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Zhang P, Wen B, Gong J, Liu Z, Zhang M, Zhou G, Zhang L, Zhang Z. Clinical prognostication and immunotherapy response prediction in esophageal squamous cell carcinoma using the DNA damage repair-associated signature. Environ Toxicol 2024; 39:2803-2816. [PMID: 38287713 DOI: 10.1002/tox.24155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/06/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND The relationship between DNA damage repair (DDR) and cancer is intricately intertwined; however, its specific role in esophageal squamous cell carcinoma (ESCC) remains enigmatic. METHODS Employing single-cell analysis, we delineated the functionality of DDR-related genes within the tumor microenvironment (TME). A diverse array of scoring mechanisms, including AUCell, UCell, singscore, ssgsea, and AddModuleScore, were harnessed to scrutinize the activity of DDR-related genes across different cell types. Differential pathway alterations between high-and low-DDR activity cell clusters were compared. Furthermore, leveraging multiple RNA-seq datasets, we constructed a robust DDR-associated signature (DAS), and through integrative multiomics analysis, we explored differences in prognosis, pathways, mutational landscapes, and immunotherapy predictions among distinct DAS groups. RESULTS Notably, high-DDR activity cell subpopulations exhibited markedly enhanced cellular communication. The DAS demonstrated uniformity across multiple datasets. The low-DAS group exhibited improved prognoses, accompanied by heightened immune infiltration and elevated immune checkpoint expression. SubMap analysis of multiple immunotherapy datasets suggested that low-DAS group may experience enhanced immunotherapy responses. The "oncopredict" R package analyzed and screened sensitive drugs for different DAS groups. CONCLUSION Through the integration of single-cell and bulk RNA-seq data, we have developed a DAS associated with prognosis and immunotherapy response. This signature holds promise for the future stratification and personalized treatment of ESCC patients in clinical settings.
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Affiliation(s)
- Pengpeng Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Bing Wen
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Department of Cardiothoracic Surgery, The Second People's Hospital of Yibin, Yibin, Sichuan, China
| | - Jialin Gong
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zuo Liu
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Mengzhe Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Guangyao Zhou
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Lianmin Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhenfa Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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Xu J, Fei P, Simon DW, Morowitz MJ, Mehta PA, Du W. Crosstalk between DNA Damage Repair and Metabolic Regulation in Hematopoietic Stem Cells. Cells 2024; 13:733. [PMID: 38727270 PMCID: PMC11083014 DOI: 10.3390/cells13090733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Self-renewal and differentiation are two characteristics of hematopoietic stem cells (HSCs). Under steady physiological conditions, most primitive HSCs remain quiescent in the bone marrow (BM). They respond to different stimuli to refresh the blood system. The transition from quiescence to activation is accompanied by major changes in metabolism, a fundamental cellular process in living organisms that produces or consumes energy. Cellular metabolism is now considered to be a key regulator of HSC maintenance. Interestingly, HSCs possess a distinct metabolic profile with a preference for glycolysis rather than oxidative phosphorylation (OXPHOS) for energy production. Byproducts from the cellular metabolism can also damage DNA. To counteract such insults, mammalian cells have evolved a complex and efficient DNA damage repair (DDR) system to eliminate various DNA lesions and guard genomic stability. Given the enormous regenerative potential coupled with the lifetime persistence of HSCs, tight control of HSC genome stability is essential. The intersection of DDR and the HSC metabolism has recently emerged as an area of intense research interest, unraveling the profound connections between genomic stability and cellular energetics. In this brief review, we delve into the interplay between DDR deficiency and the metabolic reprogramming of HSCs, shedding light on the dynamic relationship that governs the fate and functionality of these remarkable stem cells. Understanding the crosstalk between DDR and the cellular metabolism will open a new avenue of research designed to target these interacting pathways for improving HSC function and treating hematologic disorders.
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Affiliation(s)
- Jian Xu
- Division of Hematology and Oncology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15232, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Peiwen Fei
- Cancer Biology, University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI 96812, USA
| | - Dennis W. Simon
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Michael J. Morowitz
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Parinda A. Mehta
- Division of Blood and Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Wei Du
- Division of Hematology and Oncology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15232, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
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Mao X, Lee NK, Saad SE, Fong IL. Clinical translation for targeting DNA damage repair in non-small cell lung cancer: a review. Transl Lung Cancer Res 2024; 13:375-397. [PMID: 38496700 PMCID: PMC10938103 DOI: 10.21037/tlcr-23-742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/31/2024] [Indexed: 03/19/2024]
Abstract
Despite significant advancements in screening, diagnosis, and treatment of non-small cell lung cancer (NSCLC), it remains the primary cause of cancer-related deaths globally. DNA damage is caused by the exposure to exogenous and endogenous factors and the correct functioning of DNA damage repair (DDR) is essential to maintain of normal cell circulation. The presence of genomic instability, which results from defective DDR, is a critical characteristic of cancer. The changes promote the accumulation of mutations, which are implicated in cancer cells, but these may be exploited for anti-cancer therapies. NSCLC has a distinct genomic profile compared to other tumors, making precision medicine essential for targeting actionable gene mutations. Although various treatment options for NSCLC exist including chemotherapy, targeted therapy, and immunotherapy, drug resistance inevitably arises. The identification of deleterious DDR mutations in 49.6% of NSCLC patients has led to the development of novel target therapies that have the potential to improve patient outcomes. Synthetic lethal treatment using poly (ADP-ribose) polymerase (PARP) inhibitors is a breakthrough in biomarker-driven therapy. Additionally, promising new compounds targeting DDR, such as ATR, CHK1, CHK2, DNA-PK, and WEE1, had demonstrated great potential for tumor selectivity. In this review, we provide an overview of DDR pathways and discuss the clinical translation of DDR inhibitors in NSCLC, including their application as single agents or in combination with chemotherapy, radiotherapy, and immunotherapy.
