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Jhan JH, Ke HL, Liang PI, Hsu WC, Lee YC, Lin HH, Wu YR, Huang AM, Lee HY, Yeh HC, Wu WJ, Li CC, Li WM. High MRE11 Expression Level Predicts Poor Survival in Upper Tract Urothelial Carcinomas. Appl Immunohistochem Mol Morphol 2023; 31:94-100. [PMID: 36688483 DOI: 10.1097/pai.0000000000001099] [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: 06/12/2021] [Accepted: 12/07/2022] [Indexed: 01/24/2023]
Abstract
Upper tract urothelial carcinoma (UTUC) is an aggressive malignancy with characteristics of high metastasis and poor prognosis. There are some particularly different features of UTUC between the Asian and Western countries. Double-strand break repair protein MRE11 is a component of the MRN complex that is involved in the DNA repair pathway. Emerging studies have focused on the role of MRE11 in human malignancies with conflicting results. We aimed to establish the relationship between MRE11 expression and the oncological outcome of UTUC. This study retrospectively reviewed 150 patients who underwent radical nephroureterectomy with pathologically confirmed UTUC. Pathologic slides were reviewed, and clinical parameters were collected. An immunohistochemical study was performed, and the cytoplasmic and nuclear-staining results of UTUC were recorded. The expression of MRE11 was analyzed to identify correlations with various clinicopathological parameters, metastasis-free survival, and cancer-specific survival (CSS). MRE11 expression was significantly correlated with patients with a high pathologic stage ( P =0.001), perineural invasion ( P =0.015), and tumor necrosis ( P =0.034). Upon univariate analysis, a high MRE11 expression was associated with poor metastasis-free survival ( P =0.014, 95% CI 1.18, 4.38) and poor CSS ( P =0.001, 95% CI 2.45, 27.75). Upon multivariable analysis, a high MRE11 expression was associated with poor CSS ( P =0.019, 95% CI 1.28, 15.65). In summary, MRE11 expression could serve as a potential predictor of prognosis in patients with UTUC.
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Affiliation(s)
- Jhen-Hao Jhan
- Department of Urology
- Graduate Institute of Clinical Medicine
- Department of Urology, Kaohsiung Municipal Siaogang Hospital, Kaohsiung
| | - Hung-Lung Ke
- Department of Urology
- Graduate Institute of Medicine
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University
| | | | | | | | - Hui-Hui Lin
- Department of Urology
- Graduate Institute of Medicine
| | | | - A-Mei Huang
- Graduate Institute of Clinical Medicine
- Graduate Institute of Medicine
- Department of Biochemistry
| | - Hsiang-Ying Lee
- Department of Urology
- Graduate Institute of Clinical Medicine
| | - Hsin-Chih Yeh
- Department of Urology
- Graduate Institute of Clinical Medicine
| | - Wen-Jeng Wu
- Department of Urology
- Graduate Institute of Medicine
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University
| | - Ching-Chia Li
- Department of Urology
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University
| | - Wei-Ming Li
- Department of Urology
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University
- Department of Urology, Ministry of Health and Welfare Pingtung Hospital, Pingtung, Taiwan
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Salehi A, Wang L, Coates PJ, Norberg Spaak L, Gu X, Sgaramella N, Nylander K. Reiterative modeling of combined transcriptomic and proteomic features refines and improves the prediction of early recurrence in squamous cell carcinoma of head and neck. Comput Biol Med 2022; 149:105991. [PMID: 36007290 DOI: 10.1016/j.compbiomed.2022.105991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/11/2022] [Accepted: 08/14/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Patients with squamous cell carcinoma of the head and neck (SCCHN) have a high-risk of recurrence. We aimed to develop machine learning methods to identify transcriptomic and proteomic features that provide accurate classification models for predicting risk of early recurrence in SCCHN patients. METHODS Clinical, genomic, transcriptomic and proteomic features distinguishing recurrence risk were examined in SCCHN patients from The Cancer Genome Atlas (TCGA). Recurrence within one year after treatment was classified as high-risk and no recurrence as low-risk. RESULTS No significant differences in individual clinicopathological characteristics, mutation profiles or mRNA expression patterns were seen between the groups using conventional statistical analysis. Using the machine learning algorithm, extreme gradient boosting (XGBoost), ten proteins (RAD50, 4E-BP1, MYH11, MAP2K1, BECN1, NF2, RAB25, ERRFI1, KDR, SERPINE1) and five mRNAs (PLAUR, DKK1, AXIN2, ANG and VEGFA) made the greatest contribution to classification. These features were used to build improved models in XGBoost, achieving the best discrimination performance when combining transcriptomic and proteomic data, providing an accuracy of 0.939 and an Area Under the ROC Curve (AUC) of 0.951. CONCLUSIONS This study highlights machine learning to identify transcriptomic and proteomic factors that play important roles in predicting risk of recurrence in patients with SCCHN and to develop such models by iterative cycles to enhance their accuracy, thereby aiding the introduction of personalized treatment regimens.
