post-translational modification playing an essential role in many cellular processes. To date, more than eight types of ubiquitination exist, all of which are involved in distinct cellular processes based on their structural differences. Studies have indicated that activation of the ubiquitination pathway is tightly connected with inflammation-related diseases as well as cancer, especially in the non-proteolytic canonical pathway, highlighting the vital roles of ubiquitination in metabolic programming. Studies relating degradable ubiquitination through lys48 or lys11-linked pathways to cellular signaling have been well-characterized. However, emerging evidence shows that non-degradable ubiquitination (linked to lys6, lys27, lys29, lys33, lys63, and Met1) remains to be defined. In this review, we summarize the non-proteolytic ubiquitination involved in tumorigenesis and related signaling pathways, with the aim of providing a reference for future exploration of ubiquitination and the potential targets for cancer therapies.
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Affiliation(s)
- Xiu Yin
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tinghao Yan
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Han
- Department of Thyroid and Breast Surgery, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
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30
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DNA Damage Response Regulation by Histone Ubiquitination. Int J Mol Sci 2022; 23:ijms23158187. [PMID: 35897775 PMCID: PMC9332593 DOI: 10.3390/ijms23158187] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022] Open
Abstract
Cells are constantly exposed to numerous genotoxic stresses that induce DNA damage. DNA double-strand breaks (DSBs) are among the most serious damages and should be systematically repaired to preserve genomic integrity. The efficiency of repair is closely associated with chromatin structure, which is regulated by posttranslational modifications of histones, including ubiquitination. Recent evidence shows crosstalk between histone ubiquitination and DNA damage responses, suggesting an integrated model for the systematic regulation of DNA repair. There are two major pathways for DSB repair, viz., nonhomologous end joining and homologous recombination, and the choice of the pathway is partially controlled by posttranslational modifications of histones, including ubiquitination. Histone ubiquitination changes chromatin structure in the vicinity of DSBs and serves as a platform to select and recruit repair proteins; the removal of these modifications by deubiquitinating enzymes suppresses the recruitment of repair proteins and promotes the convergence of repair reactions. This article provides a comprehensive overview of the DNA damage response regulated by histone ubiquitination in response to DSBs.
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Kolobynina KG, Rapp A, Cardoso MC. Chromatin Ubiquitination Guides DNA Double Strand Break Signaling and Repair. Front Cell Dev Biol 2022; 10:928113. [PMID: 35865631 PMCID: PMC9294282 DOI: 10.3389/fcell.2022.928113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin is the context for all DNA-based molecular processes taking place in the cell nucleus. The initial chromatin structure at the site of the DNA damage determines both, lesion generation and subsequent activation of the DNA damage response (DDR) pathway. In turn, proceeding DDR changes the chromatin at the damaged site and across large fractions of the genome. Ubiquitination, besides phosphorylation and methylation, was characterized as an important chromatin post-translational modification (PTM) occurring at the DNA damage site and persisting during the duration of the DDR. Ubiquitination appears to function as a highly versatile “signal-response” network involving several types of players performing various functions. Here we discuss how ubiquitin modifiers fine-tune the DNA damage recognition and response and how the interaction with other chromatin modifications ensures cell survival.
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Kelliher J, Ghosal G, Leung JWC. New answers to the old RIDDLE: RNF168 and the DNA damage response pathway. FEBS J 2022; 289:2467-2480. [PMID: 33797206 PMCID: PMC8486888 DOI: 10.1111/febs.15857] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/12/2021] [Accepted: 03/31/2021] [Indexed: 12/31/2022]
Abstract
The chromatin-based DNA damage response pathway is tightly orchestrated by histone post-translational modifications, including histone H2A ubiquitination. Ubiquitination plays an integral role in regulating cellular processes including DNA damage signaling and repair. The ubiquitin E3 ligase RNF168 is essential in assembling a cohort of DNA repair proteins at the damaged chromatin via its enzymatic activity. RNF168 ubiquitinates histone H2A(X) at the N terminus and generates a specific docking scaffold for ubiquitin-binding motif-containing proteins. The regulation of RNF168 at damaged chromatin and the mechanistic implication in the recruitment of DNA repair proteins to the damaged sites remain an area of active investigation. Here, we review the function and regulation of RNF168 in the context of ubiquitin-mediated DNA damage signaling and repair. We will also discuss the unanswered questions that require further investigation and how understanding RNF168 targeting specificity could benefit the therapeutic development for cancer treatment.