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Affiliation(s)
- Xinru Mao
- Department of Paraclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak (UNIMAS), Kota Samarahan, Malaysia
| | - Nung Kion Lee
- Faculty of Computer Science and Information Technology, Universiti Malaysia Sarawak (UNIMAS), Kota Samarahan, Malaysia
| | | | - Isabel Lim Fong
- Department of Paraclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak (UNIMAS), Kota Samarahan, Malaysia
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Jing X, Qin X, Liu H, Liu H, Wang H, Qin J, Zhang Y, Cao S, Fan X. DNA damage response alterations in clear cell renal cell carcinoma: clinical, molecular, and prognostic implications. Eur J Med Res 2024; 29:107. [PMID: 38326910 PMCID: PMC10848511 DOI: 10.1186/s40001-024-01678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic responses. Nonetheless, the characteristics and significance of DDR alterations in clear cell renal cell carcinoma (ccRCC) remain undefined. This study aimed to explore the predictive role, molecular mechanism, and tumor immune profile of DDR genes in ccRCC. METHODS We prospectively sequenced 757 tumors and matched blood DNA samples from Chinese patients with ccRCC using next-generation sequencing (NGS) and analyzed data from 537 patients from The Cancer Genome Atlas (TCGA). A comprehensive analysis was performed. RESULTS Fifty-two percent of Chinese patients with ccRCC harbored DDR gene mutations and 57% of TCGA patients. The immunotherapy treatment prognosis of patients with DDR gene mutations was superior to that of patients without DDR gene mutations (p = 0.047). DDR gene mutations were associated with more gene mutations and a higher tumor mutation load (TMB, p < 0.001). Moreover, patients with DDR gene mutations have a distinct mutational signature compared with those with wild-type DDR. Furthermore, the DDR-mut group had elevated neoantigen load (including single-nucleotide variants (SNV) and indel neoantigen load, p = 0.037 and p = 0.002, respectively), TCR Shannon (p = 0.025), and neutrophils (p = 0.010). DDR gene mutations exhibited a distinct immune profile with significantly higher expression levels of TNFSF9, CD70, ICAM1, and indoleamine-2,3-dioxygenase (IDO) and lower expression levels of VTCN1 and IL12A. CONCLUSIONS Our data suggest that the detection of somatic mutations in DDR genes can predict the efficacy of immunotherapy in patients with ccRCC. Furthermore, we revealed the unique molecular and immune mechanisms underlying ccRCC with DDR gene mutations.
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Affiliation(s)
- Xiao Jing
- Department of Urology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangcheng Qin
- Department of Urology, Ningbo Urology and Nephrology Hospital, Ningbo, China
| | - Hao Liu
- Department of Urology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Huanhuan Liu
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Jiayue Qin
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Yanui Zhang
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Xiaodong Fan
- Department of Urology, Ningbo Urology and Nephrology Hospital, Ningbo, China.
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Qin C, Fan X, Sai X, Yin B, Zhou S, Addeo A, Bian T, Yu H. Development and validation of a DNA damage repair-related gene-based prediction model for the prognosis of lung adenocarcinoma. J Thorac Dis 2023; 15:6928-6945. [PMID: 38249902 PMCID: PMC10797339 DOI: 10.21037/jtd-23-1746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024]
Abstract
Background Lung cancer is the leading cause of morbidity and mortality among all cancer types, with lung adenocarcinoma (LUAD) being the most prevalent subtype. DNA damage repair (DDR)-related genes are closely associated with cancer progression and treatment, with emerging evidence highlighting their correlation with tumor development. However, the relationship between LUAD prognosis and DDR-related genes remains unclear. Methods RNA sequencing (RNA-seq) data and clinical information were obtained from The Cancer Genome Atlas (TCGA) database. The GSE31210 dataset, utilized for external validation, was retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed DDR genes were identified, and a DDR-related prognostic model was established and validated using Kaplan-Meier (KM) survival analysis, time-dependent receiver operating characteristic (ROC) curves, gene set enrichment analysis (GSEA), tumor mutational burden (TMB) analysis, and immune cell infiltration. A P value of less than 0.05 was considered statistically significant. Results A total of 514 patients with LUAD from TCGA database were divided into distinct subtypes to characterize the diversity within the DDR pathway. DDR-activated and DDR-suppressed subgroups showed distinct clinical characteristics, molecular characteristics, and immune profiles. Nine genes were identified as hub DDR-related genes, including CASP14, DKK1, ECT2, FLNC, HMMR, IGFBP1, KRT6A, TYMS, and FCER2. By using the expression levels of these selected genes, the corresponding risk scores for each sample was predicted. In the training group, KM survival analysis revealed that the high-risk group exhibited significantly diminished overall survival (OS) [hazard ratio (HR) =3.341, P=1.38e-08]. The corresponding area under the curve (AUC) values for the 1-year follow-up periods was 0.767, respectively. Upon validation in the external cohort, patients with higher risk scores manifested significantly reduced OS (HR =2.372, P=1.87e-03). The AUC values of the ROC curves for the 1-year OS in the validation cohort was 0.87, respectively. Moreover, advanced DDR risk score was correlated with increased TMB scores, a heightened frequency of TP53 mutations, an increased abundance of cancer-testicular antigens (CTAs), and a lower tumor immune dysfunction and exclusion (TIDE) score in patients with LUAD (P<0.05). Conclusions A nine-gene risk signature associated with DDR in LUAD was effectively developed, demonstrating its potential as a robust and reliable classification tool for clinical practice. This model exhibited the capability to accurately predict the prognosis and survival outcomes of LUAD patients.
