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Zuo Y, He J, Zhou Z, Sun J, Ouyang C, Huang H, Wang Y, Liu H, Reed SH. Long non-coding RNA LIP interacts with PARP-1 influencing the efficiency of base excision repair. Noncoding RNA Res 2024; 9:649-658. [PMID: 38577022 PMCID: PMC10987297 DOI: 10.1016/j.ncrna.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
In recent years, various long non-coding RNAs (lncRNAs) involved in DNA damage response (DDR) have been identified and studied to deepen our understanding. However, there are rare reports on the association between lncRNAs and base excision repair (BER). Our designed DNA microarray identified dozens of functionally unknown lncRNAs, and their transcription levels significantly increased upon exposure to DNA damage inducers. One of them, named LIP (Long noncoding RNA Interacts with PARP-1), exhibited a significant alteration in transcription in response to methyl methanesulfonate (MMS) and temozolomide (TMZ) treatments. LIP knockdown or knockout cell lines are sensitive to MMS and TMZ, indicating that LIP plays a crucial role in DDR. The loss or insufficiency of LIP significantly influences the efficiency of BER in human cells, and it suggests that LIP participates in the BER pathway. The interaction between LIP and a key factor in BER, poly (ADP-ribose) polymerase 1 (PARP-1), has been confirmed. We identified and characterized LIP, a lncRNA, which is involved in DDR, significantly influences BER efficiency, and interacts with the BER key factor PARP-1. This advances our understanding of the connection between lncRNAs and BER, presenting the potential for the discovery of new drug targets.
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Affiliation(s)
- You Zuo
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Jiaqian He
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Zheng Zhou
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Jingjing Sun
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Can Ouyang
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Hui Huang
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Yajuan Wang
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Hairong Liu
- College of Material Science and Engineering, Hunan University, Changsha, 410082, PR China
| | - Simon H. Reed
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
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2
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Qu H, Wang Y, Yan Q, Fan C, Zhang X, Wang D, Guo C, Chen P, Shi L, Liao Q, Zhou M, Wang F, Zeng Z, Xiang B, Xiong W. CircCDYL2 bolsters radiotherapy resistance in nasopharyngeal carcinoma by promoting RAD51 translation initiation for enhanced homologous recombination repair. J Exp Clin Cancer Res 2024; 43:122. [PMID: 38654320 PMCID: PMC11036759 DOI: 10.1186/s13046-024-03049-0] [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: 01/11/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Radiation therapy stands to be one of the primary approaches in the clinical treatment of malignant tumors. Nasopharyngeal Carcinoma, a malignancy predominantly treated with radiation therapy, provides an invaluable model for investigating the mechanisms underlying radiation therapy resistance in cancer. While some reports have suggested the involvement of circRNAs in modulating resistance to radiation therapy, the underpinning mechanisms remain unclear. METHODS RT-qPCR and in situ hybridization were used to detect the expression level of circCDYL2 in nasopharyngeal carcinoma tissue samples. The effect of circCDYL2 on radiotherapy resistance in nasopharyngeal carcinoma was demonstrated by in vitro and in vivo functional experiments. The HR-GFP reporter assay determined that circCDYL2 affected homologous recombination repair. RNA pull down, RIP, western blotting, IF, and polysome profiling assays were used to verify that circCDYL2 promoted the translation of RAD51 by binding to EIF3D protein. RESULTS We have identified circCDYL2 as highly expressed in nasopharyngeal carcinoma tissues, and it was closely associated with poor prognosis. In vitro and in vivo experiments demonstrate that circCDYL2 plays a pivotal role in promoting radiotherapy resistance in nasopharyngeal carcinoma. Our investigation unveils a specific mechanism by which circCDYL2, acting as a scaffold molecule, recruits eukaryotic translation initiation factor 3 subunit D protein (EIF3D) to the 5'-UTR of RAD51 mRNA, a crucial component of the DNA damage repair pathway to facilitate the initiation of RAD51 translation and enhance homologous recombination repair capability, and ultimately leads to radiotherapy resistance in nasopharyngeal carcinoma. CONCLUSIONS These findings establish a novel role of the circCDYL2/EIF3D/RAD51 axis in nasopharyngeal carcinoma radiotherapy resistance. Our work not only sheds light on the underlying molecular mechanism but also highlights the potential of circCDYL2 as a therapeutic sensitization target and a promising prognostic molecular marker for nasopharyngeal carcinoma.
