1
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Ng YB, Akincilar SC. Shaping DNA damage responses: Therapeutic potential of targeting telomeric proteins and DNA repair factors in cancer. Curr Opin Pharmacol 2024; 76:102460. [PMID: 38776747 DOI: 10.1016/j.coph.2024.102460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 05/25/2024]
Abstract
Shelterin proteins regulate genomic stability by preventing inappropriate DNA damage responses (DDRs) at telomeres. Unprotected telomeres lead to persistent DDR causing cell cycle inhibition, growth arrest, and apoptosis. Cancer cells rely on DDR to protect themselves from DNA lesions and exogenous DNA-damaging agents such as chemotherapy and radiotherapy. Therefore, targeting DDR machinery is a promising strategy to increase the sensitivity of cancer cells to existing cancer therapies. However, the success of these DDR inhibitors depends on other mutations, and over time, patients develop resistance to these therapies. This suggests the need for alternative approaches. One promising strategy is co-inhibiting shelterin proteins with DDR molecules, which would offset cellular fitness in DNA repair in a mutation-independent manner. This review highlights the associations and dependencies of the shelterin complex with the DDR proteins and discusses potential co-inhibition strategies that might improve the therapeutic potential of current inhibitors.
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Affiliation(s)
- Yu Bin Ng
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Semih Can Akincilar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore.
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2
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Zimmer J, Mueller L, Frank-Herrmann P, Rehnitz J, Dietrich JE, Bettendorf M, Strowitzki T, Krivega M. Low androgen signaling rescues genome integrity with innate immune response by reducing fertility in humans. Cell Death Dis 2024; 15:30. [PMID: 38212646 PMCID: PMC10784536 DOI: 10.1038/s41419-023-06397-5] [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: 08/18/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024]
Abstract
Development of the gonads under complex androgen regulation is critical for germ cells specification. In this work we addressed the relationship between androgens and genomic integrity determining human fertility. We used different study groups: individuals with Differences of Sex Development (DSD), including Complete Androgen Insensitivity Syndrome (CAIS) due to mutated androgen receptor (AR), and men with idiopathic nonobstructive azoospermia. Both showed genome integrity status influenced by androgen signaling via innate immune response activation in blood and gonads. Whole proteome analysis connected low AR to interleukin-specific gene expression, while compromised genome stability and tumorigenesis were also supported by interferons. AR expression was associated with predominant DNA damage phenotype, that eliminated AR-positive Sertoli cells as the degeneration of gonads increased. Low AR contributed to resistance from the inhibition of DNA repair in primary leukocytes. Downregulation of androgen promoted apoptosis and specific innate immune response with higher susceptibility in cells carrying genomic instability.
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Affiliation(s)
- J Zimmer
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - L Mueller
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - P Frank-Herrmann
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - J Rehnitz
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - J E Dietrich
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - M Bettendorf
- Division of Pediatric Endocrinology, Children's Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - T Strowitzki
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - M Krivega
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany.
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3
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Yalcin GD, Yilmaz KC, Dilber T, Acar A. Investigation of evolutionary dynamics for drug resistance in 3D spheroid model system using cellular barcoding technology. PLoS One 2023; 18:e0291942. [PMID: 37751451 PMCID: PMC10521976 DOI: 10.1371/journal.pone.0291942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/09/2023] [Indexed: 09/28/2023] Open
Abstract
Complex evolutionary dynamics governing the drug resistance is one of the major challenges in cancer treatment. Understanding these mechanisms requires a sequencing technology with higher resolution to delineate whether pre-existing or de novo drug mechanisms are behind the drug resistance. Combining this technology with clinically very relevant model system, namely 3D spheroids, better mimicking tumorigenesis and drug resistance have so far been lacking. Thus, we sought to establish dabrafenib and irinotecan resistant derivatives of barcoded 3D spheroids with the ultimate aim to quantify the selection-induced clonal dynamics and identify the genomic determinants in this model system. We found that dabrafenib and irinotecan induced drug resistance in 3D-HT-29 and 3D-HCT-116 spheroids are mediated by pre-existing and de novo resistant barcodes, indicating the presence of polyclonal drug resistance in this system. Moreover, whole-exome sequencing analysis found chromosomal gains and mutations associated with dabrafenib and irinotecan resistance in 3D-HT-29 and 3D-HCT-116 spheroids. Last, we show that dabrafenib and irinotecan resistance are also mediated by multiple drug resistance by detection of upregulation of the drug efflux pumps, ABCB1 and ABCG2, in our spheroid model system. Overall, we present the quantification of drug resistance and evolutionary dynamics in spheroids for the first time using cellular barcoding technology and the underlying genomic determinants of the drug resistance in our model system.