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Affiliation(s)
- Jessica Kelliher
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States,To whom correspondence should be addressed: and
| | - Justin Wai Chung Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States,To whom correspondence should be addressed: and
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Huang H, Pan R, Zhao Y, Li H, Zhu H, Wang S, Khan AA, Wang J, Liu X. L3MBTL2-mediated CGA transcriptional suppression promotes pancreatic cancer progression through modulating autophagy. iScience 2022; 25:104249. [PMID: 35521536 PMCID: PMC9061862 DOI: 10.1016/j.isci.2022.104249] [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: 03/22/2021] [Revised: 09/08/2021] [Accepted: 04/08/2022] [Indexed: 11/28/2022] Open
Abstract
L3MBTL2 is a crucial component of ncPRC1.6 and has been implicated in transcriptional repression and chromatin compaction. However, the repression mechanism of L3MBTL2 and its biological functions are largely undefined. Here, we found that L3MBTL2 plays a distinct oncogenic role in tumor development. We demonstrated that L3MBTL2 repressed downstream CGA through an H2AK119ub1-dependent mechanism. Importantly, the binding of the MGA/MAX heterodimer to the E-box on the CGA promoter enhanced the specific selective repression of CGA by L3MBTL2. CGA encodes the alpha subunit of glycoprotein hormones; however, we showed that CGA plays an individual tumor suppressor role in PDAC. Moreover, CGA-transcript1 (T1) was identified as the major transcript, and the tumor suppression function of CGA-T1 depends on its own glycosylation. Furthermore, glycosylated CGA-T1 inhibited PDAC, partly by repression of autophagy through multiple pathways, including PI3K/Akt/mTOR and TP53INP2 pathways. These findings reveal the important roles of L3MBTL2 and CGA in tumor development. L3MBTL2 plays a distinct oncogenic role in tumor development L3MBTL2 represses CGA transcription mainly by mediating ubiquitination of H2A CGA plays an individual tumor suppressor role in pancreatic cancer Glycosylated CGA inhibited PDAC partly through repression of autophagy
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Affiliation(s)
- Hua Huang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
- Corresponding author
| | - Ruining Pan
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yue Zhao
- Intensive Care Unit, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Huan Li
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Huiyu Zhu
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Sijia Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Aamir Ali Khan
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Juan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Xinhui Liu
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
- Corresponding author
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Shadfar S, Brocardo M, Atkin JD. The Complex Mechanisms by Which Neurons Die Following DNA Damage in Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23052484. [PMID: 35269632 PMCID: PMC8910227 DOI: 10.3390/ijms23052484] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 01/18/2023] Open
Abstract
Human cells are exposed to numerous exogenous and endogenous insults every day. Unlike other molecules, DNA cannot be replaced by resynthesis, hence damage to DNA can have major consequences for the cell. The DNA damage response contains overlapping signalling networks that repair DNA and hence maintain genomic integrity, and aberrant DNA damage responses are increasingly described in neurodegenerative diseases. Furthermore, DNA repair declines during aging, which is the biggest risk factor for these conditions. If unrepaired, the accumulation of DNA damage results in death to eliminate cells with defective genomes. This is particularly important for postmitotic neurons because they have a limited capacity to proliferate, thus they must be maintained for life. Neuronal death is thus an important process in neurodegenerative disorders. In addition, the inability of neurons to divide renders them susceptible to senescence or re-entry to the cell cycle. The field of cell death has expanded significantly in recent years, and many new mechanisms have been described in various cell types, including neurons. Several of these mechanisms are linked to DNA damage. In this review, we provide an overview of the cell death pathways induced by DNA damage that are relevant to neurons and discuss the possible involvement of these mechanisms in neurodegenerative conditions.
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Affiliation(s)
- Sina Shadfar
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia; (S.S.); (M.B.)
| | - Mariana Brocardo
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia; (S.S.); (M.B.)
| | - Julie D. Atkin
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia; (S.S.); (M.B.)