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Affiliation(s)
- Hongke Qu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Yumin Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
| | - Qijia Yan
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Xiangyan Zhang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Dan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Pan Chen
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Lei Shi
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China.
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3
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De Bragança S, Dillingham MS, Moreno-Herrero F. Recent insights into eukaryotic double-strand DNA break repair unveiled by single-molecule methods. Trends Genet 2023; 39:924-940. [PMID: 37806853 DOI: 10.1016/j.tig.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
Genome integrity and maintenance are essential for the viability of all organisms. A wide variety of DNA damage types have been described, but double-strand breaks (DSBs) stand out as one of the most toxic DNA lesions. Two major pathways account for the repair of DSBs: homologous recombination (HR) and non-homologous end joining (NHEJ). Both pathways involve complex DNA transactions catalyzed by proteins that sequentially or cooperatively work to repair the damage. Single-molecule methods allow visualization of these complex transactions and characterization of the protein:DNA intermediates of DNA repair, ultimately allowing a comprehensive breakdown of the mechanisms underlying each pathway. We review current understanding of the HR and NHEJ responses to DSBs in eukaryotic cells, with a particular emphasis on recent advances through the use of single-molecule techniques.
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Affiliation(s)
- Sara De Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Mark S Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain.
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4
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Chen Y, Shen H, Liu T, Cao K, Wan Z, Du Z, Wang H, Yu Y, Ma S, Lu E, Zhang W, Cai J, Gao F, Yang Y. ATR-binding lncRNA ScaRNA2 promotes cancer resistance through facilitating efficient DNA end resection during homologous recombination repair. J Exp Clin Cancer Res 2023; 42:256. [PMID: 37775817 PMCID: PMC10542231 DOI: 10.1186/s13046-023-02829-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/12/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Our previous study first showed that ATR-binding long noncoding RNA (lncRNA) is necessary for ATR function and promotes cancer resistance. However, the specific lncRNAs instrumental in ATR activation remain largely unclear, which limits our comprehensive understanding of this critical biological process. METHODS RNA immunoprecipitation (RIP) followed by RNA sequencing was employed to identify ATR-binding lncRNAs, which were further validated using RIP-qPCR assays. Immunofluorescence staining and Western blotting were applied to detect the activation of DNA damage repair factors. After the effect of scaRNA2 on cellular sensitivity to DNA-damaging reagents was determined, the effects of scaRNA2 on radiotherapy were investigated in patient-derived organoids and xenograft preclinical models. The clinical relevance of scaRNA2 was also validated in tissues isolated from rectal cancer patients. RESULTS ScaRNA2 was identified as the most enriched ATR-binding lncRNA and was found to be essential for homologous recombination (HR) mediated DNA damage repair. Furthermore, scaRNA2 knockdown abrogated the recruitment of ATR and its substrates in response to DNA damage. Mechanistically, scaRNA2 was observed to be necessary for Exo1-mediated DNA end resection and bridged the MRN complex to ATR activation. Knockdown of scaRNA2 effectively increased the sensitivity of cancer cells to multiple kinds of DNA damage-related chemoradiotherapy. Preclinically, knockdown of scaRNA2 improved the effects of radiotherapy on patient-derived organoids and xenograft models. Finally, an increase in scaRNA2 colocalized with ATR was also found in clinical patients who were resistant to radiotherapy. CONCLUSIONS ScaRNA2 was identified as the most abundant lncRNA bound to ATR and was demonstrated to bridge DNA end resection to ATR activation; thus, it could be applied as a potent target for combined cancer treatments with chemoradiotherapy.
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Affiliation(s)
- Yuanyuan Chen
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - Hui Shen
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
- Department of Central Laboratory, The First Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Tingting Liu
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - Kun Cao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - Zhijie Wan
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - Zhipeng Du
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang, China
| | - Hang Wang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - Yue Yu
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Shengzhe Ma
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Edward Lu
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - Wei Zhang
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China.
| | - Jianming Cai
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang, China.
| | - Fu Gao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China.
| | - Yanyong Yang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China.