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Affiliation(s)
- Gizem Damla Yalcin
- Department of Biological Sciences, Middle East Technical University, Çankaya, Ankara, Turkey
| | - Kubra Celikbas Yilmaz
- Department of Biological Sciences, Middle East Technical University, Çankaya, Ankara, Turkey
| | - Tugce Dilber
- Department of Biological Sciences, Middle East Technical University, Çankaya, Ankara, Turkey
| | - Ahmet Acar
- Department of Biological Sciences, Middle East Technical University, Çankaya, Ankara, Turkey
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4
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Yang J, Wang X, Hao W, Wang Y, Li Z, Han Q, Zhang C, Liu H. MicroRNA-488: A miRNA with diverse roles and clinical applications in cancer and other human diseases. Biomed Pharmacother 2023; 165:115115. [PMID: 37418982 DOI: 10.1016/j.biopha.2023.115115] [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: 05/29/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/09/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that post-transcriptionally regulate the expression of approximately 50 % of all protein-coding genes. They have been demonstrated to act as key regulators in various pathophysiological processes and play significant roles in a wide range of human diseases, particularly cancer. Current research highlights the aberrant expression of microRNA-488 (miR-488) in multiple human diseases and its critical involvement in disease initiation and progression. Moreover, the expression level of miR-488 has been linked to clinicopathological features and patient prognosis across different diseases. However, a comprehensive systematic review of miR-488 is lacking. Therefore, our study aims to consolidate the current knowledge surrounding miR-488, with a primary focus on its emerging biological functions, regulatory mechanisms, and potential clinical applications in human diseases. Through this review, we aim to establish a comprehensive understanding of the diverse roles of miR-488 in the development of various diseases.
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Affiliation(s)
- Jiao Yang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Department of Anatomy, the Basic Medical School of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China
| | - Xinfang Wang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Department of Cell biology and Genetics, the Basic Medical School of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China
| | - Wenjing Hao
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Department of Cell biology and Genetics, the Basic Medical School of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China
| | - Ying Wang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China
| | - Zhongxun Li
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China
| | - Qi Han
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China
| | - Chunming Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China.
| | - Hongliang Liu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China; Department of Cell biology and Genetics, the Basic Medical School of Shanxi Medical University, Taiyuan 030001, Shanxi, PR China.
