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Chen KL, Huang SW, Yao JJ, He SW, Gong S, Tan XR, Liang YL, Li JY, Huang SY, Li YQ, Zhao Y, Qiao H, Xu S, Zang S, Ma J, Liu N. LncRNA DYNLRB2-AS1 promotes gemcitabine resistance of nasopharyngeal carcinoma by inhibiting the ubiquitination degradation of DHX9 protein. Drug Resist Updat 2024; 76:101111. [PMID: 38908233 DOI: 10.1016/j.drup.2024.101111] [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: 03/21/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/24/2024]
Abstract
Gemcitabine (GEM) based induction chemotherapy is a standard treatment for locoregionally advanced nasopharyngeal carcinoma (NPC). However, approximately 15 % of patients are still resistant to GEM-containing chemotherapy, which leads to treatment failure. Nevertheless, the underlying mechanisms of GEM resistance remain poorly understood. Herein, based on a microarray analysis, we identified 221 dysregulated lncRNAs, of which, DYNLRB2-AS1 was one of the most upregulated lncRNAs in GEM-resistance NPC cell lines. DYNLRB2-AS1 was shown to function as contain an oncogenic lncRNA that promoted NPC GEM resistance, cell proliferation, but inhibited cell apoptosis. Mechanistically, DYNLRB2-AS1 could directly bind to the DHX9 protein and prevent its interaction with the E3 ubiquitin ligase PRPF19, and thus blocking PRPF19-mediated DHX9 degradation, which ultimately facilitated the repair of DNA damage in the presence of GEM. Clinically, higher DYNLRB2-AS1 expression indicated an unfavourable overall survival of NPC patients who received induction chemotherapy. Overall, this study identified the oncogenic lncRNA DYNLRB2-AS1 as an independent prognostic biomarker for patients with locally advanced NPC and as a potential therapeutic target for overcoming GEM chemoresistance in NPC.
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Affiliation(s)
- Kai-Lin Chen
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Department of Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Sai-Wei Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Ji-Jin Yao
- Department of Head and Neck Oncology, the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Shi-Wei He
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Sha Gong
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xi-Rong Tan
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Ye-Lin Liang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jun-Yan Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Sheng-Yan Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Ying-Qin Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yin Zhao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Han Qiao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Sha Xu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shengbing Zang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
| | - Jun Ma
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
| | - Na Liu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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Lee H, Han DW, Yoo S, Kwon O, La H, Park C, Lee H, Kang K, Uhm SJ, Song H, Do JT, Choi Y, Hong K. RNA helicase DEAD-box-5 is involved in R-loop dynamics of preimplantation embryos. Anim Biosci 2024; 37:1021-1030. [PMID: 38419548 PMCID: PMC11065950 DOI: 10.5713/ab.23.0401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/09/2023] [Accepted: 12/07/2023] [Indexed: 03/02/2024] Open
Abstract
OBJECTIVE R-loops are DNA:RNA triplex hybrids, and their metabolism is tightly regulated by transcriptional regulation, DNA damage response, and chromatin structure dynamics. R-loop homeostasis is dynamically regulated and closely associated with gene transcription in mouse zygotes. However, the factors responsible for regulating these dynamic changes in the R-loops of fertilized mouse eggs have not yet been investigated. This study examined the functions of candidate factors that interact with R-loops during zygotic gene activation. METHODS In this study, we used publicly available next-generation sequencing datasets, including low-input ribosome profiling analysis and polymerase II chromatin immunoprecipitation-sequencing (ChIP-seq), to identify potential regulators of R-loop dynamics in zygotes. These datasets were downloaded, reanalyzed, and compared with mass spectrometry data to identify candidate factors involved in regulating R-loop dynamics. To validate the functions of these candidate factors, we treated mouse zygotes with chemical inhibitors using in vitro fertilization. Immunofluorescence with an anti-R-loop antibody was then performed to quantify changes in R-loop metabolism. RESULTS We identified DEAD-box-5 (DDX5) and histone deacetylase-2 (HDAC2) as candidates that potentially regulate R-loop metabolism in oocytes, zygotes and two-cell embryos based on change of their gene translation. Our analysis revealed that the DDX5 inhibition of activity led to decreased R-loop accumulation in pronuclei, indicating its involvement in regulating R-loop dynamics. However, the inhibition of histone deacetylase-2 activity did not significantly affect R-loop levels in pronuclei. CONCLUSION These findings suggest that dynamic changes in R-loops during mouse zygote development are likely regulated by RNA helicases, particularly DDX5, in conjunction with transcriptional processes. Our study provides compelling evidence for the involvement of these factors in regulating R-loop dynamics during early embryonic development.