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5
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De Bragança S, Aicart-Ramos C, Arribas-Bosacoma R, Rivera-Calzada A, Unfried JP, Prats-Mari L, Marin-Baquero M, Fortes P, Llorca O, Moreno-Herrero F. APLF and long non-coding RNA NIHCOLE promote stable DNA synapsis in non-homologous end joining. Cell Rep 2023; 42:111917. [PMID: 36640344 DOI: 10.1016/j.celrep.2022.111917] [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: 06/08/2022] [Revised: 10/26/2022] [Accepted: 12/13/2022] [Indexed: 01/01/2023] Open
Abstract
The synapsis of DNA ends is a critical step for the repair of double-strand breaks by non-homologous end joining (NHEJ). This is performed by a multicomponent protein complex assembled around Ku70-Ku80 heterodimers and regulated by accessory factors, including long non-coding RNAs, through poorly understood mechanisms. Here, we use magnetic tweezers to investigate the contributions of core NHEJ proteins and APLF and lncRNA NIHCOLE to DNA synapsis. APLF stabilizes DNA end bridging and, together with Ku70-Ku80, establishes a minimal complex that supports DNA synapsis for several minutes under piconewton forces. We find the C-terminal acidic region of APLF to be critical for bridging. NIHCOLE increases the dwell time of the synapses by Ku70-Ku80 and APLF. This effect is further enhanced by a small and structured RNA domain within NIHCOLE. We propose a model where Ku70-Ku80 can simultaneously bind DNA, APLF, and structured RNAs to promote the stable joining of DNA ends.
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Affiliation(s)
- Sara De Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Raquel Arribas-Bosacoma
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Angel Rivera-Calzada
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Juan Pablo Unfried
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel; Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Laura Prats-Mari
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Mikel Marin-Baquero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain; Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid, Spain
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain.
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain.
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6
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The N-Myc-responsive lncRNA MILIP promotes DNA double-strand break repair through non-homologous end joining. Proc Natl Acad Sci U S A 2022; 119:e2208904119. [PMID: 36445966 PMCID: PMC9894261 DOI: 10.1073/pnas.2208904119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The protooncoprotein N-Myc, which is overexpressed in approximately 25% of neuroblastomas as the consequence of MYCN gene amplification, has long been postulated to regulate DNA double-strand break (DSB) repair in neuroblastoma cells, but experimental evidence of this function is presently scant. Here, we show that N-Myc transcriptionally activates the long noncoding RNA MILIP to promote nonhomologous end-joining (NHEJ) DNA repair through facilitating Ku70-Ku80 heterodimerization in neuroblastoma cells. High MILIP expression was associated with poor outcome and appeared as an independent prognostic factor in neuroblastoma patients. Knockdown of MILIP reduced neuroblastoma cell viability through the induction of apoptosis and inhibition of proliferation, retarded neuroblastoma xenograft growth, and sensitized neuroblastoma cells to DNA-damaging therapeutics. The effect of MILIP knockdown was associated with the accumulation of DNA DSBs in neuroblastoma cells largely due to decreased activity of the NHEJ DNA repair pathway. Mechanistical investigations revealed that binding of MILIP to Ku70 and Ku80 increased their heterodimerization, and this was required for MILIP-mediated promotion of NHEJ DNA repair. Disrupting the interaction between MILIP and Ku70 or Ku80 increased DNA DSBs and reduced cell viability with therapeutic potential revealed where targeting MILIP using Gapmers cooperated with the DNA-damaging drug cisplatin to inhibit neuroblastoma growth in vivo. Collectively, our findings identify MILIP as an N-Myc downstream effector critical for activation of the NHEJ DNA repair pathway in neuroblastoma cells, with practical implications of MILIP targeting, alone and in combination with DNA-damaging therapeutics, for neuroblastoma treatment.
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7
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CCAR2 functions downstream of the Shieldin complex to promote double-strand break end-joining. Proc Natl Acad Sci U S A 2022; 119:e2214935119. [PMID: 36442094 PMCID: PMC9894118 DOI: 10.1073/pnas.2214935119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The 53BP1-RIF1 pathway restricts the resection of DNA double-strand breaks (DSBs) and promotes blunt end-ligation by non-homologous end joining (NHEJ) repair. The Shieldin complex is a downstream effector of the 53BP1-RIF1 pathway. Here, we identify a component of this pathway, CCAR2/DBC1, which is also required for restriction of DNA end-resection. CCAR2 co-immunoprecipitates with the Shieldin complex, and knockout of CCAR2 in a BRCA1-deficient cell line results in elevated DSB end-resection, RAD51 loading, and PARP inhibitor (PARPi) resistance. Knockout of CCAR2 is epistatic with knockout of other Shieldin proteins. The S1-like RNA-binding domain of CCAR2 is required for its interaction with the Shieldin complex and for suppression of DSB end-resection. CCAR2 functions downstream of the Shieldin complex, and CCAR2 knockout cells have delayed resolution of Shieldin complex foci. Forkhead-associated (FHA)-dependent targeting of CCAR2 to DSB sites re-sensitized BRCA1-/-SHLD2-/- cells to PARPi. Taken together, CCAR2 is a functional component of the 53BP1-RIF1 pathway, promotes the refill of resected DSBs, and suppresses homologous recombination.