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Affiliation(s)
- Chu Qin
- Department of Respiratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Xiaodong Fan
- Department of Respiratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Xiaoyan Sai
- Department of Respiratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Bo Yin
- Department of Respiratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Shufang Zhou
- Department of Respiratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Alfredo Addeo
- Oncology Department, Geneva University Hospital (CH), Geneva, Switzerland
| | - Tao Bian
- Department of Respiratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Haoda Yu
- Department of Respiratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
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Shang Z, Wang Z, Zhang Y, Liu S. DNA damage repair molecular subtype derived immune signature applicable for the prognosis and immunotherapy response prediction in colon cancer. Transl Cancer Res 2023; 12:2781-2805. [PMID: 37969400 PMCID: PMC10643980 DOI: 10.21037/tcr-23-747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/17/2023] [Indexed: 11/17/2023]
Abstract
Background The DNA damage repair (DDR) pathway is one of the pathways of tumor pathogenesis, but its relationship with the immunophenotype has not been clarified in colon cancer (CC). Methods We identified the differentially expressed immune-related genes (DEIRGs) between two DDR molecular subtypes, namely, C1 and C2, and used univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) penalized Cox regression analysis to construct the risk score in the training cohort [n=1,009, a combination of The Cancer Genome Atlas (TCGA) and GSE39582]. Regarding the median risk score as the unified cutoff to classify the patients into high- and low-risk groups. Two independent cohorts (GSE17538, n=232; GSE38832, n=122) were used for external validation of the prognostic value of the risk score. The IMvigor210 cohort (n=348) was used to test the predictive value of the risk score for immunotherapy response. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were performed to discover the underlying mechanism. Immune cell infiltration was quantified by the single sample gene set enrichment analysis (ssGSEA) algorithm. Results The high-risk group showed significantly reduced overall survival (OS), disease-specific survival (DSS), disease-free survival (DFS), progression-free survival (PFS), and relapse-free survival (RFS) compared to the low-risk group, and the two groups differed significantly in lymphatic invasion, American Joint Committee on Cancer (AJCC) TNM stage, preoperative carcinoembryonic antigen (CEA) level, etc. The enrichment levels of pathways related to colorectal cancer, epithelial-mesenchymal transition (EMT), angiogenesis, hypoxia, P53, TGF-β, KRAS signaling, etc., were upregulated in the high-risk group, but DDR-related pathways were defective in the high-risk group. The immunophenotypes of the high-risk group tended to be desert and excluded, and the risk score of patients who responded to immunotherapy was significantly lower than that of patients who did not respond to immunotherapy. The higher the infiltration levels of gamma delta T cells (γδ T cells), immature dendritic cells, and T follicular helper (Tfh) cells, the more significant adverse impact on the prognosis of CC patients was exhibited and an obviously positive correlation with the risk score was showed. Conclusions An immune gene risk score associated with the DDR molecular subtype was built and verified herein; that is applicable to the prognosis and immunotherapy response prediction in CC.
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Affiliation(s)
- Zhen Shang
- Medical Department of Qingdao University, Qingdao, China
| | - Ze Wang
- Department of Emergency Medicine, Qingdao Haici Medical Treatment Group, Qingdao, China
| | - Yongtao Zhang
- Department of Orthopedics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shanglong Liu
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
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Liu T, Hu A, Chen H, Li Y, Wang Y, Guo Y, Liu T, Zhou J, Li D, Chen Q. Comprehensive analysis identifies DNA damage repair-related gene HCLS1 associated with good prognosis in lung adenocarcinoma. Transl Cancer Res 2023; 12:2613-2628. [PMID: 37969376 PMCID: PMC10643974 DOI: 10.21037/tcr-23-921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/21/2023] [Indexed: 11/17/2023]
Abstract
Background Lung cancer is the leading cause of cancer-associated mortality. Lung adenocarcinoma (LUAD) amounts to more than 40% of all lung malignancies. Therefore, developing clinically useful biomarkers for this disease is critical. DNA damage repair (DDR) is a complicated signal transduction process that ensures genomic stability. DDR should be comprehensively analyzed to elucidate their clinical significance and tumor immune microenvironment interactions. Methods In this study, DDR-related genes (DRGs) were selected to investigate their prognostic impact on LUAD. A regression-based prognostic model was established based on The Cancer Genome Atlas (TCGA)-LUAD cohort and three external Gene Expression Omnibus (GEO) validation cohorts (GSE31210, GSE68465, and GSE72094). The robust, established model could independently predict the clinical outcomes in patients. Then, the prognostic performance of risk profiles was assessed using a time-dependent receiver operating characteristic (ROC) curve, Cox regression, nomogram, and Kaplan-Meier analyses. Furthermore, the potential biological functions and infiltration status of DRGs in LUAD were investigated with ESTIMATE and CIBERSORT. Finally, the effects of HCLS1 on the clinical features, prognosis, biological function, immune infiltration, and treatment response in LUAD were systematically analyzed. Results Eleven DRGs were constructed to categorize patients into high- and low-risk groups. The risk score was an independent predictor of overall survival (OS). HCLS1 expression was downregulated in LUAD samples and linked with clinicopathological features. Multivariate Cox regression analysis using the Kaplan-Meier plotter revealed that low HCLS1 expression was independently associated with poor OS. Moreover, the HCLS1 high-expression group had higher immune-related gene expression and ESTIMATE scores. It was positively correlated with the infiltration of M1 macrophages, activated memory CD4 T cells, CD8 T cells, memory B cells, resting dendritic cells, and memory CD4 T cells, Tregs, and neutrophils. Conclusions A new classification system was developed for LUAD according to DDR characteristics. This stratification has important clinical values, reliable prognosis, and immunotherapy in patients with LUAD. Moreover, HCLS1 is a potential prognostic biomarker of LUAD that correlates with the extent of immune cell infiltration in the tumor microenvironment (TME).