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Affiliation(s)
- Amir Salehi
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
| | - Lixiao Wang
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
| | - Philip J Coates
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, 656 53, Czech Republic
| | - Lena Norberg Spaak
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
| | - Xiaolian Gu
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
| | - Nicola Sgaramella
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
| | - Karin Nylander
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden.
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Tarapara B, Shah F. An in-silico analysis to identify structural, functional and regulatory role of SNPs in hMRE11. J Biomol Struct Dyn 2022; 41:2160-2174. [PMID: 35048780 DOI: 10.1080/07391102.2022.2028678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Meiotic recombination 11 (MRE11) is a component of the tri-molecular MRE11-RAD50-NBS1 (MRN) complex, which functions as an exonuclease and endonuclease which is involved in identifying, signalling, protecting and repairing double-strand breaks in DNA (DSBs). Ataxia-telangiectasia-like disorder (ATLD) 1 and Nijmegen breakage syndrome (NBS)-like disorder are MRE11 associated diseases. In the present study, we used an integrated computational approach to identify the most deleterious SNPs and their structural and functional impact on human MRE11. Five of the 68 observed non-synonymous SNP (nsSNPs; I162T, S273C, W210C, D311Y and R364L) should be worked on due to their strong possible pathogenicity and the risk of changing protein properties. All the nsSNPs were highly conserved and decrease the protein stability located in the MRE11 nuclease and MRE11 DNA binding presumed domain. R364L and I162T were predicted to be involved in post-translational modification (PTM) sites. Furthermore, we also analysed the regulatory effect of noncoding SNPs on MRE11 gene regulation in which 6 SNPs were found to affect gene regulation. All six noncoding SNPs predicted chromatin interactive site whereas only one SNP was noted its association with miRNA binding site which disrupts 5 miRNA conserved site. These findings help future studies to get more insights into the role of these variants in the alteration of the MRE11 function. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bhoomi Tarapara
- Department of Cancer Biology, Stem Cell Biology Lab, The Gujarat Cancer and Research Institute, Ahmedabad, India
| | - Franky Shah
- Department of Cancer Biology, Stem Cell Biology Lab, The Gujarat Cancer and Research Institute, Ahmedabad, India
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Donís SP, González AP, Alves MGO, do Carmo Carvalho BF, Ferreira CCP, Almeida JD, Iruegas EP, Petronacci CMC, Peñaranda JMS, Sayáns MP. MLH1, MSH2, MRE11, and XRCC1 in Oral Leukoplakia and Oral Squamous Cell Carcinoma. Appl Immunohistochem Mol Morphol 2021; 29:613-618. [PMID: 33734109 DOI: 10.1097/pai.0000000000000929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/10/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND DNA damage is accumulated in the cells over time as the result of both exogenous and endogenous factors. The objective of this study was to analyze the immunohistochemical expression of the repair proteins in oral leukoplakia (OL) and oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS Paraffin blocks were selected from the archives of the Laboratory of Hospital Clinico Universitario de Santiago de Compostela, Spain. The sample was composed of 16 cases of OL without dysplasia, 14 cases of OL with dysplasia, and 15 cases of OSCC. The