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Takahashi K, Yan L, An N, Chida K, Tian W, Oshi M, Takabe K. RAD51 High-Expressed Hepatocellular Carcinomas are Associated With High Cell Proliferation. J Surg Res 2024; 302:250-258. [PMID: 39111128 DOI: 10.1016/j.jss.2024.07.046] [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: 03/15/2024] [Revised: 06/10/2024] [Accepted: 07/04/2024] [Indexed: 08/27/2024]
Abstract
INTRODUCTION RAD51 is a pivotal DNA repair gene managing double-stranded DNA break recognition and repair. RAD51 high expression was associated with adverse outcomes in other cancer types. This study aims to investigate the tumor microenvironment and immune landscape in the RAD51 high-expressed Hepatocellular Carcinoma (HCCs). METHODS A total of 467 patients from two large independent cohorts with clinical and transcriptomic data were obtained. The cohort was dichotomized based on the median RAD51 gene expression. xCell and Gene Set Enrichment Analysis (GSEA) were used. RESULTS RAD51 high-expressed HCCs were associated with worse recurrence-free, progression-free, disease-specific, and overall survival (all P < 0.05). While RAD51 high-expressed HCCs were associated with intratumoral heterogeneity, homologous recombination deficiency, and fraction altered scores, mutation or neoantigens were not increased in this group. xCell analysis demonstrated inconsistent immune cell infiltration between two cohorts. Cytolytic activity as well as GSEA with immune-related gene sets also demonstrated inconsistent results between two cohorts as well. On the other hand, RAD51 expression was significantly increased in higher-grade tumors, larger tumors, and higher clinical stages. RAD51 high-expressed HCCs were found to have elevated proliferation score. Furthermore, GSEA exhibited significant enrichment of all the cell proliferation-related gene sets in the Hallmark collection, including E2F targets, G2M checkpoint, Mitotic spindle, MYC targets, and MTORC1 signaling consistently in both cohorts (all false discovery rate < 0.25). CONCLUSIONS RAD51 high-expressed HCCs were associated with worse survival and with increased cell proliferation and were not necessarily associated with immune infiltration or inflammation.
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Affiliation(s)
- Keita Takahashi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Nan An
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Kohei Chida
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Wanqing Tian
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York; Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York; Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan; Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York; Department of Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan; Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan.
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Mills M, Emori C, Kumar P, Boucher Z, George J, Bolcun-Filas E. Single-cell and bulk transcriptional profiling of mouse ovaries reveals novel genes and pathways associated with DNA damage response in oocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578648. [PMID: 38352597 PMCID: PMC10862846 DOI: 10.1101/2024.02.02.578648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Immature oocytes enclosed in primordial follicles stored in female ovaries are under constant threat of DNA damage induced by endogenous and exogenous factors. Checkpoint kinase 2 (CHEK2) is a key mediator of the DNA damage response in all cells. Genetic studies have shown that CHEK2 and its downstream targets, p53 and TAp63, regulate primordial follicle elimination in response to DNA damage, however the mechanism leading to their demise is still poorly characterized. Single-cell and bulk RNA sequencing were used to determine the DNA damage response in wildtype and Chek2-deficient ovaries. A low but oocyte-lethal dose of ionizing radiation induces a DNA damage response in ovarian cells that is solely dependent on CHEK2. DNA damage activates multiple ovarian response pathways related to apoptosis, p53, interferon signaling, inflammation, cell adhesion, and intercellular communication. These pathways are differentially employed by different ovarian cell types, with oocytes disproportionately affected by radiation. Novel genes and pathways are induced by radiation specifically in oocytes, shedding light on their sensitivity to DNA damage, and implicating a coordinated response between oocytes and pre-granulosa cells within the follicle. These findings provide a foundation for future studies on the specific mechanisms regulating oocyte survival in the context of aging, as well as therapeutic and environmental genotoxic exposures.
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Affiliation(s)
- Monique Mills
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- The Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
| | - Chihiro Emori
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 5650871, Japan
| | - Parveen Kumar
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Zachary Boucher
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Joshy George
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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Kim Y, Kang BE, Gariani K, Gariani J, Lee J, Kim HJ, Lee CW, Schoonjans K, Auwerx J, Ryu D. Loss of hepatic Sirt7 accelerates diethylnitrosamine (DEN)-induced formation of hepatocellular carcinoma by impairing DNA damage repair. BMB Rep 2024; 57:98-103. [PMID: 38303560 PMCID: PMC10910089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/16/2023] [Accepted: 12/07/2023] [Indexed: 02/03/2024] Open
Abstract
The mammalian sirtuin family (SIRT1-SIRT7) has shown diverse biological roles in the regulation and maintenance of genome stability under genotoxic stress. SIRT7, one of the least studied sirtuin, has been demonstrated to be a key factor for DNA damage response (DDR). However, conflicting results have proposed that Sirt7 is an oncogenic factor to promote transformation in cancer cells. To address this inconsistency, we investigated properties of SIRT7 in hepatocellular carcinoma (HCC) regulation under DNA damage and found that loss of hepatic Sirt7 accelerated HCC progression. Specifically, the number, size, and volume of hepatic tumor colonies in diethylnitrosamine (DEN) injected Sirt7-deficient liver were markedly enhanced. Further, levels of HCC progression markers and pro-inflammatory cytokines were significantly elevated in the absence of hepatic Sirt7, unlike those in the control. In chromatin, SIRT7 was stabilized and colocalized to damage site by inhibiting the induction of γH2AX under DNA damage. Together, our findings suggest that SIRT7 is a crucial factor for DNA damage repair and that hepatic loss-of-Sirt7 can promote genomic instability and accelerate HCC development, unlike early studies describing that Sirt7 is an oncogenic factor [BMB Reports 2024; 57(2): 98-103].
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Affiliation(s)
- Yuna Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Baeki E. Kang
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea, Gwangju 61005, Korea
| | - Karim Gariani
- Service of Endocrinology, Diabetes, Nutrition and Therapeutic Patient Education, Geneva University Hospitals, Geneva 1205, Korea
| | - Joanna Gariani
- Department of Radiology, Hirslanden Grangettes Clinic, Geneva 1224, Switzerland, Gwangju 61005, Korea
| | - Junguee Lee
- Department of Pathology, Konyang University, Daejeon 35365, Korea, Gwangju 61005, Korea
| | - Hyun-Jin Kim
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea, Gwangju 61005, Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Kristina Schoonjans
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne 1015, Switzerland, Gwangju 61005, Korea
| | - Johan Auwerx
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne 1015, Switzerland, Gwangju 61005, Korea
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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4
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Lu Y, Wang S, Chi T, Zhao Y, Guo H, Wang H, Feng L. DNA damage repair-related gene signature for identifying the immune status and predicting the prognosis of hepatocellular carcinoma. Sci Rep 2023; 13:18978. [PMID: 37923899 PMCID: PMC10624694 DOI: 10.1038/s41598-023-45999-z] [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: 07/31/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
The heterogeneity of hepatocellular carcinoma (HCC) poses a challenge for accurate prognosis prediction. DNA damage repair genes (DDRGs) have an impact on a wide range of malignancies. However, the relevance of these genes in HCC prognosis has received little attention. In this study, we aimed to develop a prognostic signature to identify novel therapy options for HCC. We acquired mRNA expression profiles and clinical data for HCC patients from The Cancer Genome Atlas (TCGA) database. A polygenic prognostic model for HCC was constructed using selection operator Cox analysis and least absolute shrinkage. The model was validated using International Cancer Genome Consortium (ICGC) data. Overall survival (OS) between the high-risk and low-risk groups was compared using Kaplan‒Meier analysis. Independent predictors of OS were identified through both univariate and multivariate Cox analyses. To determine immune cell infiltration scores and activity in immune-related pathways, a single-sample gene set enrichment analysis was performed. The protein and mRNA expression levels of the prognostic genes between HCC and normal liver tissues were also examined by immunohistochemistry (IHC), immunofluorescence (IF) and quantitative real-time PCR (qRT-PCR). A novel ten-gene signature (CHD1L, HDAC1, KPNA2, MUTYH, PPP2R5B, NEIL3, POLR2L, RAD54B, RUVBL1 and SPP1) was established for HCC prognosis prediction. Patients in the high-risk group had worse OS than those in the low-risk group. Receiver operating characteristic curve analysis confirmed the predictive ability of this prognostic gene signature. Multivariate Cox analysis showed that the risk score was an independent predictor of OS. Functional analysis revealed a strong association with cell cycle and antigen binding pathways, and the risk score was highly correlated with tumor grade, tumor stage, and types of immune infiltrate. High expression levels of the prognostic genes were significantly correlated with increased sensitivity of cancer cells to antitumor drugs. IHC, IF and qRT-PCR all indicated that the prognostic genes were highly expressed in HCC relative to normal liver tissue, consistent with the results of bioinformatics analysis. Ten DDRGs were utilized to create a new signature for identifying the immunological state of HCC and predicting prognosis. In addition, blocking these genes could represent a promising treatment.