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8
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Agostini M, Mancini M, Candi E. Long non-coding RNAs affecting cell metabolism in cancer. Biol Direct 2022; 17:26. [PMID: 36182907 PMCID: PMC9526990 DOI: 10.1186/s13062-022-00341-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/27/2021] [Indexed: 11/10/2022] Open
Abstract
Metabolic reprogramming is commonly recognized as one important hallmark of cancers. Cancer cells present significant alteration of glucose metabolism, oxidative phosphorylation, and lipid metabolism. Recent findings demonstrated that long non-coding RNAs control cancer development and progression by modulating cell metabolism. Here, we give an overview of breast cancer metabolic reprogramming and the role of long non-coding RNAs in driving cancer-specific metabolic alteration.
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Affiliation(s)
- Massimiliano Agostini
- Department Experimental Medicine, University of Rome "Tor Vergata", TOR, Via Montpellier,1, 00133, Rome, Italy
| | - Mara Mancini
- IDI-IRCCS, Via Monti di Creta 104, 00166, Rome, Italy
| | - Eleonora Candi
- Department Experimental Medicine, University of Rome "Tor Vergata", TOR, Via Montpellier,1, 00133, Rome, Italy. .,IDI-IRCCS, Via Monti di Creta 104, 00166, Rome, Italy.
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9
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Yang K, Liang X, Wen K. Long non‑coding RNAs interact with RNA‑binding proteins to regulate genomic instability in cancer cells (Review). Oncol Rep 2022; 48:175. [PMID: 36004472 PMCID: PMC9478986 DOI: 10.3892/or.2022.8390] [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: 06/20/2022] [Accepted: 07/27/2022] [Indexed: 11/05/2022] Open
Abstract
Genomic instability, a feature of most cancers, contributes to malignant cell transformation and cancer progression due to the accumulation of genetic alterations. Genomic instability is reflected at numerous levels, from single nucleotide to the chromosome levels. However, the exact molecular mechanisms and regulators of genomic instability in cancer remain unclear. Growing evidence indicates that the binding of long non-coding RNAs (lncRNAs) to protein chaperones confers a variety of regulatory functions, including managing of genomic instability. The aim of the present review was to examine the roles of mitosis, telomeres, DNA repair, and epigenetics in genomic instability, and the mechanisms by which lncRNAs regulate them by binding proteins in cancer cells. This review contributes to our understanding of the role of lncRNAs and genomic instability in cancer and can potentially provide entry points and molecular targets for cancer therapies.
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Affiliation(s)
- Kai Yang
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Xiaoxiang Liang
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Kunming Wen
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
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10
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Ali A, Xiao W, Babar ME, Bi Y. Double-Stranded Break Repair in Mammalian Cells and Precise Genome Editing. Genes (Basel) 2022; 13:genes13050737. [PMID: 35627122 PMCID: PMC9142082 DOI: 10.3390/genes13050737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, double-strand breaks (DSBs) are repaired predominantly by error-prone non-homologous end joining (NHEJ), but less prevalently by error-free template-dependent homologous recombination (HR). DSB repair pathway selection is the bedrock for genome editing. NHEJ results in random mutations when repairing DSB, while HR induces high-fidelity sequence-specific variations, but with an undesirable low efficiency. In this review, we first discuss the latest insights into the action mode of NHEJ and HR in a panoramic view. We then propose the future direction of genome editing by virtue of these advancements. We suggest that by switching NHEJ to HR, full fidelity genome editing and robust gene knock-in could be enabled. We also envision that RNA molecules could be repurposed by RNA-templated DSB repair to mediate precise genetic editing.