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5
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Chen G, Luo D, Qi X, Li D, Zheng J, Luo Y, Zhang C, Ren Q, Lu Y, Chan YT, Chen B, Wu J, Wang N, Feng Y. Characterization of cuproptosis in gastric cancer and relationship with clinical and drug reactions. Front Cell Dev Biol 2023; 11:1172895. [PMID: 37351275 PMCID: PMC10283039 DOI: 10.3389/fcell.2023.1172895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/09/2023] [Indexed: 06/24/2023] Open
Abstract
Gastric cancer (GC) is the fifth most common cancer worldwide. Cuproptosis is associated with cell growth and death as well as tumorigenesis. Aiming to lucubrate the potential influence of CRGs in gastric cancer, we acquired datasets of gastric cancer patients from TCGA and GEO. The identification of molecular subtypes with CRGs expression was achieved through unsupervised learning-cluster analysis. To evaluate the application value of subtypes, the K-M survival analysis was conducted to evaluate the clinical prognostic characteristics. Subsequently, we performed Gene Set Variation Analysis (GSVA) and utilized ssGSEA to quantify the extent of immune infiltration. Further, the K-M survival analysis was used to identify the prognosis-related CRGs. Next, signature genes of diagnostic predictive value were screened using the least absolute shrinkage and selection operator (LASSO) algorithm from the expression matrix for TCGA, as well as the signature gene-related subtype was clustered by the "ConsensusClusterPlus" package. Finally, the immunological and drug sensitivity assessments of the signature gene-related subtypes were conducted. A total of 173 CRGs were identified, most of the CRGs undergo copy number variation in gastric cancer. Under different patient subtypes, immune cell levels differed significantly, and the subtype exhibiting high expression of the CRGs had a better prognosis. Furthermore, we selected 34 CRGs that were highly correlated with the prognosis of gastric cancer. By constructing a multivariate Cox proportional-hazards model and a hazard scoring system, we were able to categorize patients into high- and low-risk groups based on their hazard score. K-M analysis demonstrated a significant survival disadvantage in the high-risk group. Based on Lasso regression analysis, we screened 16 signature genes, a multivariate logistic regression model [cutoff: 0.149 (0.000, 0.974), AUC:0.987] and a prognosis network diagram was constructed and their prediction efficiency for gastric cancer prognostic diagnosis was well validated. According to the signature genes, the patients were separated to two signature subtypes. We found that patients with higher CRGs expression and better prognosis had lower levels of immune infiltration. Finally, according to the results of drug susceptibility analysis, docetaxel, 5-Fluorouracil, gemcitabin, and paclitaxel were found to be more sensitive to gastric cancer.
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Affiliation(s)
- Guoming Chen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Dongqiang Luo
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiangjun Qi
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danyun Li
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiyuan Zheng
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yang Luo
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Cheng Zhang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Qing Ren
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yuanjun Lu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yau-Tuen Chan
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Bonan Chen
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Junyu Wu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ning Wang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yibin Feng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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6
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Cao Z, Jiang H, Zhao C, Zhou H, Ma Z, Xu C, Zhang J, Jiang M, Wang Z. Up‐regulation of
PRKDC
was associated with poor renal dysfunction after renal transplantation: A multi‐centre analysis. J Cell Mol Med 2023; 27:1362-1372. [PMID: 37002788 PMCID: PMC10183702 DOI: 10.1111/jcmm.17737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
Renal transplantation is the only efficacious treatment for end-stage kidney disease. However, some people have developed renal insufficiency after transplantation, the mechanisms of which have not been well clarified. Previous studies have focused on patient factors, while the effect of gene expression in the donor kidney on post-transplant renal function has been less studied. Donor kidney clinical data and mRNA expression status were extracted from the GEO database (GSE147451). Weight gene co-expression network analysis (WGCNA) and differential gene enrichment analysis were performed. For external validation, we collected data from 122 patients who accepted renal transplantation at several hospitals and measured the level of target genes by qPCR. This study included 192 patients from the GEO data set, and 13 co-expressed genes were confirmed by WGCNA and differential gene enrichment analysis. Then, the PPI network contained 17 edges as well as 12 nodes, and four central genes (PRKDC, RFC5, RFC3 and RBM14) were identified. We found by collecting data from 122 patients who underwent renal transplantation in several hospitals and by multivariate logistic regression that acute graft-versus-host disease postoperative infection, PRKDC [Hazard Ratio (HR) = 4.44; 95% CI = [1.60, 13.68]; p = 0.006] mRNA level correlated with the renal function after transplantation. The prediction model constructed had good predictive accuracy (C-index = 0.886). Elevated levels of donor kidney PRKDC are associated with renal dysfunction after transplantation. The prediction model of renal function status for post-transplant recipients based on PRKDC has good predictive accuracy and clinical application.