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Affiliation(s)
- Yongpan Lu
- Department of Plastic Surgery, Shandong University of Traditional Chinese Medicine, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Jingshi Road, Jinan, 250014, Shandong, China
| | - Sen Wang
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Tingting Chi
- Department of Acupuncture and Rehabilitation, The Affiliated Qingdao Hai Ci Hospital of Qingdao University (West Hospital Area), Qingdao, 266000, Shandong, China
| | - Yuli Zhao
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Huimin Guo
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Jining Medical College, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Haizheng Wang
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Li Feng
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China.
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Kauke-Navarro M, Noel OF, Knoedler L, Knoedler S, Panayi AC, Stoegner VA, Huelsboemer L, Pomahac B. Novel Strategies in Transplantation: Genetic Engineering and Vascularized Composite Allotransplantation. J Surg Res 2023; 291:176-186. [PMID: 37429217 DOI: 10.1016/j.jss.2023.04.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/18/2023] [Accepted: 04/30/2023] [Indexed: 07/12/2023]
Abstract
INTRODUCTION Despite the clinical success in vascularized composite allotransplantation (VCA), systemic immunosuppression remains necessary to prevent allograft rejection. Even with potent immunosuppressive regimens (tacrolimus, mycophenolate mofetil, and steroids), most patients experience several rejection episodes, often within the same year. The risk of systemic side effects must constantly be weighed against the risk of under-immunosuppression and, thus, acute and chronic rejection. In this context, genomic editing has emerged as a potential tool to minimize the need for toxic immunosuppressive regimens and has gained attention in the fields of solid organ transplantation and xenotransplantation. This strategy may also be relevant for the future of VCA. METHODS We discuss the topic of genetic engineering and review recent developments in this field that justify investigating tools such as clustered regularly interspaced short palindromic repeats/Cas9 in the context of VCA. RESULTS We propose specific strategies for VCA based on the most recent gene expression data. This includes the well-known strategy of tolerance induction. Specifically, targeting the interaction between antigen-presenting cells and recipient-derived T cells by CD40 knockout may be effective. The novelty for VCA is a discovery that donor-derived T lymphocytes may play a special role in allograft rejection of facial transplants. We suggest targeting these cells prior to transplantation (e.g., by ex vivo perfusion of the transplant) by knocking out genes necessary for the long-term persistence of donor-derived immune cells in the allograft. CONCLUSION Despite the demonstrated feasibility of VCA in recent years, continued improvements to immunomodulatory strategies using tools like clustered regularly interspaced short palindromic repeats/Cas9 could lead to the development of approaches that mitigate the limitations associated with rejection of this life-giving procedure.
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Affiliation(s)
- Martin Kauke-Navarro
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Division of Plastic and Reconstructive Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, Connecticut
| | - Olivier F Noel
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, Connecticut
| | - Leonard Knoedler
- Department of Plastic, Hand and Reconstructive Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Samuel Knoedler
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Adriana C Panayi
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Viola A Stoegner
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, Connecticut; Department of Plastic, Aesthetic, Hand and Reconstructive Surgery, Burn Center, Hannover Medical School, Hannover, Germany
| | - Lioba Huelsboemer
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, Connecticut; Institute of Musculoskeletal Medicine, University Hospital Muenster, Münster, Germany
| | - Bohdan Pomahac
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, Connecticut.
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Du Z, Zhang F, Liu L, Shen H, Liu T, Jin J, Yu N, Wan Z, Wang H, Hu X, Chen Y, Cai J. LncRNA ANRIL promotes HR repair through regulating PARP1 expression by sponging miR-7-5p in lung cancer. BMC Cancer 2023; 23:130. [PMID: 36755223 PMCID: PMC9906921 DOI: 10.1186/s12885-023-10593-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Radiotherapy is an important treatment for lung cancer, mainly by triggering DNA double-strand breaks to induce cell death. Blocking DNA damage repair can increase the radiosensitivity of tumor cells. Recent studies have identified long noncoding RNAs as key regulators in DNA damage repair. The lncRNA ANRIL was previously shown to be involved in homologous recombination (HR) repair, but its specific mechanism has not been fully elucidated. METHODS The downstream interacting miRNAs of ANRIL were predicted according to miRanda software. Fluorescence quantitative PCR was used to detect the expression levels of ANRIL and candidate miRNAs. Clone formation experiment and cell viability assays detect cell viability after ionizing radiation. Apoptosis assay was used to detect the apoptosis of cells after 8 h of ionizing radiation. Western blot analysis and immunofluorescence assays verified the protein expression levels of the downstream target molecule PARP1 of miR-7-5p and key molecules in the HR pathway. Fluorescent reporter gene experiments were used to verify the interaction between ANRIL and miR-7-5p and between miR-7-5p and PARP1. RESULTS Bioinformatics analysis and qPCR validation suggested that miR-7-5p might be a downstream molecule of ANRIL. The expression of miR-7-5p was up-regulated after knockdown of ANRIL, and the expression of miR-7-5p was down-regulated after overexpression of ANRIL. Meanwhile, there was a negative correlation between ANRIL and miR-7-5p expression changes before and after ionizing radiation. The luciferase reporter gene assay confirmed the existence of ANRIL binding site with miR-7-5p, and found that transfection of miR-7-5p inhibitor can reduce the radiation sensitivity of ANRIL-KD cells. A downstream target molecule of miR-7-5p related to HR repair, PARP1, was screened through website prediction. Subsequently, it was confirmed by Western blot and luciferase reporter assays that miR-7-5p could down-regulate the expression of PARP1, and there was a miR-7-5p binding site on the 3'UTR of PARP1 mRNA. This suggests that ANRIL may act as a competitive endogenous RNA to bind miR-7-5p and upregulate the expression of PARP1. Western blot and immunofluorescence staining were used to detect the expression changes of HR repair factors in ANRIL-KD cells after ionizing radiation, and it was found that knockdown of ANRIL can inhibit the expression of PARP1, BRCA1 and Rad51, hinder radiation-induced HR repair, and eventually result in resensitizing ANRIL-KD cells to ionizing radiation. CONCLUSIONS Our findings provide evidence that ANRIL targets the miR-7-5p/PARP1 axis to exert its regulatory effect on HR repair, suggesting that altering ANRIL expression may be a promising strategy to overcome radiation resistance.