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
- Correspondence:
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35
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Kieffer SR, Lowndes NF. Immediate-Early, Early, and Late Responses to DNA Double Stranded Breaks. Front Genet 2022; 13:793884. [PMID: 35173769 PMCID: PMC8841529 DOI: 10.3389/fgene.2022.793884] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 12/18/2022] Open
Abstract
Loss or rearrangement of genetic information can result from incorrect responses to DNA double strand breaks (DSBs). The cellular responses to DSBs encompass a range of highly coordinated events designed to detect and respond appropriately to the damage, thereby preserving genomic integrity. In analogy with events occurring during viral infection, we appropriate the terms Immediate-Early, Early, and Late to describe the pre-repair responses to DSBs. A distinguishing feature of the Immediate-Early response is that the large protein condensates that form during the Early and Late response and are resolved upon repair, termed foci, are not visible. The Immediate-Early response encompasses initial lesion sensing, involving poly (ADP-ribose) polymerases (PARPs), KU70/80, and MRN, as well as rapid repair by so-called ‘fast-kinetic’ canonical non-homologous end joining (cNHEJ). Initial binding of PARPs and the KU70/80 complex to breaks appears to be mutually exclusive at easily ligatable DSBs that are repaired efficiently by fast-kinetic cNHEJ; a process that is PARP-, ATM-, 53BP1-, Artemis-, and resection-independent. However, at more complex breaks requiring processing, the Immediate-Early response involving PARPs and the ensuing highly dynamic PARylation (polyADP ribosylation) of many substrates may aid recruitment of both KU70/80 and MRN to DSBs. Complex DSBs rely upon the Early response, largely defined by ATM-dependent focal recruitment of many signalling molecules into large condensates, and regulated by complex chromatin dynamics. Finally, the Late response integrates information from cell cycle phase, chromatin context, and type of DSB to determine appropriate pathway choice. Critical to pathway choice is the recruitment of p53 binding protein 1 (53BP1) and breast cancer associated 1 (BRCA1). However, additional factors recruited throughout the DSB response also impact upon pathway choice, although these remain to be fully characterised. The Late response somehow channels DSBs into the appropriate high-fidelity repair pathway, typically either ‘slow-kinetic’ cNHEJ or homologous recombination (HR). Loss of specific components of the DSB repair machinery results in cells utilising remaining factors to effect repair, but often at the cost of increased mutagenesis. Here we discuss the complex regulation of the Immediate-Early, Early, and Late responses to DSBs proceeding repair itself.
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36
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Wong WPS, Wang JC, Schipma MJ, Zhang X, Edwards JR, El Muayed M. Cadmium-mediated pancreatic islet transcriptome changes in mice and cultured mouse islets. Toxicol Appl Pharmacol 2021; 433:115756. [PMID: 34666113 PMCID: PMC9873403 DOI: 10.1016/j.taap.2021.115756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/08/2021] [Accepted: 10/13/2021] [Indexed: 01/26/2023]
Abstract
Type II diabetes mellitus (T2DM) is a multifactorial disease process that is characterized by insulin resistance and impairment of insulin-producing pancreatic islets. There is evidence that environmental exposure to cadmium contributes to the development of T2DM. The presence of cadmium in human islets from the general population and the uptake of cadmium in β-cells have been reported. To identify cadmium-mediated changes in gene expression and molecular regulatory networks in pancreatic islets, we performed next-generation RNA-Sequencing (RNA-Seq) in islets following either in vivo (1 mM CdCl2 in drinking water) or ex-vivo (0.5 μM CdCl2) exposure. Both exposure regiments resulted in islet cadmium concentrations that are comparable to those found in human islets from the general population. 6-week in vivo cadmium exposure upregulates the expression of five genes: Synj2, Gjb1, Rbpjl, Try5 and 5430419D17Rik. Rbpjl is a known regulator of ctrb, a gene associated with diabetes susceptibility. With 18-week in vivo cadmium exposure, we found more comprehensive changes in gene expression profile. Pathway enrichment analysis showed that these secondary changes were clustered to molecular mechanisms related to intracellular protein trafficking to the plasma membrane. In islet culture, cadmium ex vivo significantly induces the expression of Mt1, Sphk1, Nrcam, L3mbtl2, Rnf216 and Itpr1. Mt1 and Itpr1 are known to be involved in glucose homeostasis. Collectively, findings reported here revealed a complex cadmium-mediated effect on pancreatic islet gene expression at environmentally relevant cadmium exposure conditions, providing the basis for further studies into the pathophysiological processes arising from cadmium accumulation in pancreatic islets.