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Affiliation(s)
- Hyeonji Lee
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Dong Wook Han
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen 529020,
China
| | - Seonho Yoo
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Ohbeom Kwon
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Hyeonwoo La
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Heeji Lee
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Kiye Kang
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Sang Jun Uhm
- Department of Animal Science, Sangji University, Wonju 26339,
Korea
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
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Xu Y, Jiao Y, Liu C, Miao R, Liu C, Wang Y, Ma C, Liu J. R-loop and diseases: the cell cycle matters. Mol Cancer 2024; 23:84. [PMID: 38678239 PMCID: PMC11055327 DOI: 10.1186/s12943-024-02000-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
The cell cycle is a crucial biological process that is involved in cell growth, development, and reproduction. It can be divided into G1, S, G2, and M phases, and each period is closely regulated to ensure the production of two similar daughter cells with the same genetic material. However, many obstacles influence the cell cycle, including the R-loop that is formed throughout this process. R-loop is a triple-stranded structure, composed of an RNA: DNA hybrid and a single DNA strand, which is ubiquitous in organisms from bacteria to mammals. The existence of the R-loop has important significance for the regulation of various physiological processes. However, aberrant accumulation of R-loop due to its limited resolving ability will be detrimental for cells. For example, DNA damage and genomic instability, caused by the R-loop, can activate checkpoints in the cell cycle, which in turn induce cell cycle arrest and cell death. At present, a growing number of factors have been proven to prevent or eliminate the accumulation of R-loop thereby avoiding DNA damage and mutations. Therefore, we need to gain detailed insight into the R-loop resolution factors at different stages of the cell cycle. In this review, we review the current knowledge of factors that play a role in resolving the R-loop at different stages of the cell cycle, as well as how mutations of these factors lead to the onset and progression of diseases.
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Affiliation(s)
- Yuqin Xu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yue Jiao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chengbin Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Rui Miao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunyan Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yilong Wang
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunming Ma
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Jiao Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China.
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Krishnamoorthy V, Foglizzo M, Dilley RL, Wu A, Datta A, Dutta P, Campbell LJ, Degtjarik O, Musgrove LJ, Calabrese AN, Zeqiraj E, Greenberg RA. The SPATA5-SPATA5L1 ATPase complex directs replisome proteostasis to ensure genome integrity. Cell 2024; 187:2250-2268.e31. [PMID: 38554706 PMCID: PMC11055677 DOI: 10.1016/j.cell.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 12/27/2023] [Accepted: 03/02/2024] [Indexed: 04/02/2024]
Abstract
Ubiquitin-dependent unfolding of the CMG helicase by VCP/p97 is required to terminate DNA replication. Other replisome components are not processed in the same fashion, suggesting that additional mechanisms underlie replication protein turnover. Here, we identify replisome factor interactions with a protein complex composed of AAA+ ATPases SPATA5-SPATA5L1 together with heterodimeric partners C1orf109-CINP (55LCC). An integrative structural biology approach revealed a molecular architecture of SPATA5-SPATA5L1 N-terminal domains interacting with C1orf109-CINP to form a funnel-like structure above a cylindrically shaped ATPase motor. Deficiency in the 55LCC complex elicited ubiquitin-independent proteotoxicity, replication stress, and severe chromosome instability. 55LCC showed ATPase activity that was specifically enhanced by replication fork DNA and was coupled to cysteine protease-dependent cleavage of replisome substrates in response to replication fork damage. These findings define 55LCC-mediated proteostasis as critical for replication fork progression and genome stability and provide a rationale for pathogenic variants seen in associated human neurodevelopmental disorders.