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Affiliation(s)
- Zhijun Cao
- Department of Urology, Suzhou Ninth People's Hospital Soochow University Suzhou 215000 China
- Department of Urology The First Affiliated Hospital of Soochow University Suzhou 215000 China
| | - Hao Jiang
- Department of Urology The First Affiliated Hospital of Soochow University Suzhou 215000 China
| | - Chunchun Zhao
- Department of Urology, Suzhou Municipal Hospital Nanjing Medical University Suzhou 215000 China
| | - Huifeng Zhou
- Department of Haematology The Children's Hospital of Soochow University Suzhou 215000 China
| | - Zheng Ma
- Department of Urology, Suzhou Ninth People's Hospital Soochow University Suzhou 215000 China
| | - Chen Xu
- Department of Urology, Suzhou Ninth People's Hospital Soochow University Suzhou 215000 China
| | - Jianglei Zhang
- Department of Urology The First Affiliated Hospital of Soochow University Suzhou 215000 China
| | - Minjun Jiang
- Department of Urology, Suzhou Ninth People's Hospital Soochow University Suzhou 215000 China
| | - Zhenfan Wang
- Department of Urology, Suzhou Ninth People's Hospital Soochow University Suzhou 215000 China
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7
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Novotny JP, Mariño-Enríquez A, Fletcher JA. Targeting DNA-PK. Cancer Treat Res 2023; 186:299-312. [PMID: 37978142 DOI: 10.1007/978-3-031-30065-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
This chapter explores the multifaceted roles of DNA-PK with particular focus on its functions in non-homologous end-joining (NHEJ) DNA repair. DNA-PK is the primary orchestrator of NHEJ but also regulates other biologic processes. The growing understanding of varied DNA-PK biologic roles highlights new avenues for cancer treatment. However, these multiple roles also imply challenges, particularly in combination therapies, with perhaps a higher risk of clinical toxicities than was previously envisioned. These considerations underscore the need for compelling and innovative strategies to accomplish effective clinical translation.
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8
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Wang X, Huang Z, Li L, Yang Y, Zhang J, Wang L, Yuan J, Li Y. The Role of Alternative Splicing Factors, DDB2-Related Ageing and DNA Damage Repair in the Progression and Prognosis of Stomach Adenocarcinoma Patients. Genes (Basel) 2022; 14:genes14010039. [PMID: 36672781 PMCID: PMC9858704 DOI: 10.3390/genes14010039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
DNA damage response is a key signal transduction pathway in triggering ageing and tumor progression. Abnormal alternative splicing (AS) is associated with tumors and ageing. However, the role of AS factors associated with DNA damage repair and ageing in stomach adenocarcinoma (STAD) remains unclear. We downloaded the percentage of splicing (PSI) values for AS in STAD from the TCGA SpliceSeq database. The PSI values of DNA repair gene AS events were integrated with STAD patient survival data for Cox regression analysis. The prediction model for the overall survival (OS) was constructed by the clinical traits. The tumor immune microenvironment was analyzed by CIBERSORT and ESTIMATE. We detected 824 AS events originating from 166 DNA repair genes. Cox regression analysis provided 21 prognostic AS events connected with OS statistically, and a prognostic prediction model was constructed. The expression of these AS factors was higher in STAD tumors. DDB2 high senescence levels were associated with active immune responses and better survival in STAD patients. We built a novel prognostic model founded on DNA repair genes with AS events and identified that DDB2 may be a potential biomarker to apply in clinics.
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Affiliation(s)
- Xinshu Wang
- Postgraduate Training Base of Jinzhou Medical University, Shanghai East Hospital, Shanghai 200120, China
| | - Zhiyuan Huang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Lei Li
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Yuntong Yang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Jiyuan Zhang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Li Wang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
- Correspondence: (J.Y.); (Y.L.); Tel.: +86-138-1823-3596 (J.Y.); +86-188-1730-0177 (Y.L.)
| | - Yunhui Li
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
- Ji’an Hospital, Shanghai East Hospital, Ji’an 343000, China
- Correspondence: (J.Y.); (Y.L.); Tel.: +86-138-1823-3596 (J.Y.); +86-188-1730-0177 (Y.L.)