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Affiliation(s)
- Winifred P S Wong
- Division of Endocrinology, Metabolism and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Janice C Wang
- Division of Endocrinology, Metabolism and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Matthew J Schipma
- NU Seq Core, Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Xiaomin Zhang
- Division of Transplant Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joshua R Edwards
- College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA
| | - Malek El Muayed
- Division of Endocrinology, Metabolism and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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37
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Sahay O, Barik GK, Sharma T, Pillai AD, Rapole S, Santra MK. Damsel in distress calling on her knights: Illuminating the pioneering role of E3 ubiquitin ligases in guarding the genome integrity. DNA Repair (Amst) 2021; 109:103261. [PMID: 34920250 DOI: 10.1016/j.dnarep.2021.103261] [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: 08/19/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 11/03/2022]
Abstract
The maintenance of genomic integrity is of utmost importance for the organisms to survive and to accurately inherit traits to their progenies. Any kind of DNA damage either due to defect in DNA duplication and/ or uncontrolled cell division or intracellular insults or environment radiation can result in gene mutation, chromosomal aberration and ultimately genomic instability, which may cause several diseases including cancers. Therefore, cells have evolved machineries for the surveillance of genomic integrity. Enormous exciting studies in the past indicate that ubiquitination (a posttranslational modification of proteins) plays a crucial role in maintaining the genomic integrity by diverse ways. In fact, various E3 ubiquitin ligases catalyse ubiquitination of key proteins to control their central role during cell cycle, DNA damage response (DDR) and DNA repair. Some E3 ligases promote genomic instability while others prevent it, deregulation of both of which leads to several malignancies. In this review, we consolidate the recent findings wherein the role of ubiquitination in conferring genome integrity is highlighted. We also discuss the latest discoveries on the mechanisms utilized by various E3 ligases to preserve genomic stability, with a focus on their actions during cell cycle progression and different types of DNA damage response as well as repair pathways.
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Affiliation(s)
- Osheen Sahay
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, S.P. Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Ganesh Kumar Barik
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, S.P. Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Tanisha Sharma
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, S.P. Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Ajay D Pillai
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Srikanth Rapole
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Manas Kumar Santra
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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38
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Zhang J, Lu X, MoghaddamKohi S, Shi L, Xu X, Zhu WG. Histone lysine modifying enzymes and their critical roles in DNA double-strand break repair. DNA Repair (Amst) 2021; 107:103206. [PMID: 34411909 DOI: 10.1016/j.dnarep.2021.103206] [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: 03/29/2021] [Revised: 07/24/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
Cells protect the integrity of the genome against DNA double-strand breaks through several well-characterized mechanisms including nonhomologous end-joining repair, homologous recombination repair, microhomology-mediated end-joining and single-strand annealing. However, aberrant DNA damage responses (DDRs) lead to genome instability and tumorigenesis. Clarification of the mechanisms underlying the DDR following lethal damage will facilitate the identification of therapeutic targets for cancer. Histones are small proteins that play a major role in condensing DNA into chromatin and regulating gene function. Histone modifications commonly occur in several residues including lysine, arginine, serine, threonine and tyrosine, which can be acetylated, methylated, ubiquitinated and phosphorylated. Of these, lysine modifications have been extensively explored during DDRs. Here, we focus on discussing the roles of lysine modifying enzymes involved in acetylation, methylation, and ubiquitination during the DDR. We provide a comprehensive understanding of the basis of potential epigenetic therapies driven by histone lysine modifications.
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Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Xiaopeng Lu
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Sara MoghaddamKohi
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Xingzhi Xu
- Department of Cell Biology and Medical Genetics, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
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39
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Katsuki Y, Abe M, Park SY, Wu W, Yabe H, Yabe M, van Attikum H, Nakada S, Ohta T, Seidman MM, Kim Y, Takata M. RNF168 E3 ligase participates in ubiquitin signaling and recruitment of SLX4 during DNA crosslink repair. Cell Rep 2021; 37:109879. [PMID: 34706224 PMCID: PMC11388903 DOI: 10.1016/j.celrep.2021.109879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/24/2021] [Accepted: 10/01/2021] [Indexed: 12/11/2022] Open
Abstract
SLX4/FANCP is a key Fanconi anemia (FA) protein and a DNA repair scaffold for incision around a DNA interstrand crosslink (ICL) by its partner XPF nuclease. The tandem UBZ4 ubiquitin-binding domains of SLX4 are critical for the recruitment of SLX4 to damage sites, likely by binding to K63-linked polyubiquitin chains. However, the identity of the ubiquitin E3 ligase that mediates SLX4 recruitment remains unknown. Using small interfering RNA (siRNA) screening with a GFP-tagged N-terminal half of SLX4 (termed SLX4-N), we identify the RNF168 E3 ligase as a critical factor for mitomycin C (MMC)-induced SLX4 foci formation. RNF168 and GFP-SLX4-N colocalize in MMC-induced ubiquitin foci. Accumulation of SLX4-N at psoralen-laser ICL tracks or of endogenous SLX4 at Digoxigenin-psoralen/UVA ICL is dependent on RNF168. Finally, we find that RNF168 is epistatic with SLX4 in promoting MMC tolerance. We conclude that RNF168 is a critical component of the signal transduction that recruits SLX4 to ICL damage.
