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Abdulla R, Devasia Puthenpurackal J, Pinto SM, Rekha PD, Subbannayya Y. Serum autoantibody profiling of oral squamous cell carcinoma patients reveals NUBP2 as a potential diagnostic marker. Front Oncol 2023; 13:1167691. [PMID: 37810966 PMCID: PMC10556692 DOI: 10.3389/fonc.2023.1167691] [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: 02/16/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Oral Squamous Cell Carcinoma (OSCC), a common malignancy of the head and neck region, is frequently diagnosed at advanced stages, necessitating the development of efficient diagnostic methods. Profiling autoantibodies generated against tumor-associated antigens have lately demonstrated a promising role in diagnosis, predicting disease course, and response to therapeutics and relapse. Methods In the current study, we, for the first time, aimed to identify and evaluate the diagnostic value of autoantibodies in serum samples of patients with OSCC using autoantibody profiling by an immunome protein array. The utility of anti-NUBP2 antibody and tissue positivity in OSCC was further evaluated. Results and discussion We identified a total of 53 autoantibodies with significant differential levels between OSCC and control groups, including 25 that were increased in OSCC and 28 that were decreased. These included autoantibodies against Thymidine kinase 1 (TK1), nucleotide-binding protein 2 (NUBP2), and protein pyrroline-5-carboxylate reductase 1 (PYCR1), among others. Immunohistochemical validation indicated positive staining of NUBP2 in a large majority of cases (72%). Further, analysis of OSCC data available in TCGA revealed higher NUBP2 expression correlated with better disease-free patient survival. In conclusion, the differential serum autoantibodies identified in the current study, including those for NUBP2, could be used as potential biomarkers for early diagnosis or as screening biomarkers for OSCC pending investigation in a larger cohort.
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Affiliation(s)
- Riaz Abdulla
- Department of Oral Pathology and Microbiology, Yenepoya Dental College, Yenepoya (Deemed to be University), Mangalore, India
| | - Jofy Devasia Puthenpurackal
- Department of Oral Pathology and Microbiology, Yenepoya Dental College, Yenepoya (Deemed to be University), Mangalore, India
| | - Sneha M. Pinto
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | | | - Yashwanth Subbannayya
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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2
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Song HY, Shen R, Mahasin H, Guo YN, Wang DG. DNA replication: Mechanisms and therapeutic interventions for diseases. MedComm (Beijing) 2023; 4:e210. [PMID: 36776764 PMCID: PMC9899494 DOI: 10.1002/mco2.210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 02/09/2023] Open
Abstract
Accurate and integral cellular DNA replication is modulated by multiple replication-associated proteins, which is fundamental to preserve genome stability. Furthermore, replication proteins cooperate with multiple DNA damage factors to deal with replication stress through mechanisms beyond their role in replication. Cancer cells with chronic replication stress exhibit aberrant DNA replication and DNA damage response, providing an exploitable therapeutic target in tumors. Numerous evidence has indicated that posttranslational modifications (PTMs) of replication proteins present distinct functions in DNA replication and respond to replication stress. In addition, abundant replication proteins are involved in tumorigenesis and development, which act as diagnostic and prognostic biomarkers in some tumors, implying these proteins act as therapeutic targets in clinical. Replication-target cancer therapy emerges as the times require. In this context, we outline the current investigation of the DNA replication mechanism, and simultaneously enumerate the aberrant expression of replication proteins as hallmark for various diseases, revealing their therapeutic potential for target therapy. Meanwhile, we also discuss current observations that the novel PTM of replication proteins in response to replication stress, which seems to be a promising strategy to eliminate diseases.