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Affiliation(s)
- Zhipeng Du
- grid.268099.c0000 0001 0348 3990School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang P. R. China
| | - Fangxiao Zhang
- grid.268099.c0000 0001 0348 3990School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang P. R. China
| | - Lei Liu
- grid.417279.eDepartment of Oncology, General Hospital of Central Theater Command of Chinese People’s Liberation Army, Wuhan, Hubei P. R. China
| | - Hui Shen
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China
| | - Tingting Liu
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China
| | - Jing Jin
- grid.216417.70000 0001 0379 7164Department of Occupational and Environment Health, Xiangya School of Public Health, Central South University, Changsha, Hunan P. R. China
| | - Nanxi Yu
- grid.268099.c0000 0001 0348 3990School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang P. R. China
| | - Zhijie Wan
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China
| | - Hang Wang
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China
| | - Xuguang Hu
- Department of Gastrointestinal Surgery, Changhai Hospital, Shanghai, P. R. China.
| | - Yuanyuan Chen
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China. .,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, Zhejiang, P. R. China.
| | - Jianming Cai
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang, P. R. China. .,Department of Oncology, General Hospital of Central Theater Command of Chinese People's Liberation Army, Wuhan, Hubei, P. R. China. .,Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China.
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Smith MA, Van Alsten SC, Walens A, Damrauer JS, Maduekwe UN, Broaddus RR, Love MI, Troester MA, Hoadley KA. DNA Damage Repair Classifier Defines Distinct Groups in Hepatocellular Carcinoma. Cancers (Basel) 2022; 14:cancers14174282. [PMID: 36077818 PMCID: PMC9454479 DOI: 10.3390/cancers14174282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary DNA repair pathways have been implicated in hepatocellular carcinoma outcomes. We found that hepatocellular carcinomas (HCC) could be separated into two groups (high and low) based on the overall expression of genes involved in DNA repair. Among the low repair group, there were three subgroups, one of which shared features of the high repair group. Given the important role of liver in metabolism and detoxification and its regenerative capacity, proliferation and DNA damage responses are critical in subdividing major biological categories of liver tumors. High repair samples showed more proliferative and regenerative signatures and had poorer outcomes versus the low repair that were more associated with the genes involved in normal liver biology. These biological groups suggest that dysregulation in endogenous liver processes promotes a pro-tumorigenic microenvironment that may facilitate tumor progression or identify tumors that require more substantial clinical intervention. Abstract DNA repair pathways have been associated with variability in hepatocellular carcinoma (HCC) clinical outcomes, but the mechanism through which DNA repair varies as a function of liver regeneration and other HCC characteristics is poorly understood. We curated a panel of 199 genes representing 15 DNA repair pathways to identify DNA repair expression classes and evaluate their associations with liver features and clinicopathologic variables in The Cancer Genome Atlas (TCGA) HCC study. We identified two groups in HCC, defined by low or high expression across all DNA repair pathways. The low-repair group had lower grade and retained the expression of classical liver markers, whereas the high-repair group had more clinically aggressive features, increased p53 mutant-like gene expression, and high liver regenerative gene expression. These pronounced features overshadowed the variation in the low-repair subset, but when considered separately, the low-repair samples included three subgroups: L1, L2, and L3. L3 had high DNA repair expression with worse progression-free (HR 1.24, 95% CI 0.81–1.91) and overall (HR 1.63, 95% CI 0.98–2.71) survival. High-repair outcomes were also significantly worse compared with the L1 and L2 groups. HCCs vary in DNA repair expression, and a subset of tumors with high regeneration profoundly disrupts liver biology and poor prognosis.
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Affiliation(s)
- Markia A. Smith
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sarah C. Van Alsten
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrea Walens
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeffrey S. Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ugwuji N. Maduekwe
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Russell R. Broaddus
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael I. Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melissa A. Troester
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence:
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8
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Shadfar S, Brocardo M, Atkin JD. The Complex Mechanisms by Which Neurons Die Following DNA Damage in Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23052484. [PMID: 35269632 PMCID: PMC8910227 DOI: 10.3390/ijms23052484] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 01/18/2023] Open
Abstract
Human cells are exposed to numerous exogenous and endogenous insults every day. Unlike other molecules, DNA cannot be replaced by resynthesis, hence damage to DNA can have major consequences for the cell. The DNA damage response contains overlapping signalling networks that repair DNA and hence maintain genomic integrity, and aberrant DNA damage responses are increasingly described in neurodegenerative diseases. Furthermore, DNA repair declines during aging, which is the biggest risk factor for these conditions. If unrepaired, the accumulation of DNA damage results in death to eliminate cells with defective genomes. This is particularly important for postmitotic neurons because they have a limited capacity to proliferate, thus they must be maintained for life. Neuronal death is thus an important process in neurodegenerative disorders. In addition, the inability of neurons to divide renders them susceptible to senescence or re-entry to the cell cycle. The field of cell death has expanded significantly in recent years, and many new mechanisms have been described in various cell types, including neurons. Several of these mechanisms are linked to DNA damage. In this review, we provide an overview of the cell death pathways induced by DNA damage that are relevant to neurons and discuss the possible involvement of these mechanisms in neurodegenerative conditions.
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Affiliation(s)
- Sina Shadfar
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia; (S.S.); (M.B.)
| | - Mariana Brocardo
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia; (S.S.); (M.B.)
| | - Julie D. Atkin
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia; (S.S.); (M.B.)
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
- Correspondence:
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Meyenberg M, Ferreira da Silva J, Loizou JI. Tissue Specific DNA Repair Outcomes Shape the Landscape of Genome Editing. Front Genet 2021; 12:728520. [PMID: 34539755 PMCID: PMC8446275 DOI: 10.3389/fgene.2021.728520] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/05/2021] [Indexed: 12/26/2022] Open
Abstract
The use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 has moved from bench to bedside in less than 10years, realising the vision of correcting disease through genome editing. The accuracy and safety of this approach relies on the precise control of DNA damage and repair processes to achieve the desired editing outcomes. Strategies for modulating pathway choice for repairing CRISPR-mediated DNA double-strand breaks (DSBs) have advanced the genome editing field. However, the promise of correcting genetic diseases with CRISPR-Cas9 based therapies is restrained by a lack of insight into controlling desired editing outcomes in cells of different tissue origin. Here, we review recent developments and urge for a greater understanding of tissue specific DNA repair processes of CRISPR-induced DNA breaks. We propose that integrated mapping of tissue specific DNA repair processes will fundamentally empower the implementation of precise and safe genome editing therapies for a larger variety of diseases.
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Affiliation(s)
- Mathilde Meyenberg
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Joana Ferreira da Silva
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Joanna I. Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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10
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Ferreira da Silva J, Meyenberg M, Loizou JI. Tissue specificity of DNA repair: the CRISPR compass. Trends Genet 2021; 37:958-962. [PMID: 34392967 DOI: 10.1016/j.tig.2021.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/09/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas9-mediated genome editing holds great promise for the correction of pathogenic variants in humans. However, its therapeutic implementation is hampered due to unwanted editing outcomes. A better understanding of cell type- and tissue-specific DNA repair processes will ultimately enable precise control of editing outcomes for safer and effective therapies.
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Affiliation(s)
- Joana Ferreira da Silva
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Mathilde Meyenberg
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria.