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Affiliation(s)
- Vidhya Krishnamoorthy
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Martina Foglizzo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Robert L Dilley
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA.
| | - Angela Wu
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Arindam Datta
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Parul Dutta
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Lisa J Campbell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Oksana Degtjarik
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Laura J Musgrove
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - 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 19104-6160, USA.
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5
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Huang TT, Chiang CY, Nair JR, Wilson KM, Cheng K, Lee JM. AKT1 interacts with DHX9 to Mitigate R Loop-Induced Replication Stress in Ovarian Cancer. Cancer Res 2024; 84:887-904. [PMID: 38241710 PMCID: PMC10947874 DOI: 10.1158/0008-5472.can-23-1908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/04/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
PARP inhibitor (PARPi)-resistant BRCA-mutant (BRCAm) high-grade serous ovarian cancer (HGSOC) represents a new clinical challenge with unmet therapeutic needs. Here, we performed a quantitative high-throughput drug combination screen that identified the combination of an ATR inhibitor (ATRi) and an AKT inhibitor (AKTi) as an effective treatment strategy for both PARPi-sensitive and PARPi-resistant BRCAm HGSOC. The ATRi and AKTi combination induced DNA damage and R loop-mediated replication stress (RS). Mechanistically, the kinase domain of AKT1 directly interacted with DHX9 and facilitated recruitment of DHX9 to R loops. AKTi increased ATRi-induced R loop-mediated RS by mitigating recruitment of DHX9 to R loops. Moreover, DHX9 was upregulated in tumors from patients with PARPi-resistant BRCAm HGSOC, and high coexpression of DHX9 and AKT1 correlated with worse survival. Together, this study reveals an interaction between AKT1 and DHX9 that facilitates R loop resolution and identifies combining ATRi and AKTi as a rational treatment strategy for BRCAm HGSOC irrespective of PARPi resistance status. SIGNIFICANCE Inhibition of the AKT and ATR pathways cooperatively induces R loop-associated replication stress in high-grade serous ovarian cancer, providing rationale to support the clinical development of AKT and ATR inhibitor combinations. See related commentary by Ramanarayanan and Oberdoerffer, p. 793.
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Affiliation(s)
- Tzu-Ting Huang
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chih-Yuan Chiang
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Jayakumar R. Nair
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kelli M. Wilson
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Ken Cheng
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Jung-Min Lee
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Fütterer A, Rodriguez-Acebes S, Méndez J, Gutiérrez J, Martínez-A C. PARP1, DIDO3, and DHX9 Proteins Mutually Interact in Mouse Fibroblasts, with Effects on DNA Replication Dynamics, Senescence, and Oncogenic Transformation. Cells 2024; 13:159. [PMID: 38247850 PMCID: PMC10814579 DOI: 10.3390/cells13020159] [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: 12/18/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
The regulated formation and resolution of R-loops is a natural process in physiological gene expression. Defects in R-loop metabolism can lead to DNA replication stress, which is associated with a variety of diseases and, ultimately, with cancer. The proteins PARP1, DIDO3, and DHX9 are important players in R-loop regulation. We previously described the interaction between DIDO3 and DHX9. Here, we show that, in mouse embryonic fibroblasts, the three proteins are physically linked and dependent on PARP1 activity. The C-terminal truncation of DIDO3 leads to the impairment of this interaction; concomitantly, the cells show increased replication stress and senescence. DIDO3 truncation also renders the cells partially resistant to in vitro oncogenic transformation, an effect that can be reversed by immortalization. We propose that PARP1, DIDO3, and DHX9 proteins form a ternary complex that regulates R-loop metabolism, preventing DNA replication stress and subsequent senescence.