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Affiliation(s)
- Hao-Yun Song
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - Rong Shen
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - Hamid Mahasin
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - Ya-Nan Guo
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - De-Gui Wang
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
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Dai D, Li Q, Zhou P, Huang J, Zhuang H, Wu H, Chen B. Analysis of Omics Data Reveals Nucleotide Excision Repair-Related Genes Signature in Highly-Grade Serous Ovarian Cancer to Predict Prognosis. Front Cell Dev Biol 2022; 10:874588. [PMID: 35769257 PMCID: PMC9235032 DOI: 10.3389/fcell.2022.874588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/02/2022] [Indexed: 12/31/2022] Open
Abstract
Most of the high-grade serous ovarian cancers (HGSOC) are accompanied by P53 mutations, which are related to the nucleotide excision repair (NER) pathway. This study aims to construct a risk signature based on NER-related genes that could effectively predict the prognosis for advanced patients with HGSOC. In our study, we found that two clusters of HGSOC with significantly different overall survival (OS) were identified by consensus clustering and principal component analysis (PCA). Then, a 7-gene risk signature (DDB2, POLR2D, CCNH, XPC, ERCC2, ERCC4, and RPA2) for OS prediction was developed subsequently based on TCGA cohort, and the risk score-based signature was identified as an independent prognostic indicator for HGSOC. According to the risk score, HGSOC patients were divided into high-risk group and low-risk group, in which the distinct OS and the predictive power were also successfully verified in the GEO validation sets. Then we constructed a nomogram, including the risk signature and clinical-related risk factors (age and treatment response) that predicted an individual’s risk of OS, which can be validated by assessing calibration curves. Furthermore, GSEA showed that the genes in the high-risk group were significantly enriched in cancer-related pathways, such as “MAPK signaling pathway”, “mTOR signaling pathway”, “VEGF signaling pathway” and so on. In conclusion, our study has developed a robust NER-related genes-based molecular signature for prognosis prediction, and the nomogram could be used as a convenient tool for OS evaluation and guidance of therapeutic strategies in advanced patients with HGSOC.
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Affiliation(s)
- Danian Dai
- Department of Vascular and Plastic Surgery, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qiang Li
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Pengfei Zhou
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Jianjiang Huang
- Department of Pathology, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hongkai Zhuang
- Department of General Surgery, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Hongkai Zhuang, ; Hongmei Wu, ; Bo Chen,
| | - Hongmei Wu
- Department of Pathology, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Hongkai Zhuang, ; Hongmei Wu, ; Bo Chen,
| | - Bo Chen
- Department of Breast Cancer, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Hongkai Zhuang, ; Hongmei Wu, ; Bo Chen,
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4
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Chen R, Hu B, Jiang M, Deng W, Zheng P, Fu B. Bioinformatic Analysis of the Expression and Clinical Significance of the DNA Replication Regulator MCM Complex in Bladder Cancer. Int J Gen Med 2022; 15:5465-5485. [PMID: 35698656 PMCID: PMC9188401 DOI: 10.2147/ijgm.s368573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/26/2022] [Indexed: 12/04/2022] Open
Abstract
Objective The minichromosome maintenance (MCM) complex (MCM2, MCM3, MCM4, MCM5, MCM6, and MCM7), which regulates DNA replication and cell cycle progression, is essential for the development and progression of multiple tumors, but their role in bladder cancer development remains unclear. In the present study, the biological role and clinical significance of the MCM complex in bladder cancer were systematically elucidated. Materials and Methods We analyzed DNA mutations, mRNA expression and protein levels, protein–protein interaction (PPI) networks, functional enrichment, prognostic value of MCM2/3/4/5/6/7 in bladder urothelial carcinoma (BLC) and the connections between the immune cell infiltration and the overall survival of BLC patients with the MCM expression levels using Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), the Cancer Genome Atlas database (TCGA), Human Protein Atlas, UALCAN, STRING, cBioPortal, TIMER and GSCALite databases. Results The outcomes showed that the mRNA expression level of each member of the MCM complex was significantly correlated with histologic grade and tumor histology in BLC patients. Moreover, survival analysis showed that MCM/2/3/4/5/6/7 mRNA expressions were significantly associated with prognosis in patients with bladder cancer. Moreover, we experimentally validated the overexpression of the MCM2-7 complex in the BLC. Based on functional enrichment and PPI network analysis, the MCM complex might promote the progression of bladder cancer by activating DNA replication and accelerating cell cycle progression. In addition, MCM2/3/4/5/6/7 genes were also significantly associated with tumor immune cells infiltration and the drug sensitivity in BLC. Conclusion Our study suggests that the MCM complex especially MCM2/4/6/7 might be potential molecular therapeutic targets for BLC treatment and might be useful biomarkers for diagnosis and prognosis.