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Affiliation(s)
- Tingjun Liu
- Center of Animal Laboratory, Xuzhou Medical University, Xuzhou, China
| | - Ankang Hu
- Center of Animal Laboratory, Xuzhou Medical University, Xuzhou, China
| | - Hao Chen
- Respiratory Department, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yan Li
- Respiratory Department, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yonghui Wang
- School of Life Sciences, Xuzhou Medical University, Xuzhou, China
| | - Yao Guo
- School of Life Sciences, Xuzhou Medical University, Xuzhou, China
| | - Tingya Liu
- Department of Neurology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Jie Zhou
- The Second Clinical College of Xuzhou Medical University, Xuzhou, China
| | - Debao Li
- School of Imaging, Xuzhou Medical University, Xuzhou, China
| | - Quangang Chen
- School of Life Sciences, Xuzhou Medical University, Xuzhou, China
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Zhang P, Li Q, Zhang Y, Wang Q, Yan J, Shen A, Hu B. Identification of a Novel Gene Signature with DDR and EMT Difunctionalities for Predicting Prognosis, Immune Activity, and Drug Response in Breast Cancer. Int J Environ Res Public Health 2023; 20:1221. [PMID: 36673982 PMCID: PMC9859620 DOI: 10.3390/ijerph20021221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Breast cancer, with an overall poor clinical prognosis, is one of the most heterogeneous cancers. DNA damage repair (DDR) and epithelial-mesenchymal transition (EMT) have been identified to be associated with cancer's progression. Our study aimed to explore whether genes with both functions play a more crucial role in the prognosis, immune, and therapy response of breast cancer patients. Based on the Cancer Genome Atlas (TCGA) cancer database, we used LASSO regression analysis to identify the six prognostic-related genes with both DDR and EMT functions, including TP63, YWHAZ, BRCA1, CCND2, YWHAG, and HIPK2. Based on the six genes, we defined the risk scores of the patients and reasonably analyzed the overall survival rate between the patients with the different risk scores. We found that overall survival in higher-risk-score patients was lower than in lower-risk-score patients. Subsequently, further GO and KEGG analyses for patients revealed that the levels of immune infiltration varied for patients with high and low risk scores, and the high-risk-score patients had lower immune infiltration's levels and were insensitive to treatment with chemotherapeutic agents. Furthermore, the Gene Expression Omnibus (GEO) database validated our findings. Our data suggest that TP63, YWHAZ, BRCA1, CCND2, YWHAG, and HIPK2 can be potential genetic markers of prognostic assessment, immune infiltration and chemotherapeutic drug sensitivity in breast cancer patients.
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Affiliation(s)
- Pan Zhang
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
- Key Laboratory of Watershed Science and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Quan Li
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
- Key Laboratory of Watershed Science and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Yuni Zhang
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
- Key Laboratory of Watershed Science and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Qianqian Wang
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
- Key Laboratory of Watershed Science and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Junfang Yan
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
- Key Laboratory of Watershed Science and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Aihua Shen
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
- Key Laboratory of Watershed Science and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Burong Hu
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
- Key Laboratory of Watershed Science and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
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Xiao Z, Sun L, Zheng Y, Chen H, Zheng X, Luo J, Gu C, Lin R, Huang M, Bai Y, Chen ZS, Kinslow CJ, Loh J, Lin L. DNA damage repair gene mutations predict the efficacy of platinum-based chemotherapy and immunotherapy plus platinum-based chemotherapy in advanced non-small cell lung cancer: a retrospective Chinese cohort study. Transl Lung Cancer Res 2022; 11:2539-2566. [PMID: 36636408 PMCID: PMC9830265 DOI: 10.21037/tlcr-22-746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022]
Abstract
Background Platinum-based chemotherapy (PC) and immunotherapy plus platinum-based chemotherapy (IPC) remain the first-line treatment for advanced NSCLC. But only a minority patients benefit from PC, and existing biomarkers, such as PD-L1, have been shown to be defective in predicting the efficacy of IPC. Highlighting the need to identify novel biomarkers for the efficacy of PC and IPC. DNA damage repair (DDR) mutations are known to predict response to PC in solid tumors. However, the predictive value of DDR in PC and IPC of NSCLC remains unclear. Methods Patients diagnosed with advanced or metastatic NSCLC were retrospectively included if they underwent next generation sequencing prior to starting treatment. Primary endpoints were to explore whether DDR mutations (DDRmut) are associated with clinical outcomes of PC and IPC. Secondary end point were to explore the association between DDRmut and the choice to add immunotherapy to chemotherapy, and the impact of different DDR pathways on efficacy in PC and IPC. Results DDRmut showed a strong association with tumor mutation burden-high (TMB-H) versus DDR wild-type (DDRwt) and higher rates of PD-L1 TPS ≥50% positivity. In 63 patients treated with PC, ORRs were 15.38% and 2.86% for DDRmut and DDRwt subgroup (P=0.1536), and DCRs were 88.46% and 45.72% (P=0.00097) at 6 months after PC. The DDRmut patients had significantly improved median PFS (mPFS) and median overall survival (mOS) than DDRwt group (mPFS: 7.6 vs. 3.9 months, HR =1.93, 95% CI: 1.09 to 3.14, P=0.0220. mOS: 29.9 vs. 20.7 months, HR =2.31, 95% CI: 1.09 to 4.9, P=0.0250). Moreover, among 37 patients treated with IPC, ORRs were 45% and 11.76% for DDRmut and DDRwt patients (P=0.0365), and the DCRs were 95% and 70.58% (P=0.0752), respectively at 6 months after IPC. The DDRmut patients had significantly improved mPFS compared to the DDRwt group (19.5 vs. 4.5 months, HR =3.28, 95% CI: 1.53 to 9.56, P=0.0022). In DDRmut group, mPFS of IPC recipients was significantly better than that of PC recipients (19.5 vs. 7.6 months, HR =2.09, 95% CI: 0.98 to 4.42, P=0.050). Conclusions There is potential for DDR to serve as a positive predictor of PC and IPC in advanced NSCLC patients.
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Affiliation(s)
- Zhiwei Xiao
- Oncology Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lingling Sun
- Oncology Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yating Zheng
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Hanrui Chen
- Oncology Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinting Zheng
- Oncology Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiamin Luo
- Oncology Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chuying Gu
- Oncology Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruiting Lin
- The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mengli Huang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Yuezong Bai
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY, USA
| | - Connor J. Kinslow
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Jerold Loh
- Department of Haematology-Oncology, National University Cancer Institute, Singapore (NCIS), National University Health System, Singapore, Singapore
| | - Lizhu Lin
- Oncology Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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10
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Luo L, Keyomarsi K. PARP inhibitors as single agents and in combination therapy: the most promising treatment strategies in clinical trials for BRCA-mutant ovarian and triple-negative breast cancers. Expert Opin Investig Drugs 2022; 31:607-631. [PMID: 35435784 DOI: 10.1080/13543784.2022.2067527] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Poly (ADP-ribose) polymerase inhibitors (PARPis) are an exciting class of agents that have shown efficacy, particularly for BRCA-mutant triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSOC). However, most patients who receive PARPi as their standard of care therapy inevitably develop resistance and this underscores the need to identify additional targets that can circumvent such resistance. Combination treatment strategies have been developed in preclinical and clinical studies to address the challenges of efficacy and resistance. AREAS COVERED This review examines completed or ongoing clinical trials of PARPi mono- and combination therapies. PARPi monotherapy in HER2 negative breast (HR+ and TNBC subtypes) and ovarian cancer is a focal point. The authors propose potential strategies that might overcome resistance to PARPi and discuss key questions and future directions. EXPERT OPINION While the advent of PARPis has significantly improved the treatment of tumors with defects in DNA damage and repair pathways, careful patient selection will be essential to enhance these treatments. The identification of molecular biomarkers to predict disease response and progression is an endeavor.