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9
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Yang X, Yang F, Lan L, Wen N, Li H, Sun X. Potential value of PRKDC as a therapeutic target and prognostic biomarker in pan-cancer. Medicine (Baltimore) 2022; 101:e29628. [PMID: 35801800 PMCID: PMC9259106 DOI: 10.1097/md.0000000000029628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND While protein kinase, DNA-activated, catalytic subunit (PRKDC) plays an important role in double-strand break repair to retain genomic stability, there is still no pan-cancer analysis based on large clinical information on the relationship between PRKDC and different tumors. For the first time, this research used numerous databases to perform a pan-cancer review for PRKDC to explore the possible mechanism of PRKDC in the etiology and outcomes in various tumors. METHODS PRKDC's expression profile and prognostic significance in pan-cancer were investigated based on various databases and online platforms, including TIMER2, GEPIA2, cBioPortal, CPTAC, and SangerBox. We applied the TIMER to identified the interlink of PRKDC and the immune infiltration in assorted tumors, and the SangerBox online platform was adopted to find out the relevance between PRKDC and immune checkpoint genes, tumor mutation burden, and microsatellite instability in tumors. GeneMANIA tool was employed to create a protein-protein interaction analysis, gene set enrichment analysis was conducted to performed gene enrichment analysis. RESULTS Overall, tumor tissue presented a higher degree of PRKDC expression than adjacent normal tissue. Meanwhile, patients with high PRKDC expression have a worse prognosis. PRKDC mutations were present in almost all The Cancer Genome Atlas tumors and might lead to a better survival prognosis. The PRKDC expression level was shown a positive correlation with tumor-infiltrating immune cells. PRKDC high expression cohorts were enriched in "cell cycle" "oocyte meiosis" and "RNA-degradation" signaling pathways. CONCLUSIONS This study revealed the potential value of PRKDC in tumor immunology and as a therapeutic target and prognostic biomarker in pan-cancer.
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Affiliation(s)
- Xiawei Yang
- Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Feng Yang
- Department of Gynocology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Liugen Lan
- Transplant Medical Center, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Key Laboratory of Organ Donation and Transplantation, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Key Laboratory for Transplantation Medicine, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Transplantation Medicine Research Center of Engineering Technology, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Ning Wen
- Transplant Medical Center, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Key Laboratory of Organ Donation and Transplantation, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Key Laboratory for Transplantation Medicine, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Transplantation Medicine Research Center of Engineering Technology, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Haibin Li
- Transplant Medical Center, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Key Laboratory of Organ Donation and Transplantation, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Key Laboratory for Transplantation Medicine, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Transplantation Medicine Research Center of Engineering Technology, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Xuyong Sun
- Transplant Medical Center, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Key Laboratory of Organ Donation and Transplantation, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Key Laboratory for Transplantation Medicine, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Transplantation Medicine Research Center of Engineering Technology, Nanning, Guangxi Zhuang Autonomous Region, China
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10
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Chen Y, Li Y, Xiong J, Lan B, Wang X, Liu J, Lin J, Fei Z, Zheng X, Chen C. Role of PRKDC in cancer initiation, progression, and treatment. Cancer Cell Int 2021; 21:563. [PMID: 34702253 PMCID: PMC8547028 DOI: 10.1186/s12935-021-02229-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/24/2021] [Indexed: 01/29/2023] Open
Abstract
The PRKDC gene encodes the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) protein. DNA-PKcs plays an important role in nonhomologous end joining (NHEJ) of DNA double-strand breaks (DSBs) and is also closely related to the establishment of central immune tolerance and the maintenance of chromosome stability. The occurrence and development of different types of tumors and the results of their treatment are also influenced by DNA-PKcs, and it may also predict the results of radiotherapy, chemotherapy, and therapy with immune checkpoint inhibitors (ICIs). Here, we discuss and review the structure and mechanism of action of PRKDC and DNA-PKcs and their relationship with cancer.