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Affiliation(s)
- Yoko Katsuki
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
| | - Masako Abe
- The Core Facility, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Seon Young Park
- Department of Biological Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Wenwen Wu
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Hiromasa Yabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Miharu Yabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Shinichiro Nakada
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka, Japan; Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| | - Tomohiko Ohta
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Michael M Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yonghwan Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
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40
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Sanchez A, Lee D, Kim DI, Miller KM. Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin. Front Genet 2021; 12:747734. [PMID: 34659365 PMCID: PMC8514019 DOI: 10.3389/fgene.2021.747734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/31/2021] [Indexed: 01/25/2023] Open
Abstract
DNA double-strand breaks (DSBs) are hazardous to genome integrity and can promote mutations and disease if not handled correctly. Cells respond to these dangers by engaging DNA damage response (DDR) pathways that are able to identify DNA breaks within chromatin leading ultimately to their repair. The recognition and repair of DSBs by the DDR is largely dependent on the ability of DNA damage sensing factors to bind to and interact with nucleic acids, nucleosomes and their modified forms to target these activities to the break site. These contacts orientate and localize factors to lesions within chromatin, allowing signaling and faithful repair of the break to occur. Coordinating these events requires the integration of several signaling and binding events. Studies are revealing an enormously complex array of interactions that contribute to DNA lesion recognition and repair including binding events on DNA, as well as RNA, RNA:DNA hybrids, nucleosomes, histone and non-histone protein post-translational modifications and protein-protein interactions. Here we examine several DDR pathways that highlight and provide prime examples of these emerging concepts. A combination of approaches including genetic, cellular, and structural biology have begun to reveal new insights into the molecular interactions that govern the DDR within chromatin. While many questions remain, a clearer picture has started to emerge for how DNA-templated processes including transcription, replication and DSB repair are coordinated. Multivalent interactions with several biomolecules serve as key signals to recruit and orientate proteins at DNA lesions, which is essential to integrate signaling events and coordinate the DDR within the milieu of the nucleus where competing genome functions take place. Genome architecture, chromatin structure and phase separation have emerged as additional vital regulatory mechanisms that also influence genome integrity pathways including DSB repair. Collectively, recent advancements in the field have not only provided a deeper understanding of these fundamental processes that maintain genome integrity and cellular homeostasis but have also started to identify new strategies to target deficiencies in these pathways that are prevalent in human diseases including cancer.
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Affiliation(s)
- Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Doohyung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Dae In Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
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41
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Xu Y, Hu Y, Xu T, Yan K, Zhang T, Li Q, Chang F, Guo X, Peng J, Li M, Zhao M, Zhen H, Xu L, Zheng D, Li L, Shao G. RNF8-mediated regulation of Akt promotes lung cancer cell survival and resistance to DNA damage. Cell Rep 2021; 37:109854. [PMID: 34686341 DOI: 10.1016/j.celrep.2021.109854] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 08/18/2021] [Accepted: 09/28/2021] [Indexed: 01/21/2023] Open
Abstract
Despite the tremendous success of targeted and conventional therapies for lung cancer, therapeutic resistance is a common and major clinical challenge. RNF8 is a ubiquitin E3 ligase that plays essential roles in the DNA damage response; however, its role in the pathogenesis of lung cancer is unclear. Here, we report that RNF8 is overexpressed in lung cancer and positively correlates with the expression of p-Akt and poor survival of patients with non-small-cell lung cancer. In addition, we identify RNF8 as the E3 ligase for regulating the activation of Akt by K63-linked ubiquitination under physiological and genotoxic conditions, which leads to lung cancer cell proliferation and resistance to chemotherapy. Together, our study suggests that RNF8 could be a very promising target in precision medicine for lung cancer.