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Affiliation(s)
- Akhtar Ali
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan
| | - Wei Xiao
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
| | - Masroor Ellahi Babar
- The University of Agriculture Dera Ismail Khan, Dera Ismail Khan 29220, Pakistan;
| | - Yanzhen Bi
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Correspondence: ; Tel.: +86-151-0714-8708
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11
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Zhang X, Zheng S, Hu C, Li G, Lin H, Xia R, Ye Y, He R, Li Z, Lin Q, Chen R, Zhou Q. Cancer-associated fibroblast-induced lncRNA UPK1A-AS1 confers platinum resistance in pancreatic cancer via efficient double-strand break repair. Oncogene 2022; 41:2372-2389. [PMID: 35264742 PMCID: PMC9010302 DOI: 10.1038/s41388-022-02253-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/06/2022] [Accepted: 02/16/2022] [Indexed: 12/27/2022]
Abstract
The tumor stroma of pancreatic ductal adenocarcinoma (PDAC) is characterized by an abundant and heterogeneous population of cancer-associated fibroblasts (CAFs), which are critically involved in chemoresistance. However, the underlying mechanism of CAFs in chemoresistance is unclear. Here, we show that CAFR, a CAF subset derived from platinum-resistant PDAC patients, assumes an iCAF phenotype and produces more IL8 than CAFS isolated from platinum-sensitive PDAC patients. CAFR-derived IL8 promotes oxaliplatin chemoresistance in PDAC. Based on long noncoding RNA (lncRNA) profiling in tumor cells incubated with CAF-CM, we found that UPK1A-AS1, whose expression is directly induced by IL8/NF-kappa B signaling, functions as a chemoresistance-promoting lncRNA and is critical for active IL8-induced oxaliplatin resistance. Impressively, blocking the activation of UPK1A-AS1 expression increases the oxaliplatin sensitivity of tumor cells in vivo. Mechanistically, UPK1A-AS1 strengthens the interaction between Ku70 and Ku80 to facilitate nonhomologous end joining (NHEJ), thereby enhancing DNA double-strand break (DSB) repair. Clinically, UPK1A-AS1 expression is positively correlated with IL8 expression, a poor chemotherapeutic response and a shorter progression-free survival (PFS) time in advanced PDAC patients. Collectively, our study reveals a lncRNA-mediated mechanism of CAF-derived paracrine IL8-dependent oxaliplatin resistance and highlights UPK1A-AS1 as a potential therapeutic target.
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Affiliation(s)
- Xiang Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, People's Republic of China
- Department of Pancreatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, People's Republic of China
| | - Shangyou Zheng
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, People's Republic of China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Chonghui Hu
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, People's Republic of China
- Guangdong cardiovascular Institute, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Guolin Li
- Department of Hepatobiliary, Pancreatic and Splenic surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, Guangdong, People's Republic of China
| | - Hongcao Lin
- General Surgery of Shenshan Medical Center, Memorial Hospital of Sun Yat-sen University, Shanwei, 516600, Guangdong, People's Republic of China
| | - Renpeng Xia
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, People's Republic of China
- Department of Neonatal/General Surgery, Hunan Children's Hospital, Changsha, 410007, Hunan, People's Republic of China
| | - Yuancheng Ye
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, People's Republic of China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Rihua He
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Zhihua Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, People's Republic of China
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, People's Republic of China
| | - Qing Lin
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, People's Republic of China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
- School of medicine, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China.
| | - Rufu Chen
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, People's Republic of China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
- Guangdong cardiovascular Institute, Guangzhou, 510080, Guangdong, People's Republic of China.
- School of medicine, South China University of Technology, Guangzhou, 510006, Guangdong, People's Republic of China.
| | - Quanbo Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, People's Republic of China.
- Department of Pancreatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, People's Republic of China.