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Affiliation(s)
- Ru Chen
- Department of Urology, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People’s Republic of China
- Department of Urology, The First Hospital of Putian City, Putian, Fujian, People’s Republic of China
| | - Bing Hu
- Department of Urology, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People’s Republic of China
| | - Ming Jiang
- Department of Urology, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People’s Republic of China
| | - Wen Deng
- Department of Urology, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People’s Republic of China
| | - Ping Zheng
- Department of Urology, Shangrao municipal Hospital, Shangrao, 334000, Jiangxi Province, People’s Republic of China
| | - Bin Fu
- Department of Urology, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People’s Republic of China
- Jiangxi Institute of Urology, Nanchang City, Jiangxi Province, People’s Republic of China
- Correspondence: Bin Fu, Email
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VanderVere-Carozza PS, Gavande NS, Jalal SI, Pollok KE, Ekinci E, Heyza J, Patrick SM, Masters A, Turchi JJ, Pawelczak KS. In Vivo Targeting Replication Protein A for Cancer Therapy. Front Oncol 2022; 12:826655. [PMID: 35251993 PMCID: PMC8895377 DOI: 10.3389/fonc.2022.826655] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/18/2022] [Indexed: 02/04/2023] Open
Abstract
Replication protein A (RPA) plays essential roles in DNA replication, repair, recombination, and the DNA damage response (DDR). Retrospective analysis of lung cancer patient data demonstrates high RPA expression as a negative prognostic biomarker for overall survival in smoking-related lung cancers. Similarly, relative expression of RPA is a predictive marker for response to chemotherapy. These observations are consistent with the increase in RPA expression serving as an adaptive mechanism that allows tolerance of the genotoxic stress resulting from carcinogen exposure. We have developed second-generation RPA inhibitors (RPAis) that block the RPA-DNA interaction and optimized formulation for in vivo analyses. Data demonstrate that unlike first-generation RPAis, second-generation molecules show increased cellular permeability and induce cell death via apoptosis. Second-generation RPAis elicit single-agent in vitro anticancer activity across a broad spectrum of cancers, and the cellular response suggests existence of a threshold before chemical RPA exhaustion induces cell death. Chemical RPA inhibition potentiates the anticancer activity of a series of DDR inhibitors and traditional DNA-damaging cancer therapeutics. Consistent with chemical RPA exhaustion, we demonstrate that the effects of RPAi on replication fork dynamics are similar to other known DDR inhibitors. An optimized formulation of RPAi NERx 329 was developed that resulted in single-agent anticancer activity in two non-small cell lung cancer models. These data demonstrate a unique mechanism of action of RPAis eliciting a state of chemical RPA exhaustion and suggest they will provide an effective therapeutic option for difficult-to-treat lung cancers.