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Affiliation(s)
- Yongjie Xu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yumeng Hu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tao Xu
- The Affiliated Hospital of Qingdao University, Qingdao 266021, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Zhang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Qin Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Fen Chang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xueyuan Guo
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jingyu Peng
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Mo Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Min Zhao
- Department of Oncology, Hebei Chest Hospital, Research Center of Hebei Lung Cancer Prevention and Treatment, Shijiazhuang, Hebei 050041, China
| | - Hongying Zhen
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Luzheng Xu
- Medical and Health Analysis Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Duo Zheng
- Department of Cell Biology and Genetics, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Li Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Genze Shao
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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42
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Lu X, Xu M, Zhu Q, Zhang J, Liu G, Bao Y, Gu L, Tian Y, Wen H, Zhu WG. RNF8-ubiquitinated KMT5A is required for RNF168-induced H2A ubiquitination in response to DNA damage. FASEB J 2021; 35:e21326. [PMID: 33710666 DOI: 10.1096/fj.202002234r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022]
Abstract
Histone modifications play critical roles in DNA damage repair to safeguard genome integrity. However, how different histone modifiers coordinate to build appropriate chromatin context for DNA damage repair is largely unknown. Here, we report a novel interplay between the histone methyltransferase KMT5A and two E3 ligases RNF8 and RNF168 in establishing the histone modification status for DNA damage repair. KMT5A is a newly identified substrate of RNF8 in vitro and in vivo. In response to DNA double-strand breaks (DSBs), RNF8 promotes KMT5A recruitment onto damaged chromatin in a ubiquitination-dependent manner. RNF8-induced KMT5A ubiquitination increases the binding capacity of KMT5A to RNF168. Interestingly, KMT5A not only drives a local increase in H4K20 monomethylation at DSBs, but also promotes RNF168's activity in catalyzing H2A ubiquitination. We proved that the interaction between the H2A acidic patch and KMT5A R188/R189 residues is critical for KMT5A-mediated regulation of H2A ubiquitination. Taken together, our results highlight a new role for KMT5A in linking H4K20 methylation and H2A ubiquitination and provide insight into the histone modification network during DNA damage repair.
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Affiliation(s)
- Xiaopeng Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Min Xu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Qian Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Jun Zhang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Ge Liu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Yantao Bao
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Luo Gu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Yuan Tian
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China.,Shenzhen Bay Laboratory, Shenzhen University School of Medicine, Shenzhen, China
| | - He Wen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China.,Shenzhen Bay Laboratory, Shenzhen University School of Medicine, Shenzhen, China.,International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
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43
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Non-canonical function of DGCR8 in DNA double-strand break repair signaling and tumor radioresistance. Nat Commun 2021; 12:4033. [PMID: 34188037 PMCID: PMC8242032 DOI: 10.1038/s41467-021-24298-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 06/11/2021] [Indexed: 12/21/2022] Open
Abstract
In response to DNA double-strand breaks (DSBs), repair proteins are recruited to the damaged sites. Ubiquitin signaling plays a critical role in coordinating protein recruitment during the DNA damage response. Here, we find that the microRNA biogenesis factor DGCR8 promotes tumor resistance to X-ray radiation independently of its Drosha-binding ability. Upon radiation, the kinase ATM and the deubiquitinase USP51 mediate the activation and stabilization of DGCR8 through phosphorylation and deubiquitination. Specifically, radiation-induced ATM-dependent phosphorylation of DGCR8 at serine 677 facilitates USP51 to bind, deubiquitinate, and stabilize DGCR8, which leads to the recruitment of DGCR8 and DGCR8’s binding partner RNF168 to MDC1 and RNF8 at DSBs. This, in turn, promotes ubiquitination of histone H2A, repair of DSBs, and radioresistance. Altogether, these findings reveal the non-canonical function of DGCR8 in DSB repair and suggest that radiation treatment may result in therapy-induced tumor radioresistance through ATM- and USP51-mediated activation and upregulation of DGCR8. The molecular mechanisms underlying cancer cell radioresistance need to be elucidated. In this study, the authors show that the microRNA biogenesis factor DGCR8 is stabilized by USP51 and ATM upon irradiation and by consequence it promotes the repair of DNA double-strand breaks and radioresistance by recruiting RNF168 to sites of damage.
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44
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Verma P, Greenberg RA. Communication between chromatin and homologous recombination. Curr Opin Genet Dev 2021; 71:1-9. [PMID: 34098484 DOI: 10.1016/j.gde.2021.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/13/2021] [Indexed: 12/24/2022]
Abstract
Higher-order chromatin packing serves as a structural barrier to the recognition and repair of genomic lesions. The initiation and outcome of the repair response is dictated by a highly coordinated yet complex interplay between chromatin modifying enzymes and their cognate readers, damage induced chemical modifications, nucleosome density, transcriptional state, and cell cycle-dependent availability of DNA repair machinery. The physical and chemical properties of the DNA lesions themselves further regulate the nature of ensuing chromatin responses. Here we review recent discoveries across these various contexts, where chromatin regulates the homology-guided double-strand break repair mechanism, homologous recombination, and also highlight the key knowledge gaps vital to generate a holistic understanding of this process and its contributions to genome integrity.