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12
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Xiao H, Zhang M, Wu H, Wu J, Hu X, Pei X, Li D, Zhao L, Hua Q, Meng B, Zhang X, Peng L, Cheng X, Li Z, Yang W, Zhang Q, Zhang Y, Lu Y, Pan Z. CIRKIL Exacerbates Cardiac Ischemia/Reperfusion Injury by Interacting With Ku70. Circ Res 2022; 130:e3-e17. [PMID: 35105170 DOI: 10.1161/circresaha.121.318992] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Ku70 participates in several pathological processes through mediating repair of DNA double-strand breaks. Our previous study has identified a highly conserved long noncoding RNA cardiac ischemia reperfusion associated Ku70 interacting lncRNA (CIRKIL) that was upregulated in myocardial infarction. The study aims to investigate whether CIRKIL regulates myocardial ischemia/reperfusion (I/R) through binding to Ku70. METHODS CIRKIL transgenic and knockout mice were subjected to 45-minute ischemia and 24-hour reperfusion to establish myocardial I/R model. RNA pull-down and RNA immunoprecipitation assay were used to detect the interaction between CIRKIL and Ku70. RESULTS The expression of CIRKIL was increased in I/R myocardium and H2O2-treated cardiomyocytes. Overexpression of CIRKIL increased the expression of γH2A.X, a specific marker of DNA double-strand breaks and aggravated cardiomyocyte apoptosis, whereas knockdown of CIRKIL produced the opposite changes. Transgenic overexpression of CIRKIL aggravated cardiac dysfunction, enlarged infarct area, and worsened cardiomyocyte damage in I/R mice. Knockout of CIRKIL alleviated myocardial I/R injury. Mechanistically, CIRKIL directly bound to Ku70 to subsequently decrease nuclear translocation of Ku70 and impair DNA double-strand breaks repair. Concurrent overexpression of Ku70 mitigated CIRKIL overexpression-induced myocardial I/R injury. Furthermore, knockdown of human CIRKIL significantly suppressed cell damage induced by H2O2 in adult human ventricular cardiomyocytes and human induced pluripotent stem cell-derived cardiomyocytes. CONCLUSIONS CIRKIL is a detrimental factor in I/R injury acting via regulating nuclear translocation of Ku70 and DNA double-strand breaks repair. Thus, CIRKIL might be considered as a novel molecular target for the treatment of cardiac conditions associated with I/R injury.
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Affiliation(s)
- Hongwen Xiao
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Mingyu Zhang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Hao Wu
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.).,College of Pharmacy and Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin Medical University, P.R. China. (H.W., D.L., Q.H., Y.L.)
| | - Jiaxu Wu
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Xiaoxi Hu
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Xinyu Pei
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Danyang Li
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.).,College of Pharmacy and Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin Medical University, P.R. China. (H.W., D.L., Q.H., Y.L.)
| | - Lu Zhao
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Qi Hua
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.).,College of Pharmacy and Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin Medical University, P.R. China. (H.W., D.L., Q.H., Y.L.)
| | - Bo Meng
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Xiaowen Zhang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Lili Peng
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Xiaoling Cheng
- Department of Medicinal Chemistry, Harbin Medical University, P.R. China. (X.C.)
| | - Zhuoyun Li
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Wanqi Yang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Qi Zhang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Yang Zhang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Yanjie Lu
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.).,College of Pharmacy and Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin Medical University, P.R. China. (H.W., D.L., Q.H., Y.L.)
| | - Zhenwei Pan
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
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13
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Unfried JP, Marín-Baquero M, Rivera-Calzada Á, Razquin N, Martín-Cuevas EM, de Bragança S, Aicart-Ramos C, McCoy C, Prats-Mari L, Arribas-Bosacoma R, Lee L, Caruso S, Zucman-Rossi J, Sangro B, Williams G, Moreno-Herrero F, Llorca O, Lees-Miller SP, Fortes P. Long Noncoding RNA NIHCOLE Promotes Ligation Efficiency of DNA Double-Strand Breaks in Hepatocellular Carcinoma. Cancer Res 2021; 81:4910-4925. [PMID: 34321241 PMCID: PMC8488005 DOI: 10.1158/0008-5472.can-21-0463] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/25/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Abstract
Long noncoding RNAs (lncRNA) are emerging as key players in cancer as parts of poorly understood molecular mechanisms. Here, we investigated lncRNAs that play a role in hepatocellular carcinoma (HCC) and identified NIHCOLE, a novel lncRNA induced in HCC with oncogenic potential and a role in the ligation efficiency of DNA double-stranded breaks (DSB). NIHCOLE expression was associated with poor prognosis and survival of HCC patients. Depletion of NIHCOLE from HCC cells led to impaired proliferation and increased apoptosis. NIHCOLE deficiency led to accumulation of DNA damage due to a specific decrease in the activity of the nonhomologous end-joining (NHEJ) pathway of DSB repair. DNA damage induction in NIHCOLE-depleted cells further decreased HCC cell growth. NIHCOLE was associated with DSB markers and recruited several molecules of the Ku70/Ku80 heterodimer. Further, NIHCOLE putative structural domains supported stable multimeric complexes formed by several NHEJ factors including Ku70/80, APLF, XRCC4, and DNA ligase IV. NHEJ reconstitution assays showed that NIHCOLE promoted the ligation efficiency of blunt-ended DSBs. Collectively, these data show that NIHCOLE serves as a scaffold and facilitator of NHEJ machinery and confers an advantage to HCC cells, which could be exploited as a targetable vulnerability. SIGNIFICANCE: This study characterizes the role of lncRNA NIHCOLE in DNA repair and cellular fitness in HCC, thus implicating it as a therapeutic target.See related commentary by Barcena-Varela and Lujambio, p. 4899.