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Affiliation(s)
| | - Navnath S. Gavande
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States,Department of Pharmaceutical Sciences, Wayne State University College of Pharmacy and Health Sciences, Detroit, MI, United States
| | - Shadia I. Jalal
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Karen E. Pollok
- Herman B. Wells Center for Pediatric Research, Departments of Pediatrics, Pharmacology and Toxicology, Medical and Molecular Genetics Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, United States
| | - Elmira Ekinci
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, MI, United States
| | - Joshua Heyza
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, MI, United States
| | - Steve M. Patrick
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, MI, United States
| | - Andi Masters
- Indiana University Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - John J. Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States,NERx BioSciences, Indianapolis, IN, United States,*Correspondence: John J. Turchi, ; Katherine S. Pawelczak,
| | - Katherine S. Pawelczak
- NERx BioSciences, Indianapolis, IN, United States,*Correspondence: John J. Turchi, ; Katherine S. Pawelczak,
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van Breda SG, Mathijs K, Pieters HJ, Sági-Kiss V, Kuhnle GG, Georgiadis P, Saccani G, Parolari G, Virgili R, Sinha R, Hemke G, Hung Y, Verbeke W, Masclee AA, Vleugels-Simon CB, van Bodegraven AA, de Kok TM. Replacement of Nitrite in Meat Products by Natural Bioactive Compounds Results in Reduced Exposure to N-Nitroso Compounds: The PHYTOME Project. Mol Nutr Food Res 2021; 65:e2001214. [PMID: 34382747 PMCID: PMC8530897 DOI: 10.1002/mnfr.202001214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 07/16/2021] [Indexed: 11/07/2022]
Abstract
SCOPE It has been proposed that endogenously form N-nitroso compounds (NOCs) are partly responsible for the link between red meat consumption and colorectal cancer (CRC) risk. As nitrite has been indicated as critical factor in the formation of NOCs, the impact of replacing the additive sodium nitrite (E250) by botanical extracts in the PHYTOME project is evaluated. METHOD AND RESULTS A human dietary intervention study is conducted in which healthy subjects consume 300 g of meat for 2 weeks, in subsequent order: conventional processed red meat, white meat, and processed red meat with standard or reduced levels of nitrite and added phytochemicals. Consumption of red meat products enriched with phytochemicals leads to a significant reduction in the faecal excretion of NOCs, as compared to traditionally processed red meat products. Gene expression changes identify cell proliferation as main affects molecular mechanism. High nitrate levels in drinking water in combination with processed red meat intake further stimulates NOC formation, an effect that could be mitigated by replacement of E250 by natural plant extracts. CONCLUSION These findings suggest that addition of natural extracts to conventionally processed red meat products may help to reduce CRC risk, which is mechanistically support by gene expression analyses.
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Affiliation(s)
- Simone G van Breda
- Department of Toxicogenomics, GROW-school for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, the Netherlands
| | - Karen Mathijs
- Department of Toxicogenomics, GROW-school for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, the Netherlands
| | - Harm-Jan Pieters
- Department of Toxicogenomics, GROW-school for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, the Netherlands
| | - Virág Sági-Kiss
- Department of Food & Nutritional Sciences, University of Reading, Reading, UK
| | - Gunter G Kuhnle
- Department of Food & Nutritional Sciences, University of Reading, Reading, UK
| | - Panagiotis Georgiadis
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | - Giovanna Saccani
- SSICA-Experimental Station for the Food Preserving Industry, Parma, Italy
| | - Giovanni Parolari
- SSICA-Experimental Station for the Food Preserving Industry, Parma, Italy
| | - Roberta Virgili
- SSICA-Experimental Station for the Food Preserving Industry, Parma, Italy
| | - Rashmi Sinha
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gert Hemke
- Hemke Nutriconsult, Prins Clauslaan 70, 5684 GB Best, The Netherlands
| | - Yung Hung
- Department of Agricultural Economics, Ghent University, Coupure links 653, Gent, 9000, Belgium
| | - Wim Verbeke
- Department of Agricultural Economics, Ghent University, Coupure links 653, Gent, 9000, Belgium
| | - Ad A Masclee
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | | | - Theo M de Kok
- Department of Toxicogenomics, GROW-school for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, the Netherlands
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- Department of Toxicogenomics, GROW-school for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, the Netherlands
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Li Y, Zou J, Zhang Q, Quan F, Cao L, Zhang X, Liu J, Wu D. Systemic Analysis of the DNA Replication Regulator MCM Complex in Ovarian Cancer and Its Prognostic Value. Front Oncol 2021; 11:681261. [PMID: 34178669 PMCID: PMC8220296 DOI: 10.3389/fonc.2021.681261] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/18/2021] [Indexed: 01/11/2023] Open
Abstract
Microliposome maintenance (MCM) 2, MCM3, MCM4, MCM5, MCM6, and MCM7 are DNA replication regulators and are involved in the progression of multiple cancer types, but their role in ovarian cancer is still unclear. The purpose of this study is to clarify the biological function and prognostic value of the MCM complex in ovarian cancer (OS) progression. We analyzed DNA alterations, mRNA and protein levels, protein structure, PPI network, functional enrichment, and prognostic value in OC based on the Oncomine, cBioPortal, TCGA, CPTAC, PDB, GeneMANIA, DAVID, KEGG, and GSCALite databases. The results indicated that the protein levels of these DNA replication regulators were increased significantly. Moreover, survival analysis showed a prognostic signature based on the MCM complex, which performed moderately well in terms of OS prognostic prediction. Additionally, protein structure, functional enrichment, and PPI network analyses indicated that the MCM complex synergistically promoted OC progression by accelerating DNA replication and the cell cycle. In conclusion, our study suggested that the MCM complex might be a potential target and prognostic marker for OC patients.