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Affiliation(s)
- Linjie Luo
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Khandan Keyomarsi
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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11
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Leng Y, Dang S, Yin F, Gao T, Xiao X, Zhang Y, Chen L, Qin C, Lai N, Zhan XY, Huang K, Luo C, Kang Y, Wang N, Li Y, Liang Y, Huang B. GDPLichi: a DNA Damage Repair-Related Gene Classifier for Predicting Lung Adenocarcinoma Immune Checkpoint Inhibitors Response. Front Oncol 2021; 11:733533. [PMID: 34970479 PMCID: PMC8713481 DOI: 10.3389/fonc.2021.733533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/27/2021] [Indexed: 12/26/2022] Open
Abstract
Lung cancer is one of the most common and mortal malignancies, usually with a poor prognosis in its advanced or recurrent stages. Recently, immune checkpoint inhibitors (ICIs) immunotherapy has revolutionized the treatment of human cancers including lung adenocarcinoma (LUAD), and significantly improved patients' prognoses. However, the prognostic and predictive outcomes differ because of tumor heterogeneity. Here, we present an effective method, GDPLichi (Genes of DNA damage repair to predict LUAD immune checkpoint inhibitors response), as the signature to predict the LUAD patient's response to the ICIs. GDPLichi utilized only 7 maker genes from 8 DDR pathways to construct the predictive model and classified LUAD patients into two subgroups: low- and high-risk groups. The high-risk group was featured by worse prognosis and decreased B cells, CD8+ T cells, CD8+ central memory T cells, hematopoietic stem cells (HSC), myeloid dendritic cells (MDC), and immune scores as compared to the low-risk group. However, our research also suggests that the high-risk group was more sensitive to ICIs, which might be explained by increased TMB, neoantigen, immune checkpoint molecules, and immune suppression genes' expression, but lower TIDE score as compared to the low-risk group. This conclusion was verified in three other LUAD cohort datasets (GSE30219, GSE31210, GSE50081).
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Affiliation(s)
- Yang Leng
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shiying Dang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Fei Yin
- Department of Thoracic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Tianshun Gao
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xing Xiao
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yi Zhang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Lin Chen
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Changfei Qin
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Nannan Lai
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xiao-Yong Zhan
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Ke Huang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Chuanming Luo
- Center for Clinical Neuroscience, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yang Kang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Nan Wang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yun Li
- Department of Thoracic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yuhong Liang
- School of Medicine, Southern University Of Science And Technology, Shenzhen, China
| | - Bihui Huang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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12
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He L, Lomberk G. Collateral Victim or Rescue Worker?-The Role of Histone Methyltransferases in DNA Damage Repair and Their Targeting for Therapeutic Opportunities in Cancer. Front Cell Dev Biol 2021; 9:735107. [PMID: 34869318 PMCID: PMC8636273 DOI: 10.3389/fcell.2021.735107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/01/2021] [Indexed: 01/25/2023] Open
Abstract
Disrupted DNA damage signaling greatly threatens cell integrity and plays significant roles in cancer. With recent advances in understanding the human genome and gene regulation in the context of DNA damage, chromatin biology, specifically biology of histone post-translational modifications (PTMs), has emerged as a popular field of study with great promise for cancer therapeutics. Here, we discuss how key histone methylation pathways contribute to DNA damage repair and impact tumorigenesis within this context, as well as the potential for their targeting as part of therapeutic strategies in cancer.
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Affiliation(s)
- Lishu He
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Gwen Lomberk
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States,*Correspondence: Gwen Lomberk,
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13
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Teng PC, Huang SP, Liu CH, Lin TY, Cho YC, Lai YL, Wang SC, Yeh HC, Chuu CP, Chen DN, Cheng WC, Li CY. Identification of DNA Damage Repair-Associated Prognostic Biomarkers for Prostate Cancer Using Transcriptomic Data Analysis. Int J Mol Sci 2021; 22:11771. [PMID: 34769200 DOI: 10.3390/ijms222111771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/19/2021] [Accepted: 10/29/2021] [Indexed: 02/08/2023] Open
Abstract
In the recent decade, the importance of DNA damage repair (DDR) and its clinical application have been firmly recognized in prostate cancer (PC). For example, olaparib was just approved in May 2020 to treat metastatic castration-resistant PC with homologous recombination repair-mutated genes; however, not all patients can benefit from olaparib, and the treatment response depends on patient-specific mutations. This highlights the need to understand the detailed DDR biology further and develop DDR-based biomarkers. In this study, we establish a four-gene panel of which the expression is significantly associated with overall survival (OS) and progression-free survival (PFS) in PC patients from the TCGA-PRAD database. This panel includes DNTT, EXO1, NEIL3, and EME2 genes. Patients with higher expression of the four identified genes have significantly worse OS and PFS. This significance also exists in a multivariate Cox regression model adjusting for age, PSA, TNM stages, and Gleason scores. Moreover, the expression of the four-gene panel is highly correlated with aggressiveness based on well-known PAM50 and PCS subtyping classifiers. Using publicly available databases, we successfully validate the four-gene panel as having the potential to serve as a prognostic and predictive biomarker for PC specifically based on DDR biology.