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Affiliation(s)
- Priyanka Verma
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Roger A Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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45
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Gao M, Guo G, Huang J, Hou X, Ham H, Kim W, Zhao F, Tu X, Zhou Q, Zhang C, Zhu Q, Liu J, Yan Y, Xu Z, Yin P, Luo K, Weroha J, Deng M, Billadeau DD, Lou Z. DOCK7 protects against replication stress by promoting RPA stability on chromatin. Nucleic Acids Res 2021; 49:3322-3337. [PMID: 33704464 PMCID: PMC8034614 DOI: 10.1093/nar/gkab134] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/21/2021] [Accepted: 03/02/2021] [Indexed: 02/05/2023] Open
Abstract
RPA is a critical factor for DNA replication and replication stress response. Surprisingly, we found that chromatin RPA stability is tightly regulated. We report that the GDP/GTP exchange factor DOCK7 acts as a critical replication stress regulator to promote RPA stability on chromatin. DOCK7 is phosphorylated by ATR and then recruited by MDC1 to the chromatin and replication fork during replication stress. DOCK7-mediated Rac1/Cdc42 activation leads to the activation of PAK1, which subsequently phosphorylates RPA1 at S135 and T180 to stabilize chromatin-loaded RPA1 and ensure proper replication stress response. Moreover, DOCK7 is overexpressed in ovarian cancer and depleting DOCK7 sensitizes cancer cells to camptothecin. Taken together, our results highlight a novel role for DOCK7 in regulation of the replication stress response and highlight potential therapeutic targets to overcome chemoresistance in cancer.
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Affiliation(s)
- Ming Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jinzhou Huang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaonan Hou
- Department of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Hyoungjun Ham
- Department of Biochemistry and Molecular Biology, Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Wootae Kim
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Fei Zhao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xinyi Tu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qin Zhou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chao Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qian Zhu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jiaqi Liu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuanliang Yan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhijie Xu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ping Yin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kuntian Luo
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - John Weroha
- Department of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Min Deng
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel D Billadeau
- Department of Biochemistry and Molecular Biology, Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
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46
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Tang M, Li S, Chen J. Ubiquitylation in DNA double-strand break repair. DNA Repair (Amst) 2021; 103:103129. [PMID: 33990032 DOI: 10.1016/j.dnarep.2021.103129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 12/28/2022]
Abstract
Genome integrity is constantly challenged by various DNA lesions with DNA double-strand breaks (DSBs) as the most cytotoxic lesions. In order to faithfully repair DSBs, DNA damage response (DDR) signaling networks have evolved, which organize many multi-protein complexes to deal with the encountered DNA damage. Spatiotemporal dynamics of these protein complexes at DSBs are mainly modulated by post-translational modifications (PTMs). One of the most well-studied PTMs in DDR is ubiquitylation which can orchestrate cellular responses to DSBs, promote accurate DNA repair, and maintain genome integrity. Here, we summarize the recent advances of ubiquitin-dependent signaling in DDR and discuss how ubiquitylation crosstalks with other PTMs to control fundamental biological processes in DSB repair.
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Affiliation(s)
- Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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47
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DNA double-strand break repair: Putting zinc fingers on the sore spot. Semin Cell Dev Biol 2021; 113:65-74. [DOI: 10.1016/j.semcdb.2020.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/22/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022]
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48
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Guo G, Gao M, Gao X, Zhu B, Huang J, Tu X, Kim W, Zhao F, Zhou Q, Zhu S, Wu Z, Yan Y, Zhang Y, Zeng X, Zhu Q, Yin P, Luo K, Sun J, Deng M, Lou Z. Reciprocal regulation of RIG-I and XRCC4 connects DNA repair with RIG-I immune signaling. Nat Commun 2021; 12:2187. [PMID: 33846346 PMCID: PMC8041803 DOI: 10.1038/s41467-021-22484-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/16/2021] [Indexed: 02/08/2023] Open
Abstract
The RNA-sensing pathway contributes to type I interferon (IFN) production induced by DNA damaging agents. However, the potential involvement of RNA sensors in DNA repair is unknown. Here, we found that retinoic acid-inducible gene I (RIG-I), a key cytosolic RNA sensor that recognizes RNA virus and initiates the MAVS-IRF3-type I IFN signaling cascade, is recruited to double-stranded breaks (DSBs) and suppresses non-homologous end joining (NHEJ). Mechanistically, RIG-I interacts with XRCC4, and the RIG-I/XRCC4 interaction impedes the formation of XRCC4/LIG4/XLF complex at DSBs. High expression of RIG-I compromises DNA repair and sensitizes cancer cells to irradiation treatment. In contrast, depletion of RIG-I renders cells resistant to irradiation in vitro and in vivo. In addition, this mechanism suggests a protective role of RIG-I in hindering retrovirus integration into the host genome by suppressing the NHEJ pathway. Reciprocally, XRCC4, while suppressed for its DNA repair function, has a critical role in RIG-I immune signaling through RIG-I interaction. XRCC4 promotes RIG-I signaling by enhancing oligomerization and ubiquitination of RIG-I, thereby suppressing RNA virus replication in host cells. In vivo, silencing XRCC4 in mouse lung promotes influenza virus replication in mice and these mice display faster body weight loss, poorer survival, and a greater degree of lung injury caused by influenza virus infection. This reciprocal regulation of RIG-I and XRCC4 reveals a new function of RIG-I in suppressing DNA repair and virus integration into the host genome, and meanwhile endues XRCC4 with a crucial role in potentiating innate immune response, thereby helping host to prevail in the battle against virus.