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Affiliation(s)
- Yukun Li
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Juan Zou
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Qunfeng Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Feifei Quan
- Department of Obstetrics and Gynecology, Foshan First People's Hospital, Foshan, China
| | - Lu Cao
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Xiaodi Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Jue Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Daichao Wu
- Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, University of South China, Hengyang, China.,Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, United States
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Dueva R, Iliakis G. Replication protein A: a multifunctional protein with roles in DNA replication, repair and beyond. NAR Cancer 2020; 2:zcaa022. [PMID: 34316690 PMCID: PMC8210275 DOI: 10.1093/narcan/zcaa022] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) forms continuously during DNA replication and is an important intermediate during recombination-mediated repair of damaged DNA. Replication protein A (RPA) is the major eukaryotic ssDNA-binding protein. As such, RPA protects the transiently formed ssDNA from nucleolytic degradation and serves as a physical platform for the recruitment of DNA damage response factors. Prominent and well-studied RPA-interacting partners are the tumor suppressor protein p53, the RAD51 recombinase and the ATR-interacting proteins ATRIP and ETAA1. RPA interactions are also documented with the helicases BLM, WRN and SMARCAL1/HARP, as well as the nucleotide excision repair proteins XPA, XPG and XPF–ERCC1. Besides its well-studied roles in DNA replication (restart) and repair, accumulating evidence shows that RPA is engaged in DNA activities in a broader biological context, including nucleosome assembly on nascent chromatin, regulation of gene expression, telomere maintenance and numerous other aspects of nucleic acid metabolism. In addition, novel RPA inhibitors show promising effects in cancer treatment, as single agents or in combination with chemotherapeutics. Since the biochemical properties of RPA and its roles in DNA repair have been extensively reviewed, here we focus on recent discoveries describing several non-canonical functions.
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Affiliation(s)
- Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
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9
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Li X, Tian R, Gao H, Yan F, Ying L, Yang Y, Yang P, Gao Y. Identification of Significant Gene Signatures and Prognostic Biomarkers for Patients With Cervical Cancer by Integrated Bioinformatic Methods. Technol Cancer Res Treat 2018; 17:1533033818767455. [PMID: 29642758 PMCID: PMC5900817 DOI: 10.1177/1533033818767455] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cervical cancer is the leading cause of death with gynecological malignancies. We aimed to explore the molecular mechanism of carcinogenesis and biomarkers for cervical cancer by integrated bioinformatic analysis. We employed RNA-sequencing details of 254 cervical squamous cell carcinomas and 3 normal samples from The Cancer Genome Atlas. To explore the distinct pathways, messenger RNA expression was submitted to a Gene Set Enrichment Analysis. Kyoto Encyclopedia of Genes and Genomes and protein–protein interaction network analysis of differentially expressed genes were performed. Then, we conducted pathway enrichment analysis for modules acquired in protein–protein interaction analysis and obtained a list of pathways in every module. After intersecting the results from the 3 approaches, we evaluated the survival rates of both mutual pathways and genes in the pathway, and 5 survival-related genes were obtained. Finally, Cox hazards ratio analysis of these 5 genes was performed. DNA replication pathway (P < .001; 12 genes included) was suggested to have the strongest association with the prognosis of cervical squamous cancer. In total, 5 of the 12 genes, namely, minichromosome maintenance 2, minichromosome maintenance 4, minichromosome maintenance 5, proliferating cell nuclear antigen, and ribonuclease H2 subunit A were significantly correlated with survival. Minichromosome maintenance 5 was shown as an independent prognostic biomarker for patients with cervical cancer. This study identified a distinct pathway (DNA replication). Five genes which may be prognostic biomarkers and minichromosome maintenance 5 were identified as independent prognostic biomarkers for patients with cervical cancer.