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11
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Ben-Shlomo A, Deng N, Ding E, Yamamoto M, Mamelak A, Chesnokova V, Labadzhyan A, Melmed S. DNA damage and growth hormone hypersecretion in pituitary somatotroph adenomas. J Clin Invest 2021; 130:5738-5755. [PMID: 32673291 DOI: 10.1172/jci138540] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/14/2020] [Indexed: 12/22/2022] Open
Abstract
Drivers of sporadic benign pituitary adenoma growth are largely unknown. Whole-exome sequencing of 159 prospectively resected pituitary adenomas showed that somatic copy number alteration (SCNA) rather than mutation is a hallmark of hormone-secreting adenomas and that SCNAs correlate with adenoma phenotype. Using single-gene SCNA pathway analysis, we observed that both cAMP and Fanconi anemia DNA damage repair pathways were affected by SCNAs in growth hormone-secreting (GH-secreting) somatotroph adenomas. As somatotroph differentiation and GH secretion are dependent on cAMP activation and we previously showed DNA damage, aneuploidy, and senescence in somatotroph adenomas, we studied links between cAMP signaling and DNA damage. Stimulation of cAMP in C57BL/6 mouse primary pituitary cultures using forskolin or a long-acting GH-releasing hormone (GHRH) analog increased GH production and DNA damage measured by H2AX phosphorylation and a comet assay. Octreotide, a somatostatin receptor ligand that targets somatotroph adenoma GH secretion in patients with acromegaly, inhibited cAMP and GH and reversed DNA damage induction. In vivo long-acting GHRH treatment also induced pituitary DNA damage in mice. We conclude that cAMP, which induces somatotroph proliferation and GH secretion, may concomitantly induce DNA damage, potentially linking hormone hypersecretion to SCNA and genome instability. These results elucidating somatotroph adenoma pathophysiology identify pathways for targeted treatment.
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Affiliation(s)
| | - Nan Deng
- Biostatistics and Bioinformatics Research Center, Samuel Oschin Comprehensive Cancer Institute, and
| | | | | | - Adam Mamelak
- Pituitary Center, Department of Medicine.,Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
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12
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The Role of PARP1 in Monocyte and Macrophage Commitment and Specification: Future Perspectives and Limitations for the Treatment of Monocyte and Macrophage Relevant Diseases with PARP Inhibitors. Cells 2020; 9:cells9092040. [PMID: 32900001 PMCID: PMC7565932 DOI: 10.3390/cells9092040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022] Open
Abstract
Modulation of PARP1 expression, changes in its enzymatic activity, post-translational modifications, and inflammasome-dependent cleavage play an important role in the development of monocytes and numerous subtypes of highly specialized macrophages. Transcription of PARP1 is governed by the proliferation status of cells at each step of their development. Higher abundance of PARP1 in embryonic stem cells and in hematopoietic precursors supports their self-renewal and pluri-/multipotency, whereas a low level of the enzyme in monocytes determines the pattern of surface receptors and signal transducers that are functionally linked to the NFκB pathway. In macrophages, the involvement of PARP1 in regulation of transcription, signaling, inflammasome activity, metabolism, and redox balance supports macrophage polarization towards the pro-inflammatory phenotype (M1), which drives host defense against pathogens. On the other hand, it seems to limit the development of a variety of subsets of anti-inflammatory myeloid effectors (M2), which help to remove tissue debris and achieve healing. PARP inhibitors, which prevent protein ADP-ribosylation, and PARP1‒DNA traps, which capture the enzyme on chromatin, may allow us to modulate immune responses and the development of particular cell types. They can be also effective in the treatment of monocytic leukemia and other cancers by reverting the anti- to the proinflammatory phenotype in tumor-associated macrophages.
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13
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Bermúdez-Guzmán L, Leal A. DNA repair deficiency in neuropathogenesis: when all roads lead to mitochondria. Transl Neurodegener 2019; 8:14. [PMID: 31110700 PMCID: PMC6511134 DOI: 10.1186/s40035-019-0156-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/24/2019] [Indexed: 12/18/2022] Open
Abstract
Mutations in DNA repair enzymes can cause two neurological clinical manifestations: a developmental impairment and a degenerative disease. Polynucleotide kinase 3'-phosphatase (PNKP) is an enzyme that is actively involved in DNA repair in both single and double strand break repair systems. Mutations in this protein or others in the same pathway are responsible for a complex group of diseases with a broad clinical spectrum. Besides, mitochondrial dysfunction also has been consolidated as a hallmark of brain degeneration. Here we provide evidence that supports a shared role between mitochondrial dysfunction and DNA repair defects in the pathogenesis of the nervous system. As models, we analyze PNKP-related disorders, focusing on Charcot-Marie-Tooth disease and ataxia. A better understanding of the molecular dynamics of this relationship could provide improved diagnosis and treatment for neurological diseases.
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Affiliation(s)
- Luis Bermúdez-Guzmán
- Section of Genetics and Biotechnology, School of Biology, Universidad de Costa Rica, San José, 11501 Costa Rica
| | - Alejandro Leal
- Section of Genetics and Biotechnology, School of Biology, Universidad de Costa Rica, San José, 11501 Costa Rica
- Neuroscience Research Center, Universidad de Costa Rica, San José, Costa Rica
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14
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van de Vrugt HJ, Harmsen T, Riepsaame J, Alexantya G, van Mil SE, de Vries Y, Bin Ali R, Huijbers IJ, Dorsman JC, Wolthuis RMF, Te Riele H. Effective CRISPR/Cas9-mediated correction of a Fanconi anemia defect by error-prone end joining or templated repair. Sci Rep 2019; 9:768. [PMID: 30683899 PMCID: PMC6347620 DOI: 10.1038/s41598-018-36506-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022] Open
Abstract
Fanconi anemia (FA) is a cancer predisposition syndrome characterized by congenital abnormalities, bone marrow failure, and hypersensitivity to aldehydes and crosslinking agents. For FA patients, gene editing holds promise for therapeutic applications aimed at functionally restoring mutated genes in hematopoietic stem cells. However, intrinsic FA DNA repair defects may obstruct gene editing feasibility. Here, we report on the CRISPR/Cas9-mediated correction of a disruptive mutation in Fancf. Our experiments revealed that gene editing could effectively restore Fancf function via error-prone end joining resulting in a 27% increased survival in the presence of mitomycin C. In addition, templated gene correction could be achieved after double strand or single strand break formation. Although templated gene editing efficiencies were low (≤6%), FA corrected embryonic stem cells acquired a strong proliferative advantage over non-corrected cells, even without imposing genotoxic stress. Notably, Cas9 nickase activity resulted in mono-allelic gene editing and avoidance of undesired mutagenesis. In conclusion: DNA repair defects associated with FANCF deficiency do not prohibit CRISPR/Cas9 gene correction. Our data provide a solid basis for the application of pre-clinical models to further explore the potential of gene editing against FA, with the eventual aim to obtain therapeutic strategies against bone marrow failure.
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Affiliation(s)
- Henri J van de Vrugt
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands.
| | - Tim Harmsen
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Joey Riepsaame
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Genome Engineering Oxford, Sir William Dunn School of Pathology, University of Oxford South Parks Road, OX1 3RE, Oxford, UK
| | - Georgina Alexantya
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Saskia E van Mil
- Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands
| | - Yne de Vries
- Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands
| | - Rahmen Bin Ali
- Mouse Clinic for Cancer and Aging research (MCCA) Transgenic Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Ivo J Huijbers
- Mouse Clinic for Cancer and Aging research (MCCA) Transgenic Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Josephine C Dorsman
- Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands
| | - Rob M F Wolthuis
- Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands
| | - Hein Te Riele
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands.
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15
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Zhang W, Wang G, Liang A. DNA Damage Response in Quiescent Hematopoietic Stem Cells and Leukemia Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1143:147-171. [PMID: 31338819 DOI: 10.1007/978-981-13-7342-8_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In humans, hematopoietic stem cells (HSCs) adopt unique responsive pathways counteracting with the DNA-damaging assaults to weigh the balance between the maintenance of normal stem cell poor for whole-life blood regeneration and the transformation to leukemia stem cells (LSCs) for leukemia initiation. LSCs also take actions of combating with the attack launched by externally therapeutic drugs that can kill most leukemic cells, to avoid extermination and promote disease relapse. Therefore, the collection of knowledge about all these underlined mechanisms would present a preponderance for later studies. In this chapter, the universal DNA damage response (DDR) mechanisms were firstly introduced, and then DDR of HSCs were presented focusing on the DNA double-strand breaks in the quiescent state of HSCs, which poses a big advantage in promoting its transformation into preleukemic HSCs. Lastly, the DDR of LSCs were summarized based on the major outcomes triggered by different pathways in specific leukemia, upon which some aspects for future investigations were envisioned under our currently limited scope of knowledge.