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Affiliation(s)
- Agnes Fütterer
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain;
| | - Sara Rodriguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (S.R.-A.); (J.M.)
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (S.R.-A.); (J.M.)
| | - Julio Gutiérrez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain;
| | - Carlos Martínez-A
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain;
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7
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Yang S, Winstone L, Mondal S, Wu Y. Helicases in R-loop Formation and Resolution. J Biol Chem 2023; 299:105307. [PMID: 37778731 PMCID: PMC10641170 DOI: 10.1016/j.jbc.2023.105307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023] Open
Abstract
With the development and wide usage of CRISPR technology, the presence of R-loop structures, which consist of an RNA-DNA hybrid and a displaced single-strand (ss) DNA, has become well accepted. R-loop structures have been implicated in a variety of circumstances and play critical roles in the metabolism of nucleic acid and relevant biological processes, including transcription, DNA repair, and telomere maintenance. Helicases are enzymes that use an ATP-driven motor force to unwind double-strand (ds) DNA, dsRNA, or RNA-DNA hybrids. Additionally, certain helicases have strand-annealing activity. Thus, helicases possess unique positions for R-loop biogenesis: they utilize their strand-annealing activity to promote the hybridization of RNA to DNA, leading to the formation of R-loops; conversely, they utilize their unwinding activity to separate RNA-DNA hybrids and resolve R-loops. Indeed, numerous helicases such as senataxin (SETX), Aquarius (AQR), WRN, BLM, RTEL1, PIF1, FANCM, ATRX (alpha-thalassemia/mental retardation, X-linked), CasDinG, and several DEAD/H-box proteins are reported to resolve R-loops; while other helicases, such as Cas3 and UPF1, are reported to stimulate R-loop formation. Moreover, helicases like DDX1, DDX17, and DHX9 have been identified in both R-loop formation and resolution. In this review, we will summarize the latest understandings regarding the roles of helicases in R-loop metabolism. Additionally, we will highlight challenges associated with drug discovery in the context of targeting these R-loop helicases.
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Affiliation(s)
- Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sohaumn Mondal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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Sun J, Zhang X, Sun Y. C1orf109 promotes malignant phenotype of liver cancer via wnt signaling pathway in a CK2-dependent manner. J Mol Histol 2023; 54:135-145. [PMID: 36988773 DOI: 10.1007/s10735-023-10117-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/27/2023] [Indexed: 03/30/2023]
Abstract
Chromosome 1 open reading frame 109 (C1orf09) is a protein whose expression pattern and biological function in humans, particularly in malignant tumors, have not been explored. In this study, both bioinformatics and immunohistochemical staining revealed that C1orf109 was overexpressed in the cytoplasm of liver cancer cells, and the positive ratio of C1orf109 in liver cancer samples (42.5%, 37/87) was significantly higher than that in normal liver tissues (10%, 3/30, P = 0.0012). C1orf109 expression was correlated with an advanced TNM stage (P = 0.017) and vascular invasion (P = 0.023) and predicted the poor overall survival of patients with liver cancer (P = 0.001). C1orf109 facilitated tumor growth, colony formation, migration, and invasion by activating Wnt signaling by upregulating non-phosphorylated β-catenin and its downstream target genes such as CyclinD1, c-myc, and MMP7. Our results also suggest that C1orf109 interacts and co-localizes with casein kinase II (CK2) to activate Wnt signaling. Treatment with a CK2-specific inhibitor markedly counteracted the increased expression of CyclinD1, c-Myc, and MMP7, as well as the upregulation of tumor proliferation and invasion caused by C1orf109 overexpression. Taken together, our results indicate that C1orf109 accelerates liver cancer cell proliferation and invasion by strengthening the Wnt signaling pathway in a CK2-dependent manner.
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Affiliation(s)
- Jing Sun
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiupeng Zhang
- Department of Pathology, the First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yefei Sun
- Department of Gastrointestinal Surgery & Hernia and Abdominal Wall Surgery, the First Hospital, China Medical University, No.155, North Nanjing Street, Heping District, 110001, Shenyang, Liaoning, China.