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Affiliation(s)
- Xiaofang Li
- 1 Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Run Tian
- 2 Department of Orthopedics, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Hugh Gao
- 3 Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Feng Yan
- 3 Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Le Ying
- 3 Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia.,4 Department of Tea Science, Zhejiang University, Hangzhou, People's Republic of China
| | - Yongkang Yang
- 1 Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Pei Yang
- 2 Department of Orthopedics, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yan'e Gao
- 1 Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
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Replication Protein A Availability during DNA Replication Stress Is a Major Determinant of Cisplatin Resistance in Ovarian Cancer Cells. Cancer Res 2018; 78:5561-5573. [DOI: 10.1158/0008-5472.can-18-0618] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/11/2018] [Accepted: 07/27/2018] [Indexed: 11/16/2022]
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11
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A quantitative proteomics-based signature of platinum sensitivity in ovarian cancer cell lines. Biochem J 2015; 465:433-42. [PMID: 25406946 DOI: 10.1042/bj20141087] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Although DNA encodes the molecular instructions that underlie the control of cell function, it is the proteins that are primarily responsible for implementing those instructions. Therefore quantitative analyses of the proteome would be expected to yield insights into important candidates for the detection and treatment of disease. We present an iTRAQ (isobaric tag for relative and absolute quantification)-based proteomic analysis of ten ovarian cancer cell lines and two normal ovarian surface epithelial cell lines. We profiled the abundance of 2659 cellular proteins of which 1273 were common to all 12 cell lines. Of the 1273, 75 proteins exhibited elevated expression and 164 proteins had diminished expression in the cancerous cells compared with the normal cell lines. The iTRAQ expression profiles allowed us to segregate cell lines based upon sensitivity and resistance to carboplatin. Importantly, we observed no substantial correlation between protein abundance and RNA expression or epigenetic DNA methylation data. Furthermore, we could not discriminate between sensitivity and resistance to carboplatin on the basis of RNA expression and DNA methylation data alone. The present study illustrates the importance of proteomics-based discovery for defining the basis for the carboplatin response in ovarian cancer and highlights candidate proteins, particularly involved in cellular redox regulation, homologous recombination and DNA damage repair, which otherwise could not have been predicted from whole genome and expression data sources alone.
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12
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ICan: an integrated co-alteration network to identify ovarian cancer-related genes. PLoS One 2015; 10:e0116095. [PMID: 25803614 PMCID: PMC4372216 DOI: 10.1371/journal.pone.0116095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 12/04/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Over the last decade, an increasing number of integrative studies on cancer-related genes have been published. Integrative analyses aim to overcome the limitation of a single data type, and provide a more complete view of carcinogenesis. The vast majority of these studies used sample-matched data of gene expression and copy number to investigate the impact of copy number alteration on gene expression, and to predict and prioritize candidate oncogenes and tumor suppressor genes. However, correlations between genes were neglected in these studies. Our work aimed to evaluate the co-alteration of copy number, methylation and expression, allowing us to identify cancer-related genes and essential functional modules in cancer. RESULTS We built the Integrated Co-alteration network (ICan) based on multi-omics data, and analyzed the network to uncover cancer-related genes. After comparison with random networks, we identified 155 ovarian cancer-related genes, including well-known (TP53, BRCA1, RB1 and PTEN) and also novel cancer-related genes, such as PDPN and EphA2. We compared the results with a conventional method: CNAmet, and obtained a significantly better area under the curve value (ICan: 0.8179, CNAmet: 0.5183). CONCLUSION In this paper, we describe a framework to find cancer-related genes based on an Integrated Co-alteration network. Our results proved that ICan could precisely identify candidate cancer genes and provide increased mechanistic understanding of carcinogenesis. This work suggested a new research direction for biological network analyses involving multi-omics data.
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