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MESH Headings
- Biomarkers, Tumor
- Carcinoma, Hepatocellular/diagnosis
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/mortality
- Cell Line, Tumor
- DNA Breaks, Double-Stranded
- DNA End-Joining Repair
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- High-Throughput Nucleotide Sequencing
- Humans
- Liver Neoplasms/diagnosis
- Liver Neoplasms/genetics
- Liver Neoplasms/mortality
- Models, Biological
- Nucleic Acid Conformation
- Nucleotide Motifs
- Prognosis
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
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Affiliation(s)
- Juan P Unfried
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain.
| | - Mikel Marín-Baquero
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Ángel Rivera-Calzada
- Structural Biology Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Nerea Razquin
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Eva M Martín-Cuevas
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sara de Bragança
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Christopher McCoy
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Laura Prats-Mari
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Raquel Arribas-Bosacoma
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, Functional Genomics of Solid Tumors laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, Functional Genomics of Solid Tumors laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France
| | - Bruno Sangro
- University of Navarra Clinic (CUN), Liver Unit, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid, Spain
| | - Gareth Williams
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Oscar Llorca
- Structural Biology Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain.
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid, Spain
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14
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Shaw A, Gullerova M. Home and Away: The Role of Non-Coding RNA in Intracellular and Intercellular DNA Damage Response. Genes (Basel) 2021; 12:1475. [PMID: 34680868 PMCID: PMC8535248 DOI: 10.3390/genes12101475] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/14/2022] Open
Abstract
Non-coding RNA (ncRNA) has recently emerged as a vital component of the DNA damage response (DDR), which was previously believed to be solely regulated by proteins. Many species of ncRNA can directly or indirectly influence DDR and enhance DNA repair, particularly in response to double-strand DNA breaks, which may hold therapeutic potential in the context of cancer. These include long non-coding RNA (lncRNA), microRNA, damage-induced lncRNA, DNA damage response small RNA, and DNA:RNA hybrid structures, which can be categorised as cis or trans based on the location of their synthesis relative to DNA damage sites. Mechanisms of RNA-dependent DDR include the recruitment or scaffolding of repair factors at DNA break sites, the regulation of repair factor expression, and the stabilisation of repair intermediates. DDR can also be communicated intercellularly via exosomes, leading to bystander responses in healthy neighbour cells to generate a population-wide response to damage. Many microRNA species have been directly implicated in the propagation of bystander DNA damage, autophagy, and radioresistance, which may prove significant for enhancing cancer treatment via radiotherapy. Here, we review recent developments centred around ncRNA and their contributions to intracellular and intercellular DDR mechanisms.
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Affiliation(s)
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK;
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15
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VAV2 is required for DNA repair and implicated in cancer radiotherapy resistance. Signal Transduct Target Ther 2021; 6:322. [PMID: 34462423 PMCID: PMC8405816 DOI: 10.1038/s41392-021-00735-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 07/19/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023] Open
Abstract
Radiotherapy remains the mainstay for treatment of various types of human cancer; however, the clinical efficacy is often limited by radioresistance, in which the underlying mechanism is largely unknown. Here, using esophageal squamous cell carcinoma (ESCC) as a model, we demonstrate that guanine nucleotide exchange factor 2 (VAV2), which is overexpressed in most human cancers, plays an important role in primary and secondary radioresistance. We have discovered for the first time that VAV2 is required for the Ku70/Ku80 complex formation and participates in non-homologous end joining repair of DNA damages caused by ionizing radiation. We show that VAV2 overexpression substantially upregulates signal transducer and activator of transcription 1 (STAT1) and the STAT1 inhibitor Fludarabine can significantly promote the sensitivity of radioresistant patient-derived ESCC xenografts in vivo in mice to radiotherapy. These results shed new light on the mechanism of cancer radioresistance, which may be important for improving clinical radiotherapy.