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Affiliation(s)
- Wenjun Zhang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guangming Wang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Aibin Liang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.
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16
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The DNA damage response is developmentally regulated in the African trypanosome. DNA Repair (Amst) 2018; 73:78-90. [PMID: 30470509 PMCID: PMC6329875 DOI: 10.1016/j.dnarep.2018.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/12/2018] [Accepted: 11/12/2018] [Indexed: 01/19/2023]
Abstract
Genomes are affected by a wide range of damage, which has resulted in the evolution of a number of widely conserved DNA repair pathways. Most of these repair reactions have been described in the African trypanosome Trypanosoma brucei, which is a genetically tractable eukaryotic microbe and important human and animal parasite, but little work has considered how the DNA damage response operates throughout the T. brucei life cycle. Using quantitative PCR we have assessed damage induction and repair in both the nuclear and mitochondrial genomes of the parasite. We show differing kinetics of repair for three forms of DNA damage, and dramatic differences in repair between replicative life cycle forms found in the testse fly midgut and the mammal. We find that mammal-infective T. brucei cells repair oxidative and crosslink-induced DNA damage more efficiently than tsetse-infective cells and, moreover, very distinct patterns of induction and repair of DNA alkylating damage in the two life cycle forms. We also reveal robust repair of DNA lesions in the highly unusual T. brucei mitochondrial genome (the kinetoplast). By examining mutants we show that nuclear alkylation damage is repaired by the concerted action of two repair pathways, and that Rad51 acts in kinetoplast repair. Finally, we correlate repair with cell cycle arrest and cell growth, revealing that induced DNA damage has strikingly differing effects on the two life cycle stages, with distinct timing of alkylation-induced cell cycle arrest and higher levels of damage induced death in mammal-infective cells. Our data reveal that T. brucei regulates the DNA damage response during its life cycle, a capacity that may be shared by many microbial pathogens that exist in variant environments during growth and transmission.
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17
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Hydrogen Peroxide-Induced DNA Damage and Repair through the Differentiation of Human Adipose-Derived Mesenchymal Stem Cells. Stem Cells Int 2018; 2018:1615497. [PMID: 30405718 PMCID: PMC6199883 DOI: 10.1155/2018/1615497] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 06/19/2018] [Accepted: 07/26/2018] [Indexed: 11/18/2022] Open
Abstract
Human adipose-derived mesenchymal stem cells (hADMSCs) are recognized as a potential tool in cell tissue therapy because of their capacity to proliferate and differentiate in vitro. Several studies have addressed their use in regenerative medicine; however, little is known regarding their response to DNA damage and in particular to the reactive oxygen species (ROS) that are present in the microenvironment of implantation. In this study, we used the ROS-inducing agent hydrogen peroxide to explore the responses of (1) hADMSCs and (2) derived terminally differentiated adipocytes to oxidatively generated DNA damage. Using single cell gel electrophoresis, a dose-related increase was found for both DNA breaks and oxidative lesions (formamidopyrimidine DNA glycosylase-sensitive sites) upon exposure of hADMSCs to hydrogen peroxide. DNA repair capacity of hADMSCs was affected in cells exposed to 150 and 200 μM of hydrogen peroxide. An increase in the basal levels of DNA breaks and oxidative DNA lesions was observed through adipocyte differentiation. In addition, hydrogen peroxide-induced DNA damage increased through adipocyte differentiation; DNA repair capacity also decreased. This study is the first follow-up report on DNA repair capacity during adipogenic differentiation. Remarkably, in terminally differentiated adipocytes, DNA breakage repair is abolished while the repair of DNA oxidative lesions remains efficient.
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18
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Xia Y, Jiang L, Zhong T. The role of HIF-1α in chemo-/radioresistant tumors. Onco Targets Ther 2018; 11:3003-3011. [PMID: 29872312 PMCID: PMC5973460 DOI: 10.2147/ott.s158206] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Chemo-/radioresistance is a major obstacle in clinical oncology. The precise failure mechanisms of chemo-/radioresistance are multifactorial failures. It is now widely accepted that a tumor hypoxia microenvironment contributes significantly to chemo-/radioresistance. Hypoxia is the most common and obvious neoplastic microenvironment and is due to the rapid proliferation of tumor cells. HIF-1α is a principal molecular mediator of adaptability to hypoxia in tumor cells. HIF-1α activation leads to the transcription of a plethora of target genes that promote physiological changes associated with chemo-/radioresistance, including increasing the ability of DNA repair, the inhibition of apoptosis, and alterations of the cellular metabolism. Moreover, recent findings suggest that HIF-1α-activated autophagy is a crucial factor in the promotion of cell survival under the distressed microenvironment, thereby leading to the chemo-/radioresistance. This chapter presents an overview of the role of HIF-1α in chemo-/radioresistance of tumor cells.
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Affiliation(s)
- Yu Xia
- The Graduate School, Gannan Medical University, Ganzhou, People's Republic of China
| | - Lixia Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, People's Republic of China
| | - Tianyu Zhong
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, People's Republic of China
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He M, Lin Y, Tang Y, Liu Y, Zhou W, Li C, Sun G, Guo M. miR-638 suppresses DNA damage repair by targeting SMC1A expression in terminally differentiated cells. Aging (Albany NY) 2017; 8:1442-56. [PMID: 27405111 PMCID: PMC4993341 DOI: 10.18632/aging.100998] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/28/2016] [Indexed: 12/27/2022]
Abstract
The reduction of DNA damage repair capacity in terminally differentiated cells may be involved in sensitivity to cancer chemotherapy drugs; however, the underlying molecular mechanism is still not fully understood. Herein, we evaluated the role of miR-638 in the regulation of DNA damage repair in terminally differentiated cells. Our results show that miR-638 expression was up-regulated during cellular terminal differentiation and involved in mediating DNA damage repair processes. Results from a luciferase reporting experiment show that structural maintenance of chromosomes (SMC)1A was a potential target of miR-638; this was verified by western blot assays during cell differentiation and DNA damage induction. Overexpression of miR-638 enhanced the sensitivity of cancer cells to cisplatin, thus reducing cell viability in response to chemotherapy drug treatment. Furthermore, miR-638 overexpression affected DNA damage repair processes by interfering with the recruitment of the DNA damage repair-related protein, γH2AX, to DNA break sites. These findings indicate that miR-638 might act as a sensitizer in cancer chemotherapy and accompany chemotherapy drugs to enhance chemotherapeutic efficacy and to improve the chance of recovery from cancer.
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Affiliation(s)
- Mingyang He
- College of Life Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Yi Lin
- College of Life Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Yunlan Tang
- College of Life Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Yi Liu
- College of Life Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Weiwei Zhou
- College of Life Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Chuang Li
- College of Life Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Guihong Sun
- School of Basic Medical Sciences, Wuhan University, 430071 Wuhan, P.R. China
| | - Mingxiong Guo
- College of Life Sciences, Wuhan University, 430072 Wuhan, P. R. China
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DNA Damage as a Driver for Growth Delay: Chromosome Instability Syndromes with Intrauterine Growth Retardation. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8193892. [PMID: 29238724 PMCID: PMC5702399 DOI: 10.1155/2017/8193892] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 06/16/2017] [Accepted: 07/17/2017] [Indexed: 12/20/2022]
Abstract
DNA is constantly exposed to endogenous and exogenous mutagenic stimuli that are capable of producing diverse lesions. In order to protect the integrity of the genetic material, a wide array of DNA repair systems that can target each specific lesion has evolved. Despite the availability of several repair pathways, a common general program known as the DNA damage response (DDR) is stimulated to promote lesion detection, signaling, and repair in order to maintain genetic integrity. The genes that participate in these pathways are subject to mutation; a loss in their function would result in impaired DNA repair and genomic instability. When the DDR is constitutionally altered, every cell of the organism, starting from development, will show DNA damage and subsequent genomic instability. The cellular response to this is either uncontrolled proliferation and cell cycle deregulation that ensues overgrowth, or apoptosis and senescence that result in tissue hypoplasia. These diverging growth abnormalities can clinically translate as cancer or growth retardation; both features can be found in chromosome instability syndromes (CIS). The analysis of the clinical, cellular, and molecular phenotypes of CIS with intrauterine growth retardation allows inferring that replication alteration is their unifying feature.