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Chiu CL, Li CG, Verschueren E, Wen RM, Zhang D, Gordon CA, Zhao H, Giaccia AJ, Brooks JD. NUSAP1 Binds ILF2 to Modulate R-Loop Accumulation and DNA Damage in Prostate Cancer. Int J Mol Sci 2023; 24:6258. [PMID: 37047232 PMCID: PMC10093842 DOI: 10.3390/ijms24076258] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Increased expression of NUSAP1 has been identified as a robust prognostic biomarker in prostate cancer and other malignancies. We have previously shown that NUSAP1 is positively regulated by E2F1 and promotes cancer invasion and metastasis. To further understand the biological function of NUSAP1, we used affinity purification and mass spectrometry proteomic analysis to identify NUSAP1 interactors. We identified 85 unique proteins in the NUSAP1 interactome, including ILF2, DHX9, and other RNA-binding proteins. Using proteomic approaches, we uncovered a function for NUSAP1 in maintaining R-loops and in DNA damage response through its interaction with ILF2. Co-immunoprecipitation and colocalization using confocal microscopy verified the interactions of NUSAP1 with ILF2 and DHX9, and RNA/DNA hybrids. We showed that the microtubule and charged helical domains of NUSAP1 were necessary for the protein-protein interactions. Depletion of ILF2 alone further increased camptothecin-induced R-loop accumulation and DNA damage, and NUSAP1 depletion abolished this effect. In human prostate adenocarcinoma, NUSAP1 and ILF2 mRNA expression levels are positively correlated, elevated, and associated with poor clinical outcomes. Our study identifies a novel role for NUSAP1 in regulating R-loop formation and accumulation in response to DNA damage through its interactions with ILF2 and hence provides a potential therapeutic target.
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Affiliation(s)
- Chun-Lung Chiu
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caiyun G. Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Erik Verschueren
- ULUA Besloten Vennootschap, Arendstraat 29, 2018 Antwerpen, Belgium
| | - Ru M. Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dalin Zhang
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Catherine A. Gordon
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hongjuan Zhao
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amato J. Giaccia
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Medical Research Council/Cancer Research United Kingdom Oxford Institute for Radiation Oncology and Gray Laboratory, University of Oxford, Oxford OX3 7DQ, UK
| | - James D. Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Cancer Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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10
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England-Mason G, Merrill SM, Gladish N, Moore SR, Giesbrecht GF, Letourneau N, MacIsaac JL, MacDonald AM, Kinniburgh DW, Ponsonby AL, Saffery R, Martin JW, Kobor MS, Dewey D. Prenatal exposure to phthalates and peripheral blood and buccal epithelial DNA methylation in infants: An epigenome-wide association study. ENVIRONMENT INTERNATIONAL 2022; 163:107183. [PMID: 35325772 DOI: 10.1016/j.envint.2022.107183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Prenatal exposure to phthalates has been associated with adverse health and neurodevelopmental outcomes. DNA methylation (DNAm) alterations may be a mechanism underlying these effects, but prior investigations of prenatal exposure to phthalates and neonatal DNAm profiles are limited to placental tissue and umbilical cord blood. OBJECTIVE Conduct an epigenome-wide association study (EWAS) of the associations between prenatal exposure to phthalates and DNAm in two accessible infant tissues, venous buffy coat blood and buccal epithelial cells (BECs). METHODS Participants included 152 maternal-infant pairs from the Alberta Pregnancy Outcomes and Nutrition (APrON) study. Maternal second trimester urine samples were analyzed for nine phthalate metabolites. Blood (n = 74) or BECs (n = 78) were collected from 3-month-old infants and profiled for DNAm using the Infinium HumanMethylation450 (450K) BeadChip. Robust linear regressions were used to investigate the associations between high (HMWPs) and low molecular weight phthalates (LMWPs) and change in methylation levels at variable Cytosine-phosphate-Guanine (CpG) sites in infant tissues, as well as the sensitivity of associations to potential confounders. RESULTS One candidate CpG in gene RNF39 reported by a previous study examining prenatal exposure to phthalates and cord blood DNAm was replicated. The EWAS identified 12 high-confidence CpGs in blood and another 12 in BECs associated with HMWPs and/or LMWPs. Prenatal exposure to bisphenol A (BPA) associated with two of the CpGs associated with HMWPs in BECs. DISCUSSION Prenatal exposure to phthalates was associated with DNAm variation at CpGs annotated to genes associated with endocrine hormone activity (i.e., SLCO4A1, TPO), immune pathways and DNA damage (i.e., RASGEF1B, KAZN, HLA-A, MYO18A, DIP2C, C1or109), and neurodevelopment (i.e., AMPH, NOTCH3, DNAJC5). Future studies that characterize the stability of these associations in larger samples, multiple cohorts, across tissues, and investigate the potential associations between these biomarkers and relevant health and neurodevelopmental outcomes are needed.