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16
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Audoynaud C, Vagner S, Lambert S. Non-homologous end-joining at challenged replication forks: an RNA connection? Trends Genet 2021; 37:973-985. [PMID: 34238592 DOI: 10.1016/j.tig.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022]
Abstract
Defective DNA replication, known as 'replication stress', is a source of DNA damage, a hallmark of numerous human diseases, including cancer, developmental defect, neurological disorders, and premature aging. Recent work indicates that non-homologous end-joining (NHEJ) is unexpectedly active during DNA replication to repair replication-born DNA lesions and to safeguard replication fork integrity. However, erroneous NHEJ events are deleterious to genome stability. RNAs are novel regulators of NHEJ activity through their ability to modulate the assembly of repair complexes in trans. At DNA damage sites, RNAs and DNA-embedded ribonucleotides modulate repair efficiency and fidelity. We discuss here how RNAs and associated proteins, including RNA binding proteins, may regulate NHEJ to sustain genome stability during DNA replication.
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Affiliation(s)
- Charlotte Audoynaud
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Stéphan Vagner
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France.
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17
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Fijen C, Rothenberg E. The evolving complexity of DNA damage foci: RNA, condensates and chromatin in DNA double-strand break repair. DNA Repair (Amst) 2021; 105:103170. [PMID: 34256335 DOI: 10.1016/j.dnarep.2021.103170] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/08/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023]
Abstract
Formation of biomolecular condensates is increasingly recognized as a mechanism employed by cells to deal with stress and to optimize enzymatic reactions. Recent studies have characterized several DNA repair foci as phase-separated condensates, behaving like liquid droplets. Concomitantly, the apparent importance of long non-coding RNAs and RNA-binding proteins for the repair of double-strand breaks has raised many questions about their exact contribution to the repair process. Here we discuss how RNA molecules can participate in condensate formation and how RNA-binding proteins can act as molecular scaffolds. We furthermore summarize our current knowledge about how properties of condensates can influence the choice of repair pathway (homologous recombination or non-homologous end joining) and identify the open questions in this field of emerging importance.
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Affiliation(s)
- Carel Fijen
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
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18
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Niu M, Shan M, Liu Y, Song Y, Han JG, Sun S, Liang XS, Zhang GQ. DCTPP1, an Oncogene Regulated by miR-378a-3p, Promotes Proliferation of Breast Cancer via DNA Repair Signaling Pathway. Front Oncol 2021; 11:641931. [PMID: 34113564 PMCID: PMC8185175 DOI: 10.3389/fonc.2021.641931] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
Breast cancer (BRCA) is one of the most deadly cancers worldwide, with poor survival rates that could be due to its high proliferation. Human all-alpha dCTP pyrophosphatase 1 (DCTPP1) is implicated in numerous diseases, including cancers. However, its role in BRCA is unclear. In this study, we used bioinformatic analyses of the ONCOMINE, UALCAN, and GEPIA databases to determine the expression pattern of DCTPP1 in BRCA. We found that elevated DCTPP1 levels correlate with poor BRCA prognosis. DCTPP1 silencing inhibited BRCA cell proliferation and induced apoptosis in vitro, as well as in vivo. Our data show that this tumorigenic effect depends on DNA repair signaling. Moreover, we found that DCTPP1 is directly modulated by miR-378a-3p, whose downregulation is linked to BRCA progression. Our results showed down-regulation of miR-378a-3p in BRCA. Upregulation of miR-378a-3p, on the other hand, can inhibit BRCA cell growth and proliferation. This study shows that reduced miR-378a-3p level enhances DCTPP1 expression in BRCA, which promotes proliferation by activating DNA repair signaling in BRCA.
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Affiliation(s)
- Ming Niu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ming Shan
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yang Liu
- Research Institute of Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yanni Song
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ji-Guang Han
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shanshan Sun
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiao-Shuan Liang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Guo-Qiang Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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19
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Genetic variations associated with long noncoding RNAs. Essays Biochem 2020; 64:867-873. [DOI: 10.1042/ebc20200033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
Abstract
Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome, including the long noncoding RNA (lncRNA) regions. The changes at locus might produce numerous effects in a variety of aspects. Multiple bioinformatics resources and tools were also developed for systematically dealing with genetic variations associated with lncRNAs. Moreover, correlation of the genetic variations in lncRNAs with immune disease, cancers, and other disease as well as development process were all included for discussion. In this essay, we summarized how and in what aspects these changes would affect lncRNA functions.
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