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14
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Santoni M, Cimadamore A, Massari F, Sorgentoni G, Cheng L, Lopez-Beltran A, Battelli N, Montironi R. Narrative review: predicting future molecular and clinical profiles of prostate cancer in the United States. Transl Androl Urol 2021; 10:1562-1568. [PMID: 33850790 PMCID: PMC8039584 DOI: 10.21037/tau-20-1439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prostate cancer represents the most frequent tumor in men, accounting for the 21% of all diagnosed tumors, with 191,930 new cases and 33,330 deaths estimated in 2020. Advanced prostate cancer represents a heterogeneous disease, ranging from hormone naive or hormone sensitive to castration resistant. The therapeutic armamentarium for this disease has been implemented in the last years by novel hormonal therapies and chemotherapies. However, the percentage of patients who achieve complete responses still results negligible. On this scenario, the design of clinical trials investigating new therapeutic approaches represent a dramatic medical need. Predicting cancer incidence may be fundamental to design specific clinical trials, to optimize the allocation of economic resources, and to plan future cancer control programs. ERG, SPOP and DDR genes alterations can act as therapeutic targets in prostate cancer patients and can be tested to identify a gene-selected patient population to enrol in specific trials. According to our predictions, ERG gene fusions will be the most predominant molecular subtype, accounting for 69,050 new cases in 2030. Mutation in SPOP gene will be diagnosed in 16,512 tumors, corresponding to the number of cases associated with alterations in DDR genes (including 7,956 BRCA2 mutated tumors). In this article, we analyzed and discussed the future molecular and clinical profiles of prostate cancer in the United States, aimed to describe a series of distinct subpopulations and to quantify potential clinical trial candidates in the next years.
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Affiliation(s)
| | - Alessia Cimadamore
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, Ancona, Italy
| | - Francesco Massari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, Ancona, Italy
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15
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Song Y, Huang J, Liang D, Hu Y, Mao B, Li Q, Sun H, Yang Y, Zhang J, Zhang H, Chen H, Liu H, Zhang S. DNA Damage Repair Gene Mutations Are Indicative of a Favorable Prognosis in Colorectal Cancer Treated With Immune Checkpoint Inhibitors. Front Oncol 2021; 10:549777. [PMID: 33680909 PMCID: PMC7934780 DOI: 10.3389/fonc.2020.549777] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 12/18/2020] [Indexed: 01/05/2023] Open
Abstract
Background DNA damage repair (DDR) genes were recently implicated in the anti-tumor immune response. Therefore, it is worthwhile to unravel the implications of DDR pathways in the shaping of immune responsiveness in colorectal cancer (CRC) patients receiving immune checkpoint inhibitors (ICI). Methods We analyzed publicly available genomic data from a cohort treated with ICI from Memorial Sloan Kettering Cancer Center (MSK ICI cohort). To characterize the impact of the DDR mutation, the genomic data of The Cancer Genome Atlas (TCGA) colorectal adenocarcinoma (COADREAD) dataset was explored. We also analyzed the incidence of DDR mutation and microsatellite instability-high (MSI-H) in a Chinese CRC cohort using panel sequencing. Results The DDR pathway was commonly mutated (21.8%) in the multicancer MSK ICI cohort, with the highest frequency of 36.4% in CRCs. Survival analysis showed that DDR mutation correlated with an improved overall survival (OS) in CRCs and pan-cancer in the MSK ICI cohort. However, no significant associations were identified in the TCGA COADREAD and MSK non-ICI CRCs. DDR mutation was associated with higher tumor mutational burden (TMB) levels and increased immune cell infiltration and immune checkpoint molecule expression in the TCGA COADREAD dataset. Last, we investigated the DDR mutational pattern and its associations with MSI-H and other genomic features in a Chinese CRC cohort. Notably, MSI-H and DDR mutation was present in 5.7% and 13.4% of cases, respectively, which suggests that DDR identifies a higher proportion of potential responders than MSI-H. Conclusion Our data suggest that DDR mutation as an indication of enhanced cancer immunity, and it may function as a biomarker for patients with CRCs receiving ICI treatment. The high incidence of DDR mutation in the Chinese CRC cohort emphasizes the future utility of panel-based DDR evaluation in guiding ICI treatment.
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Affiliation(s)
- Yipeng Song
- Department of Radiation Oncology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Jian Huang
- Institute of Oncology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dandan Liang
- Medical Department, Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Ying Hu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Beibei Mao
- Medical Department, Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Qiujing Li
- Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, China
| | - Huaibo Sun
- Medical Department, Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Ying Yang
- Medical Department, Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Jiao Zhang
- Medical Department, Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Henghui Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Huan Chen
- Medical Department, Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Hao Liu
- Department of Oncology, Sichuan Provincial People's Hospital, Chengdu, China
| | - Shukun Zhang
- Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, China
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16
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Michmerhuizen AR, Chandler B, Olsen E, Wilder-Romans K, Moubadder L, Liu M, Pesch AM, Zhang A, Ritter C, Ward ST, Santola A, Nyati S, Rae JM, Hayes D, Feng FY, Spratt D, Wahl D, Eisner J, Pierce LJ, Speers C. Seviteronel, a Novel CYP17 Lyase Inhibitor and Androgen Receptor Antagonist, Radiosensitizes AR-Positive Triple Negative Breast Cancer Cells. Front Endocrinol (Lausanne) 2020; 11:35. [PMID: 32117061 PMCID: PMC7027396 DOI: 10.3389/fendo.2020.00035] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/17/2020] [Indexed: 12/21/2022] Open
Abstract
Increased rates of locoregional recurrence (LR) have been observed in triple negative breast cancer (TNBC) despite multimodality therapy, including radiation (RT). Recent data suggest inhibiting the androgen receptor (AR) may be an effective radiosensitizing strategy, and AR is expressed in 15-35% of TNBC tumors. The aim of this study was to determine whether seviteronel (INO-464), a novel CYP17 lyase inhibitor and AR antagonist, is able to radiosensitize AR-positive (AR+) TNBC models. In cell viability assays, seviteronel and enzalutamide exhibited limited effect as a single agent (IC50 > 10 μM). Using clonogenic survival assays, however, AR knockdown and AR inhibition with seviteronel were effective at radiosensitizing cells with radiation enhancement ratios of 1.20-1.89 in models of TNBC with high AR expression. AR-negative (AR-) models, regardless of their estrogen receptor expression, were not radiosensitized with seviteronel treatment at concentrations up to 5 μM. Radiosensitization of AR+ TNBC models was at least partially dependent on impaired dsDNA break repair with significant delays in repair at 6, 16, and 24 h as measured by immunofluorescent staining of γH2AX foci. Similar effects were observed in an in vivo AR+ TNBC xenograft model where there was a significant reduction in tumor volume and a delay to tumor doubling and tripling times in mice treated with seviteronel and radiation. Following combination treatment with seviteronel and radiation, increased binding of AR occurred at DNA damage response genes, including genes involved both in homologous recombination and non-homologous end joining. This trend was not observed with combination treatment of enzalutamide and RT, suggesting that seviteronel may have a different mechanism of radiosensitization compared to other AR inhibitors. Enzalutamide and seviteronel treatment also had different effects on AR and AR target genes as measured by immunoblot and qPCR. These results implicate AR as a mediator of radioresistance in AR+ TNBC models and support the use of seviteronel as a radiosensitizing agent in AR+ TNBC.