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Affiliation(s)
- Gillian England-Mason
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Sarah M Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Nicole Gladish
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Sarah R Moore
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Gerald F Giesbrecht
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Psychology, Faculty of Arts, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nicole Letourneau
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Faculty of Nursing, University of Calgary, Calgary, Alberta, Canada; Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute, Calgary, Alberta, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Amy M MacDonald
- Alberta Centre for Toxicology, University of Calgary, Calgary, Alberta, Canada
| | - David W Kinniburgh
- Alberta Centre for Toxicology, University of Calgary, Calgary, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan W Martin
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Södermanland, Sweden
| | - Michael S Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; Program in Child and Brain Development, CIFAR, Toronto, Ontario, Canada
| | - Deborah Dewey
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute, Calgary, Alberta, Canada.
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11
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Dou P, Li Y, Sun H, Xie W, Zhang X, Zhang X, Zhang D, Qiao S, Ci Y, Nie H, Han F, Li Y. C1orf109L binding DHX9 promotes DNA damage depended on the R-loop accumulation and enhances camptothecin chemosensitivity. Cell Prolif 2020; 53:e12875. [PMID: 32761833 PMCID: PMC7507383 DOI: 10.1111/cpr.12875] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/14/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Objectives R‐loop is a three‐stranded nucleic acid structure of RNA/DNA hybrid, which occurs naturally during transcription, and more R‐loop accumulation can trigger serious DNA damage. There has been increasing attention to the issue of R‐loop accumulation acted as a target for cancer therapy. However, the regulation of R‐loop‐associated proteins is poorly explored. Material and method Quantitative real‐time PCR and Western blot were used to measure the expression of C1orf109 in cell lines. In addition, C1orf109L (C1orf109 longest isoform) protein binding partner was identified and validated using immunoprecipitation‐mass spectrometric (IP‐MS) and immunoprecipitation assays. DNA‐RNA immunoprecipitation (DR‐IP) and immunofluorescence determined the C1orf109L location on R‐loop. R‐loop accumulation was determined by immunofluorescence. Cell cycle was determined by flow cytometry. Finally, time‐lapse assay and cell counting were conducted to determined cell survival in response to camptothecin (CPT). Results We found that C1orf109L could mediate cell cycle arrest in the G2/M phase and DNA damage depended on R‐loop accumulation. Meanwhile, C1orf109L could bind with DHX9 to trigger R‐loop accumulation. And C1orf109L was competitive with PARP1 binding to DHX9, which would block the function of DHX9‐PARP1 to prevent the R‐loop accumulation. Furthermore, C1orf109L could enhance the chemosensitivity of CPT, a chemotherapeutic drug capable of promoting R‐loop formation. Conclusions Our data demonstrate that C1orf109L triggers R‐loop accumulation and DNA damage to arrest cell cycle.
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Affiliation(s)
- Peng Dou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Yiqun Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Haoxiu Sun
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Wanqiu Xie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Xiaoqing Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Xiaohan Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Dandan Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Shupei Qiao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Yanpeng Ci
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Fang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
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