patients' clinical data were collected and immunohistochemical analysis was performed for MLH1, MSH2, MRE11, and XRCC1. The data were submitted to the χ2 and the Kruskal-Wallis (P≤0.05) tests. RESULTS MSH2 was overexpressed in OSCC (P=0.020) and was positive in 100% of patients with OL with dysplasia or OSCC (P=0.019). Positivity for MLH1 was significantly associated with comorbidity (P=0.040), especially in patients who presented with 2 or more pathologies (P=0.028). XRCC1 positivity was also associated with comorbidity (P=0.039). No significant associations were found for the MRE11A expression. Although the simultaneous positivity for the 4 markers was observed in presence of comorbidities (P=0.006). CONCLUSIONS This study supports the effect of the overexpression of MSH2 protein in samples of OL with dysplasia and OSCC, most notably in patients who present with comorbidities and negativity for OL without dysplasia.
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Affiliation(s)
| | | | | | - Bruna F do Carmo Carvalho
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos, São Paulo, Brazil
| | - Camila C P Ferreira
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos, São Paulo, Brazil
| | - Janete Dias Almeida
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos, São Paulo, Brazil
| | - Elena Padín Iruegas
- Translational Oncology Laboratory, Idichus Foundation, Santiago de Compostela, Galicia, Spain
| | | | - José M Suárez Peñaranda
- Department of Pathology, Clinical Hospital, Santiago de Compostela
- Department of Forensic Sciences and Pathology, University of Santiago de Compostela
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Podralska M, Dzikiewicz-Krawczyk A, Mosor M, Żurawek M, Iżykowska K, Słomski R, Rydzanicz M, Gabryel P, Dyszkiewicz W, Ziółkowska-Suchanek I. The most frequent Polish ATM mutations are not susceptibility factors for tobacco-related cancers. Arch Med Sci 2021; 17:1158-1163. [PMID: 34522244 PMCID: PMC8425226 DOI: 10.5114/aoms.2020.94155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/10/2018] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION The inactivation of both alleles of the ATM gene leads to ataxia-telangiectasia syndrome, whereas carriers of monoallelic mutations in the ATM gene are associated with increased risk of different types of cancer. Three substitutions in the ATM gene (c.6095G>A, c.7630-2A>C, c.5932G>T) are the most common mutations causing ataxia-telangiectasia among Polish patients. The aim of this study was to determine whether these ATM mutations are associated with increased risk of tobacco-related cancers. MATERIAL AND METHODS 783 Polish patients with tobacco-related cancers were included in the study (468 with lung cancer, 153 with a single laryngeal cancer, 86 with multiple primary tumors localized in the larynx and 76 multiple primary tumors localized in the head or neck). The control group consisted of 464 healthy subjects from the Polish population. Three ATM mutations - c.5932G>T, c.6095G>A, c.7630-2A>C - were tested among selected patients. Molecular analyses were performed using high resolution melting analysis and restriction fragment length polymorphism. RESULTS In the present study, we detected only one mutation, c.7630-2A>C, and no carriers of c.5932G>T, c.6095G>A mutations in the ATM gene among Polish patients with tobacco-related cancers. A patient with c.7630-2A>C mutation was diagnosed with lung adenocarcinoma, the most common type of lung cancer. One carrier of c.6095G>A mutation was found in the control group. CONCLUSIONS The results indicate that the studied ATM variants do not seem to be associated with tobacco-related cancers in Poland.