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22
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Zhao H, Jiang H, Li Z, Zhuang Y, Liu Y, Zhou S, Xiao Y, Xie C, Zhou F, Zhou Y. 2-Methoxyestradiol enhances radiosensitivity in radioresistant melanoma MDA-MB-435R cells by regulating glycolysis via HIF-1α/PDK1 axis. Int J Oncol 2017; 50:1531-1540. [PMID: 28339028 PMCID: PMC5403226 DOI: 10.3892/ijo.2017.3924] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/13/2017] [Indexed: 02/06/2023] Open
Abstract
HIF-1α overexpression is associated with radio-resistance of various cancers. A radioresistant human melanoma cell model MDA-MB-435R (435R) was established by us previously. Compared with the parental cells MDA-MB-435 (435S), an elevated level of HIF-1α expression in 435R cells was demonstrated in our recent experiments. Therefore, in the current study, we sought to determine whether selective HIF-1α inhibitors could radiosensitize the 435R cells to X-ray, and to identify the potential mechanisms. Our data demonstrated that inhibition of HIF-1α with 2-methoxyestradiol (2-MeOE2) significantly enhanced radiosensitivity of 435R cells. 2-MeOE2 increased DNA damage and ratio of apoptosis cells induced by irradiation. Whereas, cell proliferation and the expression of pyruvate dehydrogenase kinase 1 (PDK1) were decreased after 2-MeOE2 treatment. The change of expression of GLUT1, LDHA and the cellular ATP level and extracellular lactate production indicates that 2-MeOE2 suppressed glycolytic state of 435R cells. In addition, the radioresistance, glycolytic state and cell proliferation of 435R cells were also decreased after inhibiting pyruvate dehydrogenase kinase 1 (PDK1) with dichloroacetate (DCA). DCA could also increase DNA damage and ratio of apoptotic cells induced by irradiation. These results also suggest that inhibition of HIF-1α with 2-MeOE2 sensitizes radioresistant melanoma cells 435R to X-ray irradiation through targeting the glycolysis that is regulated by PDK1. Selective inhibitors of HIF-1α and glycolysis are potential drugs to enhance radio sensitivity of melanoma cells.
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Affiliation(s)
- Hong Zhao
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuchang, Wuhan, Hubei 430071, P.R. China
| | - Huangang Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuchang, Wuhan, Hubei 430071, P.R. China
| | - Zheng Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuchang, Wuhan, Hubei 430071, P.R. China
| | - Yafei Zhuang
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuchang, Wuhan, Hubei 430071, P.R. China
| | - Yinyin Liu
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuchang, Wuhan, Hubei 430071, P.R. China
| | - Shuliang Zhou
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuchang, Wuhan, Hubei 430071, P.R. China
| | - Youde Xiao
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuchang, Wuhan, Hubei 430071, P.R. China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuchang, Wuhan, Hubei 430071, P.R. China
| | - Fuxiang Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuchang, Wuhan, Hubei 430071, P.R. China
| | - Yunfeng Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuchang, Wuhan, Hubei 430071, P.R. China
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Fayzullina S, Martin LJ. DNA Damage Response and DNA Repair in Skeletal Myocytes From a Mouse Model of Spinal Muscular Atrophy. J Neuropathol Exp Neurol 2016; 75:889-902. [PMID: 27452406 DOI: 10.1093/jnen/nlw064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We studied DNA damage response (DDR) and DNA repair capacities of skeletal muscle cells from a mouse model of infantile spinal muscular atrophy (SMA) caused by loss-of-function mutation of survival of motor neuron (Smn). Primary myocyte cultures derived from skeletal muscle satellite cells of neonatal control and mutant SMN mice had similar myotube length, myonuclei, satellite cell marker Pax7 and differentiated myotube marker myosin, and acetylcholine receptor clustering. DNA damage was induced in differentiated skeletal myotubes by γ-irradiation, etoposide, and methyl methanesulfonate (MMS). Unexposed control and SMA myotubes had stable genome integrity. After γ-irradiation and etoposide, myotubes repaired most DNA damage equally. Control and mutant myotubes exposed to MMS exhibited equivalent DNA damage without repair. Control and SMA myotube nuclei contained DDR proteins phospho-p53 and phospho-H2AX foci that, with DNA damage, dispersed and then re-formed similarly after recovery. We conclude that mouse primary satellite cell-derived myotubes effectively respond to and repair DNA strand-breaks, while DNA alkylation repair is underrepresented. Morphological differentiation, genome stability, genome sensor, and DNA strand-break repair potential are preserved in mouse SMA myocytes; thus, reduced SMN does not interfere with myocyte differentiation, genome integrity, and DNA repair, and faulty DNA repair is unlikely pathogenic in SMA.
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Affiliation(s)
- Saniya Fayzullina
- From the Department of Pathology, Division of Neuropathology, and the Pathobiology Graduate Training Program, Johns Hopkins School of Medicine, Baltimore, Maryland, USA (SF, LJM)
| | - Lee J Martin
- From the Department of Pathology, Division of Neuropathology, and the Pathobiology Graduate Training Program, Johns Hopkins School of Medicine, Baltimore, Maryland, USA (SF, LJM)
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Li L, Zhu T, Gao YF, Zheng W, Wang CJ, Xiao L, Huang MS, Yin JY, Zhou HH, Liu ZQ. Targeting DNA Damage Response in the Radio(Chemo)therapy of Non-Small Cell Lung Cancer. Int J Mol Sci 2016; 17:ijms17060839. [PMID: 27258253 PMCID: PMC4926373 DOI: 10.3390/ijms17060839] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/03/2016] [Accepted: 05/24/2016] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide due to its high incidence and mortality. As the most common lung cancer, non-small cell lung cancer (NSCLC) is a terrible threat to human health. Despite improvements in diagnosis and combined treatments including surgical resection, radiotherapy and chemotherapy, the overall survival for NSCLC patients still remains poor. DNA damage is considered to be the primary cause of lung cancer development and is normally recognized and repaired by the intrinsic DNA damage response machinery. The role of DNA repair pathways in radio(chemo)therapy-resistant cancers has become an area of significant interest in the clinical setting. Meanwhile, some studies have proved that genetic and epigenetic factors can alter the DNA damage response and repair, which results in changes of the radiation and chemotherapy curative effect in NSCLC. In this review, we focus on the effect of genetic polymorphisms and epigenetic factors such as miRNA regulation and lncRNA regulation participating in DNA damage repair in response to radio(chemo)therapy in NSCLC. These may provide novel information on the radio(chemo)therapy of NSCLC based on the individual DNA damage response.