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Affiliation(s)
- Guijie Guo
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Ming Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Xiaochen Gao
- Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Bibo Zhu
- Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Jinzhou Huang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Xinyi Tu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Wootae Kim
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Fei Zhao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Qin Zhou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Shouhai Zhu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Zheming Wu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Yuanliang Yan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Yong Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Xiangyu Zeng
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Qian Zhu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Ping Yin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Kuntian Luo
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jie Sun
- Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Min Deng
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
- Department of Oncology, Mayo Clinic, Rochester, MN, USA.
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
- Department of Oncology, Mayo Clinic, Rochester, MN, USA.
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49
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Sadoughi F, Maleki Dana P, Asemi Z, Yousefi B. DNA damage response and repair in osteosarcoma: Defects, regulation and therapeutic implications. DNA Repair (Amst) 2021; 102:103105. [PMID: 33836418 DOI: 10.1016/j.dnarep.2021.103105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/20/2021] [Indexed: 01/03/2023]
Abstract
Osteosarcoma (OS) is the most common primary bone malignancy in children and adolescents which has the survival rate of 20% in its advanced stages. Osteosarcomas are mostly resistance to our common treatments. DNA damage response (DDR) is a specialized multistep process containing abundant proteins which are necessary for the survival of any cell and organism. DDR machinery detects a diversity of DNA lesions and inhibits the cell cycle progression if these lesions are not repairable. DDR is involved in aging, age-related diseases, and cancer. In recent years, DDR inhibitors have gained the attention of researches due to their potentials in offering novel therapeutic targets and improving the response of many cancers to either chemo- or radio-therapy. In this regard, we tried to gather a great body of evidence about the role of DDR ingredients in osteosarcoma's initiation/progression, prognosis, and treatment.
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Affiliation(s)
- Fatemeh Sadoughi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Parisa Maleki Dana
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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50
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Nakamura K, Kustatscher G, Alabert C, Hödl M, Forne I, Völker-Albert M, Satpathy S, Beyer TE, Mailand N, Choudhary C, Imhof A, Rappsilber J, Groth A. Proteome dynamics at broken replication forks reveal a distinct ATM-directed repair response suppressing DNA double-strand break ubiquitination. Mol Cell 2021; 81:1084-1099.e6. [PMID: 33450211 PMCID: PMC7939521 DOI: 10.1016/j.molcel.2020.12.025] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/29/2022]
Abstract
Cells have evolved an elaborate DNA repair network to ensure complete and accurate DNA replication. Defects in these repair machineries can fuel genome instability and drive carcinogenesis while creating vulnerabilities that may be exploited in therapy. Here, we use nascent chromatin capture (NCC) proteomics to characterize the repair of replication-associated DNA double-strand breaks (DSBs) triggered by topoisomerase 1 (TOP1) inhibitors. We reveal profound changes in the fork proteome, including the chromatin environment and nuclear membrane interactions, and identify three classes of repair factors according to their enrichment at broken and/or stalled forks. ATM inhibition dramatically rewired the broken fork proteome, revealing that ataxia telangiectasia mutated (ATM) signalling stimulates DNA end resection, recruits PLK1, and concomitantly suppresses the canonical DSB ubiquitination response by preventing accumulation of RNF168 and BRCA1-A. This work and collection of replication fork proteomes provide a new framework to understand how cells orchestrate homologous recombination repair of replication-associated DSBs.
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Affiliation(s)
- Kyosuke Nakamura
- The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Constance Alabert
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Martina Hödl
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ignasi Forne
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg- Martinsried, Germany
| | - Moritz Völker-Albert
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg- Martinsried, Germany
| | - Shankha Satpathy
- The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Tracey E Beyer
- The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Niels Mailand
- The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Axel Imhof
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg- Martinsried, Germany
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany.
| | - Anja Groth
- The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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