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Affiliation(s)
- Anna R. Michmerhuizen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Benjamin Chandler
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
- Cancer Biology Program, University of Michigan, Ann Arbor, MI, United States
| | - Eric Olsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - Kari Wilder-Romans
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - Leah Moubadder
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - Meilan Liu
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - Andrea M. Pesch
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, United States
| | - Amanda Zhang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - Cassandra Ritter
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - S. Tanner Ward
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - Alyssa Santola
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - Shyam Nyati
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - James M. Rae
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, United States
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Hayes
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Felix Y. Feng
- Department of Urology, Medicine and Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Daniel Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Wahl
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
| | - Joel Eisner
- Innocrin Pharmaceuticals Inc., Durham, NC, United States
| | - Lori J. Pierce
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Corey Speers
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Corey Speers
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17
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Kornberg Z, Chou J, Feng FY, Ryan CJ. Prostate cancer in the era of "Omic" medicine: recognizing the importance of DNA damage repair pathways. Ann Transl Med 2018; 6:161. [PMID: 29911109 PMCID: PMC5985268 DOI: 10.21037/atm.2018.05.06] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/02/2018] [Indexed: 02/01/2023]
Abstract
Data from recent high-throughput studies analyzing local and advanced prostate cancer have revealed an incredible amount of biological diversity, which has led to the classification of distinct molecular tumor subtypes. While integrating prostate cancer genomics with clinical medicine is still at its infancy, new approaches to treat prostate cancer are well underway and being studied. With the recognition that DNA damage repair (DDR) mutations play an important role in the pathogenesis of this disease, clinicians can begin to utilize genomic information in complex treatment decisions for prostate cancer patients. In this Review, we discuss the role of DDR mutations in prostate cancer, including deficiencies in homologous repair and mismatch repair (MMR), and how this information is revolutionizing the treatment landscape. In addition, we highlight the potential resistance mechanisms that may result as we begin to target these pathways in isolation and discuss potential combinatorial approaches that may delay or overcome resistance.
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Affiliation(s)
- Zachary Kornberg
- Department of Radiation Oncology, Division of Hematology and Oncology, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Jonathan Chou
- Department of Medicine, Division of Hematology and Oncology, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Felix Y. Feng
- Department of Radiation Oncology, Division of Hematology and Oncology, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Charles J. Ryan
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
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18
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Bordignon V, Di Domenico EG, Trento E, D'Agosto G, Cavallo I, Pontone M, Pimpinelli F, Mariani L, Ensoli F. How Human Papillomavirus Replication and Immune Evasion Strategies Take Advantage of the Host DNA Damage Repair Machinery. Viruses 2017; 9:v9120390. [PMID: 29257060 PMCID: PMC5744164 DOI: 10.3390/v9120390] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/11/2022] Open
Abstract
The DNA damage response (DDR) is a complex signalling network activated when DNA is altered by intrinsic or extrinsic agents. DDR plays important roles in genome stability and cell cycle regulation, as well as in tumour transformation. Viruses have evolved successful life cycle strategies in order to ensure a chronic persistence in the host, virtually avoiding systemic sequelae and death. This process promotes the periodic shedding of large amounts of infectious particles to maintain a virus reservoir in individual hosts, while allowing virus spreading within the community. To achieve such a successful lifestyle, the human papilloma virus (HPV) needs to escape the host defence systems. The key to understanding how this is achieved is in the virus replication process that provides by itself an evasion mechanism by inhibiting and delaying the host immune response against the viral infection. Numerous studies have demonstrated that HPV exploits both the ataxia-telangiectasia mutated (ATM) and ataxia-telangiectasia and rad3-related (ATR) DDR pathways to replicate its genome and maintain a persistent infection by downregulating the innate and cell-mediated immunity. This review outlines how HPV interacts with the ATM- and ATR-dependent DDR machinery during the viral life cycle to create an environment favourable to viral replication, and how the interaction with the signal transducers and activators of transcription (STAT) protein family and the deregulation of the Janus kinase (JAK)-STAT pathways may impact the expression of interferon-inducible genes and the innate immune responses.