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Affiliation(s)
- Ling Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Tao Zhu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Yuan-Feng Gao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Wei Zheng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Chen-Jing Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Ling Xiao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Ma-Sha Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
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25
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Hofstetter C, Kampka JM, Huppertz S, Weber H, Schlosser A, Müller AM, Becker M. Inhibition of KDM6 activity during murine ESC differentiation induces DNA damage. J Cell Sci 2016; 129:788-803. [PMID: 26759175 DOI: 10.1242/jcs.175174] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 01/05/2016] [Indexed: 12/30/2022] Open
Abstract
Pluripotent embryonic stem cells (ESCs) are characterised by their capacity to self-renew indefinitely while maintaining the potential to differentiate into all cell types of an adult organism. Both the undifferentiated and differentiated states are defined by specific gene expression programs that are regulated at the chromatin level. Here, we have analysed the contribution of the H3K27me2- and H3K27me23-specific demethylases KDM6A and KDM6B to murine ESC differentiation by employing the GSK-J4 inhibitor, which is specific for KDM6 proteins, and by targeted gene knockout (KO) and knockdown. We observe that inhibition of the H3K27 demethylase activity induces DNA damage along with activation of the DNA damage response (DDR) and cell death in differentiating but not in undifferentiated ESCs. Laser microirradiation experiments revealed that the H3K27me3 mark, but not the KDM6B protein, colocalise with γH2AX-positive sites of DNA damage in differentiating ESCs. Lack of H3K27me3 attenuates the GSK-J4-induced DDR in differentiating Eed-KO ESCs. Collectively, our findings indicate that differentiating ESCs depend on KDM6 and that the H3K27me3 demethylase activity is crucially involved in DDR and survival of differentiating ESCs.
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Affiliation(s)
- Christine Hofstetter
- Institute for Medical Radiation and Cell Research (MSZ) in the Center of Experimental Molecular Medicine (ZEMM), University of Würzburg, Würzburg 97078, Germany
| | - Justyna M Kampka
- Institute for Medical Radiation and Cell Research (MSZ) in the Center of Experimental Molecular Medicine (ZEMM), University of Würzburg, Würzburg 97078, Germany
| | - Sascha Huppertz
- Institute for Medical Radiation and Cell Research (MSZ) in the Center of Experimental Molecular Medicine (ZEMM), University of Würzburg, Würzburg 97078, Germany
| | - Heike Weber
- Microarray Core Unit, Interdisciplinary Center for Clinical Science, University of Würzburg, Würzburg 97078, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg 97078, Germany
| | - Albrecht M Müller
- Institute for Medical Radiation and Cell Research (MSZ) in the Center of Experimental Molecular Medicine (ZEMM), University of Würzburg, Würzburg 97078, Germany
| | - Matthias Becker
- Institute for Medical Radiation and Cell Research (MSZ) in the Center of Experimental Molecular Medicine (ZEMM), University of Würzburg, Würzburg 97078, Germany
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Nagahashi M, Matsuda Y, Moro K, Tsuchida J, Soma D, Hirose Y, Kobayashi T, Kosugi SI, Takabe K, Komatsu M, Wakai T. DNA damage response and sphingolipid signaling in liver diseases. Surg Today 2015; 46:995-1005. [PMID: 26514817 DOI: 10.1007/s00595-015-1270-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 10/04/2015] [Indexed: 02/06/2023]
Abstract
Patients with unresectable hepatocellular carcinoma (HCC) cannot generally be cured by systemic chemotherapy or radiotherapy due to their poor response to conventional therapeutic agents. The development of novel and efficient targeted therapies to increase their treatment options depends on the elucidation of the molecular mechanisms that underlie the pathogenesis of HCC. The DNA damage response (DDR) is a network of cell-signaling events that are triggered by DNA damage. Its dysregulation is thought to be one of the key mechanisms underlying the generation of HCC. Sphingosine-1-phosphate (S1P), a lipid mediator, has emerged as an important signaling molecule that has been found to be involved in many cellular functions. In the liver, the alteration of S1P signaling potentially affects the DDR pathways. In this review, we explore the role of the DDR in hepatocarcinogenesis of various etiologies, including hepatitis B and C infection and non-alcoholic steatohepatitis. Furthermore, we discuss the metabolism and functions of S1P that may affect the hepatic DDR. The elucidation of the pathogenic role of S1P may create new avenues of research into therapeutic strategies for patients with HCC.
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Affiliation(s)
- Masayuki Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan.
| | - Yasunobu Matsuda
- Department of Medical Technology, Niigata University Graduate School of Health Sciences, 2-746 Asahimachi-dori, Chuo-ku, Niigata, 951-8518, Japan
| | - Kazuki Moro
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Junko Tsuchida
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Daiki Soma
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Yuki Hirose
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Takashi Kobayashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Shin-Ichi Kosugi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Kazuaki Takabe
- Division of Surgical Oncology, Department of Surgery, Virginia Commonwealth University School of Medicine and the Massey Cancer Center, West Hospital 7-402, 1200 East Broad Street, Richmond, VA, 23298-0011, USA
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
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Mieloch AA, Suchorska WM. The concept of radiation-enhanced stem cell differentiation. Radiol Oncol 2015; 49:209-16. [PMID: 26401125 PMCID: PMC4577216 DOI: 10.1515/raon-2015-0022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/05/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Efficient stem cell differentiation is considered to be the holy grail of regenerative medicine. Pursuing the most productive method of directed differentiation has been the subject of numerous studies, resulting in the development of many effective protocols. However, the necessity for further improvement in differentiation efficiency remains. This review contains a description of molecular processes underlying the response of stem cells to ionizing radiation, indicating its potential application in differentiation procedures. In the first part, the radiation-induced damage response in various types of stem cells is described. Second, the role of the p53 protein in embryonic and adult stem cells is highlighted. Last, the hypothesis on the mitochondrial involvement in stem cell development including its response to ionizing radiation is presented. CONCLUSIONS In summary, despite the many threats of ionizing radiation concerning genomic instability, subjecting cells to the appropriate dosage of ionizing radiation may become a useful method for enhancing directed differentiation in certain stem cell types.
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Affiliation(s)
- Adam A. Mieloch
- Radiobiology Laboratory, Department of Medical Physics, The Greater Poland Cancer Centre
| | - Wiktoria M. Suchorska
- Radiobiology Laboratory, Department of Medical Physics, The Greater Poland Cancer Centre
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28
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Kostyuk S, Smirnova T, Kameneva L, Porokhovnik L, Speranskij A, Ershova E, Stukalov S, Izevskaya V, Veiko N. GC-Rich Extracellular DNA Induces Oxidative Stress, Double-Strand DNA Breaks, and DNA Damage Response in Human Adipose-Derived Mesenchymal Stem Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:782123. [PMID: 26273425 PMCID: PMC4529983 DOI: 10.1155/2015/782123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 01/14/2015] [Accepted: 01/15/2015] [Indexed: 12/24/2022]
Abstract
BACKGROUND Cell free DNA (cfDNA) circulates throughout the bloodstream of both healthy people and patients with various diseases. CfDNA is substantially enriched in its GC-content as compared with human genomic DNA. PRINCIPAL FINDINGS Exposure of haMSCs to GC-DNA induces short-term oxidative stress (determined with H2DCFH-DA) and results in both single- and double-strand DNA breaks (comet assay and γH2AX, foci). As a result in the cells significantly increases the expression of repair genes (BRCA1 (RT-PCR), PCNA (FACS)) and antiapoptotic genes (BCL2 (RT-PCR and FACS), BCL2A1, BCL2L1, BIRC3, and BIRC2 (RT-PCR)). Under the action of GC-DNA the potential of mitochondria was increased. Here we show that GC-rich extracellular DNA stimulates adipocyte differentiation of human adipose-derived mesenchymal stem cells (haMSCs). Exposure to GC-DNA leads to an increase in the level of RNAPPARG2 and LPL (RT-PCR), in the level of fatty acid binding protein FABP4 (FACS analysis) and in the level of fat (Oil Red O). CONCLUSIONS GC-rich fragments in the pool of cfDNA can potentially induce oxidative stress and DNA damage response and affect the direction of mesenchymal stem cells differentiation in human adipose-derived mesenchymal stem cells. Such a response may be one of the causes of obesity or osteoporosis.