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Affiliation(s)
- Yu Chen
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-Immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China
| | - Yi Li
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Jiani Xiong
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-Immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Bin Lan
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Shanghai Center for Systems Biomedicine Research, Shanghai Jiao Tong University, Shanghai, China
| | - Xuefeng Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,The First Affiliated Hospital of Soochow University and State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Soochow University, Suzhou, Jiangsu, China
| | - Jun Liu
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-Immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Jing Lin
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-Immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China
| | - Zhaodong Fei
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Xiaobin Zheng
- Cancer Bio-Immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Department of Radiation Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Chuanben Chen
- Cancer Bio-Immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China. .,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China. .,Department of Radiation Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.
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11
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Genomic alterations associated with mutational signatures, DNA damage repair and chromatin remodeling pathways in cervical carcinoma. NPJ Genom Med 2021; 6:82. [PMID: 34620846 PMCID: PMC8497615 DOI: 10.1038/s41525-021-00244-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/23/2021] [Indexed: 11/08/2022] Open
Abstract
Despite recent advances in the prevention of cervical cancer, the disease remains a leading cause of cancer-related deaths in women worldwide. By applying the GISTIC2.0 and/or the MutSig2CV algorithms on 430 whole-exome-sequenced cervical carcinomas, we identified previously unreported significantly mutated genes (SMGs) (including MSN, GPX1, SPRED3, FAS, and KRT8), amplifications (including NFIA, GNL1, TGIF1, and WDR87) and deletions (including MIR562, PVRL1, and NTM). Subset analyses of 327 squamous cell carcinomas and 86 non-squamous cell carcinomas revealed previously unreported SMGs in BAP1 and IL28A, respectively. Distinctive copy number alterations related to tumors predominantly enriched for *CpG- and Tp*C mutations were observed. CD274, GRB2, KRAS, and EGFR were uniquely significantly amplified within the Tp*C-enriched tumors. A high frequency of aberrations within DNA damage repair and chromatin remodeling genes were detected. Facilitated by the large sample size derived from combining multiple datasets, this study reveals potential targets and prognostic markers for cervical cancer.
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12
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Conconi D, Redaelli S, Lissoni AA, Cilibrasi C, Perego P, Gautiero E, Sala E, Paderno M, Dalprà L, Landoni F, Lavitrano M, Roversi G, Bentivegna A. Genomic and Epigenomic Profile of Uterine Smooth Muscle Tumors of Uncertain Malignant Potential (STUMPs) Revealed Similarities and Differences with Leiomyomas and Leiomyosarcomas. Int J Mol Sci 2021; 22:1580. [PMID: 33557274 PMCID: PMC7914585 DOI: 10.3390/ijms22041580] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 01/20/2023] Open
Abstract
Uterine smooth muscle tumors of uncertain malignant potential (STUMPs) represent a heterogeneous group of tumors that cannot be histologically diagnosed as unequivocally benign or malignant. For this reason, many authors are working to obtain a better definition of diagnostic and prognostic criteria. In this work, we analyzed the genomic and epigenomic profile of uterine smooth muscle tumors (USMTs) in order to find similarities and differences between STUMPs, leiomyosarcomas (LMSs) and leiomyomas (LMs), and possibly identify prognostic factors in this group of tumors. Array-CGH data on 23 USMTs demonstrated the presence of a more similar genomic profile between STUMPs and LMSs. Some genes, such as PRKDC and PUM2, with a potential prognostic value, were never previously associated with STUMP. The methylation data appears to be very promising, especially with regards to the divergent profile found in the sample that relapsed, characterized by an overall CGI hypomethylation. Finally, the Gene Ontology analysis highlighted some cancer genes that could play a pivotal role in the unexpected aggressive behavior that can be found in some of these tumors. These genes could prove to be prognostic markers in the future.