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Affiliation(s)
- Valentina Bordignon
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Enea Gino Di Domenico
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Elisabetta Trento
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Giovanna D'Agosto
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Ilaria Cavallo
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Martina Pontone
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Fulvia Pimpinelli
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Luciano Mariani
- HPV Unit, Department of Gynaecologic Oncology, National Cancer Institute Regina Elena, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Fabrizio Ensoli
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
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Kalisperati P, Spanou E, Pateras IS, Korkolopoulou P, Varvarigou A, Karavokyros I, Gorgoulis VG, Vlachoyiannopoulos PG, Sougioultzis S. Inflammation, DNA Damage, Helicobacter pylori and Gastric Tumorigenesis. Front Genet 2017; 8:20. [PMID: 28289428 PMCID: PMC5326759 DOI: 10.3389/fgene.2017.00020] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/08/2017] [Indexed: 12/13/2022] Open
Abstract
Helicobacter pylori (H. pylori) is a Gram negative bacterium that colonizes the stomach of almost half human population. It has evolved to escape immune surveillance, establishes lifelong inflammation, predisposing to genomic instability and DNA damage, notably double strand breaks. The epithelial host cell responds by activation of DNA damage repair (DDR) machinery that seems to be compromised by the infection. It is therefore now accepted that genetic damage is a major mechanism operating in cases of H. pylori induced carcinogenesis. Here, we review the data on the molecular pathways involved in DNA damage and DDR activation during H. pylori infection.
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Affiliation(s)
- Polyxeni Kalisperati
- Gastroenterology Unit, Department of Pathophysiology, School of Medicine, National and Kapodistrian University Athens, Greece
| | - Evangelia Spanou
- Gastroenterology Unit, Department of Pathophysiology, School of Medicine, National and Kapodistrian University Athens, Greece
| | - Ioannis S Pateras
- Department of Histology and Embryology, School of Medicine, National and Kapodistrian University Athens, Greece
| | - Penelope Korkolopoulou
- 1st Department of Pathology, Laiko Hospital, School of Medicine, National and Kapodistrian University of Athens Athens, Greece
| | | | - Ioannis Karavokyros
- 1st Department of Surgery, Laiko Hospital, University of Athens, School of Medicine Athens, Greece
| | - Vassilis G Gorgoulis
- Department of Histology and Embryology, School of Medicine, National and Kapodistrian UniversityAthens, Greece; Biomedical Research Foundation of the Academy of AthensAthens, Greece; Faculty of Biology, Medicine and Health Manchester Cancer Research Centre, Manchester Academic Health Sciences Centre, The University of ManchesterManchester, UK
| | | | - Stavros Sougioultzis
- Gastroenterology Unit, Department of Pathophysiology, School of Medicine, National and Kapodistrian University Athens, Greece
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Li W, Gu X, Zhang X, Kong J, Ding N, Qi Y, Zhang Y, Wang J, Huang D. Cadmium delays non-homologous end joining (NHEJ) repair via inhibition of DNA-PKcs phosphorylation and downregulation of XRCC4 and Ligase IV. Mutat Res 2015. [PMID: 26201248 DOI: 10.1016/j.mrfmmm.2015.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although studies have shown that cadmium (Cd) interfered with DNA damage repair (DDR), whether Cd could affect non-homologous end joining (NHEJ) repair remains elusive. To further understand the effect of Cd on DDR, we used X-ray irradiation of Hela cells as an in vitro model system, along with γH2AX and 53BP1 as markers for DNA damage. Results showed that X-ray significantly increased γH2AX and 53BP1 foci in Hela cells (p < 0.01), all of which are characteristic of accrued DNA damage. The number of foci declined rapidly over time (1-8h postirradiation), indicating an initiation of NHEJ process. However, the disappearance of γH2AX and 53BP1 foci was remarkably slowed by Cd pretreatment (p < 0.01), suggesting that Cd reduced the efficiency of NHEJ. To further elucidate the mechanisms of Cd toxicity, several markers of NHEJ pathway including Ku70, DNA-PKcs, XRCC4 and Ligase IV were examined. Our data showed that Cd altered the phosphorylation of DNA-PKcs, and reduced the expression of both XRCC4 and Ligase IV in irradiated cells. These observations are indicative of the impairment of NHEJ-dependent DNA repair pathways. In addition, zinc (Zn) mitigated the effects of Cd on NHEJ, suggesting that the Cd-induced NHEJ alteration may partly result from the displacement of Zn or from an interference with the normal function of Zn-containing proteins by Cd. Our findings provide a new insight into the toxicity of Cd on NHEJ repair and its underlying mechanisms in human cells.
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Affiliation(s)
- Weiwei Li
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xueyan Gu
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaoning Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jinxin Kong
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Nan Ding
- Gansu Key laboratory of Space Radiobiology, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yongmei Qi
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yingmei Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jufang Wang
- Gansu Key laboratory of Space Radiobiology, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Dejun Huang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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Vikrant, Nakhwa P, Badgujar DC, Kumar R, Rathore KKS, Varma AK. Structural and functional characterization of the MERIT40 to understand its role in DNA repair. J Biomol Struct Dyn 2013; 32:2017-32. [PMID: 24125081 DOI: 10.1080/07391102.2013.843473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
MERIT40 (MEdiator of RAP80 Interaction and Targeting 40) is a novel associate of the BRCA1-complex and plays an essential role in DNA damage repair. It is the least characterized protein of BRCA1-complex and mainly responsible for maintaining the complex integrity. However, its structural and functional aspects of regulating the complex stability still remain elusive. Here, we carried out a comprehensive examination of MERIT40 biophysical properties and identified its novel interacting partner which would help to understand its role in BRCA1-complex. The recombinant protein was purified by affinity chromatography and unfolding pathway was determined using spectroscopic and calorimetric methods. Molecular model was generated using combinatorial approaches of modeling, and monomer-monomer docking was carried out to identify dimeric interface. Disordered region of MERIT40 was hatchet using trypsin and chymotrypsin to illustrate the existence of stable domain whose function was speculated through DALI search. Our findings suggest that MERIT40 forms a dimer in a concentration-independent manner. Its central region shows remarkable stability towards the protease digestion and has structural similarity with vWA-like region, a domain mainly present in complement activation factors. MERIT40 undergoes a three-state unfolding transition pathway with a dimeric intermediate. It interacts with adaptor molecule of BRCA1-complex, called ABRAXAS, thus help in extending the bridging interaction among various members which further stabilizes the whole complex. The results presented in this paper provide first-hand information on structural and folding behavior of MERIT40. These findings will help in elucidating the role of protein-protein interactions in stabilization of BRCA1-complex.
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Affiliation(s)
- Vikrant
- a Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer , Kharghar, Navi Mumbai , Maharashtra 410 210 , India
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