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Affiliation(s)
- Svetlana Kostyuk
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Mosskvorechie Street 1, Moscow 115478, Russia
| | - Tatiana Smirnova
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Mosskvorechie Street 1, Moscow 115478, Russia
| | - Larisa Kameneva
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Mosskvorechie Street 1, Moscow 115478, Russia
| | - Lev Porokhovnik
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Mosskvorechie Street 1, Moscow 115478, Russia
| | - Anatolij Speranskij
- V.A. Nasonova Research Institute of Rheumatology, Russian Academy of Medical Sciences, Russia
| | - Elizaveta Ershova
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Mosskvorechie Street 1, Moscow 115478, Russia
| | - Sergey Stukalov
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Mosskvorechie Street 1, Moscow 115478, Russia
| | - Vera Izevskaya
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Mosskvorechie Street 1, Moscow 115478, Russia
| | - Natalia Veiko
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Mosskvorechie Street 1, Moscow 115478, Russia
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29
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Koyuncu S, Irmak D, Saez I, Vilchez D. Defining the General Principles of Stem Cell Aging: Lessons from Organismal Models. CURRENT STEM CELL REPORTS 2015. [DOI: 10.1007/s40778-015-0017-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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30
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Taleei R, Girard PM, Nikjoo H. DSB repair model for mammalian cells in early S and G1 phases of the cell cycle: application to damage induced by ionizing radiation of different quality. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 779:5-14. [PMID: 25813721 DOI: 10.1016/j.mrgentox.2015.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 01/01/2023]
Abstract
The purpose of this work is to test the hypothesis that kinetics of double strand breaks (DSB) repair is governed by complexity of DSB. To test the hypothesis we used our recent published mechanistic mathematical model of DSB repair for DSB induced by selected protons, deuterons, and helium ions of different energies representing radiations of different qualities. In light of recent advances in experimental and computational techniques, the most appropriate method to study cellular responses in radiation therapy, and exposures to low doses of ionizing radiations is using mechanistic approaches. To this end, we proposed a 'bottom-up' approach to study cellular response that starts with the DNA damage. Monte Carlo track structure method was employed to simulate initial damage induced in the genomic DNA by direct and indirect effects. Among the different types of DNA damage, DSB are known to be induced in simple and complex forms. The DSB repair model in G1 and early S phases of the cell cycle was employed to calculate the repair kinetics. The model considers the repair of simple and complex DSB, and the DSB produced in the heterochromatin. The inverse sampling method was used to calculate the repair kinetics for each individual DSB. The overall repair kinetics for 500 DSB induced by single tracks of the radiation under test were compared with experimental results. The results show that the model is capable of predicting the repair kinetics for the DSB induced by radiations of different qualities within an accepted range of uncertainty.
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Affiliation(s)
- Reza Taleei
- Department of Radiation Physics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter M Girard
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institute, Stockholm SE171 76, Sweden
| | - Hooshang Nikjoo
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institute, Stockholm SE171 76, Sweden.
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31
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Zhang C, Peng G. Non-coding RNAs: An emerging player in DNA damage response. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 763:202-11. [DOI: 10.1016/j.mrrev.2014.11.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 01/02/2023]
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32
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Stem cell aging: mechanisms, regulators and therapeutic opportunities. Nat Med 2014; 20:870-80. [PMID: 25100532 DOI: 10.1038/nm.3651] [Citation(s) in RCA: 479] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 07/09/2014] [Indexed: 12/14/2022]
Abstract
Aging tissues experience a progressive decline in homeostatic and regenerative capacities, which has been attributed to degenerative changes in tissue-specific stem cells, stem cell niches and systemic cues that regulate stem cell activity. Understanding the molecular pathways involved in this age-dependent deterioration of stem cell function will be critical for developing new therapies for diseases of aging that target the specific causes of age-related functional decline. Here we explore key molecular pathways that are commonly perturbed as tissues and stem cells age and degenerate. We further consider experimental evidence both supporting and refuting the notion that modulation of these pathways per se can reverse aging phenotypes. Finally, we ask whether stem cell aging establishes an epigenetic 'memory' that is indelibly written or one that can be reset.
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FANCA knockout in human embryonic stem cells causes a severe growth disadvantage. Stem Cell Res 2014; 13:240-50. [PMID: 25108529 DOI: 10.1016/j.scr.2014.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/16/2014] [Accepted: 07/20/2014] [Indexed: 11/22/2022] Open
Abstract
Fanconi anemia (FA) is an autosomal recessive disorder characterized by progressive bone marrow failure (BMF) during childhood, aside from numerous congenital abnormalities. FA mouse models have been generated; however, they do not fully mimic the hematopoietic phenotype. As there is mounting evidence that the hematopoietic impairment starts already in utero, a human pluripotent stem cell model would constitute a more appropriate system to investigate the mechanisms underlying BMF in FA and its developmental basis. Using zinc finger nuclease (ZFN) technology, we have created a knockout of FANCA in human embryonic stem cells (hESC). We introduced a selection cassette into exon 2 thereby disrupting the FANCA coding sequence and found that whereas mono-allelically targeted cells retain an unaltered proliferation potential, disruption of the second allele causes a severe growth disadvantage. As a result, heterogeneous cultures arise due to the presence of cells still carrying an unaffected FANCA allele, quickly outgrowing the knockout cells. When pure cultures of FANCA knockout hESC are pursued either through selection or single cell cloning, this rapidly results in growth arrest and such cultures cannot be maintained. These data highlight the importance of a functional FA pathway at the pluripotent stem cell stage.
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Involvement of DNA damage response pathways in hepatocellular carcinoma. BIOMED RESEARCH INTERNATIONAL 2014; 2014:153867. [PMID: 24877058 PMCID: PMC4022277 DOI: 10.1155/2014/153867] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/23/2014] [Accepted: 03/25/2014] [Indexed: 12/16/2022]
Abstract
Hepatocellular carcinoma (HCC) has been known as one of the most lethal human malignancies, due to the difficulty of early detection, chemoresistance, and radioresistance, and is characterized by active angiogenesis and metastasis, which account for rapid recurrence and poor survival. Its development has been closely associated with multiple risk factors, including hepatitis B and C virus infection, alcohol consumption, obesity, and diet contamination. Genetic alterations and genomic instability, probably resulted from unrepaired DNA lesions, are increasingly recognized as a common feature of human HCC. Dysregulation of DNA damage repair and signaling to cell cycle checkpoints, known as the DNA damage response (DDR), is associated with a predisposition to cancer and affects responses to DNA-damaging anticancer therapy. It has been demonstrated that various HCC-associated risk factors are able to promote DNA damages, formation of DNA adducts, and chromosomal aberrations. Hence, alterations in the DDR pathways may accumulate these lesions to trigger hepatocarcinogenesis and also to facilitate advanced HCC progression. This review collects some of the most known information about the link between HCC-associated risk factors and DDR pathways in HCC. Hopefully, the review will remind the researchers and clinicians of further characterizing and validating the roles of these DDR pathways in HCC.
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35
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McKinnon PJ. Maintaining genome stability in the nervous system. Nat Neurosci 2013; 16:1523-9. [PMID: 24165679 PMCID: PMC4112580 DOI: 10.1038/nn.3537] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/11/2013] [Indexed: 01/09/2023]
Abstract
Active maintenance of genome stability is a prerequisite for the development and function of the nervous system. The high replication index during neurogenesis and the long life of mature neurons highlight the need for efficient cellular programs to safeguard genetic fidelity. Multiple DNA damage response pathways ensure that replication stress and other types of DNA lesions, such as oxidative damage, do not affect neural homeostasis. Numerous human neurologic syndromes result from defective DNA damage signaling and compromised genome integrity. These syndromes can involve different neuropathology, which highlights the diverse maintenance roles that are required for genome stability in the nervous system. Understanding how DNA damage signaling pathways promote neural development and preserve homeostasis is essential for understanding fundamental brain function.
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Affiliation(s)
- Peter J. McKinnon
- Department of Genetics, St Jude Children’s Research Hospital, Memphis TN, USA
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