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Affiliation(s)
- Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
| | - Serena Redaelli
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
| | - Andrea Alberto Lissoni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
- Clinic of Obstetrics and Gynecology, San Gerardo Hospital, 20900 Monza, Italy
| | - Chiara Cilibrasi
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RH, UK;
| | - Patrizia Perego
- Division of Pathology, San Gerardo Hospital, 20900 Monza, Italy;
| | - Eugenio Gautiero
- Medical Genetics Laboratory, San Gerardo Hospital, 20900 Monza, Italy; (E.G.); (E.S.)
| | - Elena Sala
- Medical Genetics Laboratory, San Gerardo Hospital, 20900 Monza, Italy; (E.G.); (E.S.)
| | - Mariachiara Paderno
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
- Clinic of Obstetrics and Gynecology, San Gerardo Hospital, 20900 Monza, Italy
| | - Leda Dalprà
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
| | - Fabio Landoni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
- Clinic of Obstetrics and Gynecology, San Gerardo Hospital, 20900 Monza, Italy
| | - Marialuisa Lavitrano
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
| | - Gaia Roversi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
- Medical Genetics Laboratory, San Gerardo Hospital, 20900 Monza, Italy; (E.G.); (E.S.)
| | - Angela Bentivegna
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
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13
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Lu J, Huang XY, Wang YH, Xie JW, Wang JB, Lin JX, Chen QY, Cao LL, Li P, Huang CM, Zheng CH. POC1A acts as a promising prognostic biomarker associated with high tumor immune cell infiltration in gastric cancer. Aging (Albany NY) 2020; 12:18982-19011. [PMID: 33052878 PMCID: PMC7732308 DOI: 10.18632/aging.103624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/04/2020] [Indexed: 01/24/2023]
Abstract
The effect of POC1 centriolar protein A (POC1A) on gastric cancer (GC) has not been clearly defined. In this study, POC1A expression and clinical information in patients with GC were analyzed. Multiple databases were used to investigate the genes that were co-expressed with POC1A and genes whose changes co-occurred with genetic alternations of POC1A. Moreover, the TISIDB and TIMER databases were used to analyze immune infiltration. The GSE54129 GC dataset and LASSO regression model (tumor vs. normal) were employed, and 6 significant differentially expressed genes (LAMP5, CEBPB, ARMC9, PAOX, VMP1, POC1A) were identified. POC1A was selected for its high expression in adjacent tissues, which was confirmed with IHC. High POC1A expression was related to better overall and recurrence-free survival. GO and KEGG analyses demonstrated that POC1A may regulate the cell cycle, DNA replication and cell growth. Furthermore, POC1A was found to be correlated with immune infiltration levels in GC according to the TISIDB and TIMER databases. These findings indicate that POC1A acts as a tumor suppressor in GC by regulating the cell cycle and cell growth. In addition, POC1A preferentially regulates the immune infiltration of GC via several immune genes. However, the specific mechanism requires further study.
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Affiliation(s)
- Jun Lu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Xiao-Yan Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Yao-Hui Wang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Jian-Wei Xie
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Jia-Bin Wang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Jian-Xian Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Qi-Yue Chen
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Long-Long Cao
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Ping Li
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Chang-Ming Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Chao-Hui Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
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14
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Yin Y, He Q, Li Y, Long J, Lei X, Li Z, Zhu W. Emerging functions of PRKDC in the initiation and progression of cancer. TUMORI JOURNAL 2020; 107:483-488. [PMID: 32867618 DOI: 10.1177/0300891620950472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is encoded by the protein kinase, DNA-activated, catalytic polypeptide (PRKDC) gene. DNA-PKcs plays a major role in nonhomologous end joining DNA repair, and it has been identified to be an important factor in tumor progression and metastasis. DNA-PKcs may have opposite effects in diseases, depending on the cell and tissue types. In this review, we discuss its role in various tumors. High levels of DNA-PKcs are directly associated with prognosis, neoplasm recurrence rates, and overall survival. Our results suggest that DNA-PKcs may serve as a therapeutic target for advanced malignancies.
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Affiliation(s)
- Yuting Yin
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Qinglian He
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Yuling Li
- Department of Pathology, Dongguan Hospital of Southern Medical University, Dongguan, Guangdong Province, China
| | - Jiali Long
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Xue Lei
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Ziqi Li
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Wei Zhu
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
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