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Affiliation(s)
- Marta Podralska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Maria Mosor
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Żurawek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Piotr Gabryel
- Department of Thoracic Surgery, Poznan University of Medical Sciences, Poznan, Poland
| | - Wojciech Dyszkiewicz
- Department of Thoracic Surgery, Poznan University of Medical Sciences, Poznan, Poland
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Rahimian E, Amini A, Alikarami F, Pezeshki SMS, Saki N, Safa M. DNA repair pathways as guardians of the genome: Therapeutic potential and possible prognostic role in hematologic neoplasms. DNA Repair (Amst) 2020; 96:102951. [PMID: 32971475 DOI: 10.1016/j.dnarep.2020.102951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 11/30/2022]
Abstract
DNA repair pathways, which are also identified as guardians of the genome, protect cells from frequent damage that can lead to DNA breaks. The most deleterious types of damage are double-strand breaks (DSBs), which are repaired by homologous recombination (HR) and non-homologous end joining (NHEJ). Single strand breaks (SSBs) can be corrected through base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). Failure to restore DNA lesions or inappropriately repaired DNA damage culminates in genomic instability and changes in the regulation of cellular functions. Intriguingly, particular mutations and translocations are accompanied by special types of leukemia. Besides, expression patterns of certain repair genes are altered in different hematologic malignancies. Moreover, analysis of mutations in key mediators of DNA damage repair (DDR) pathways, as well as investigation of their expression and function, may provide us with emerging biomarkers of response/resistance to treatment. Therefore, defective DDR pathways can offer a rational starting point for developing DNA repair-targeted drugs. In this review, we address genetic alterations and gene/protein expression changes, as well as provide an overview of DNA repair pathways.
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Affiliation(s)
- Elahe Rahimian
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Amini
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Alikarami
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA 19104, USA
| | - Seyed Mohammad Sadegh Pezeshki
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
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Expression of DNA repair genes in oral squamous cell carcinoma using reverse transcription-quantitative polymerase chain reaction. Oral Surg Oral Med Oral Pathol Oral Radiol 2020; 130:298-305. [PMID: 32682592 DOI: 10.1016/j.oooo.2020.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/14/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE The aim of this study was to evaluate the expression of DNA repair genes in cases of oral squamous cell carcinoma (OSCC). STUDY DESIGN Expression of the MLH1, MSH2, MLH3, ATM, MRE11A, XRCC1, and PMS2 genes was evaluated by reverse transcription-quantitative polymerase chain reaction in the OSCC group (32 patients) and the control group (15 patients). The groups were compared by using the Mann-Whitney test, with Bonferroni correction. Associations between gene expression levels and clinical data were explored by using Pearson's and Spearman's correlation coefficients, with P value less than .05 indicating a significant difference. RESULTS The MLH1, MSH2, MLH3, ATM, MRE11A, XRCC1, and PMS2 genes were downregulated in the OSCC group compared with the control group, with significant values for MLH1 (P < .0001); MSH2 (P = .038); MLH3 (P < .0001); ATM (P < .0001); MRE11A (P < .0001); XRCC1 (P = .0004); and PMS2 (P = .008). Analysis of the correlation between gene expression and clinical data only revealed a significant negative correlation between age and expression of the PMS2 gene. CONCLUSIONS Expression of the DNA repair genes MLH1, MSH2, MLH3, ATM, MRE11 AMRE11A, XRCC1, and PMS2 was reduced in OSCC.
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Zhang WL, Zhu ZL, Huang MC, Tang YJ, Tang YL, Liang XH. Susceptibility of Multiple Primary Cancers in Patients With Head and Neck Cancer: Nature or Nurture? Front Oncol 2019; 9:1275. [PMID: 31824853 PMCID: PMC6882292 DOI: 10.3389/fonc.2019.01275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/04/2019] [Indexed: 02/05/2023] Open
Abstract
Multiple primary cancers (MPCs) are major obstacles to long-term survival in head and neck cancer (HNSCC), however, the molecular mechanism underlying multiple carcinogenesis remains unclear. “Field cancerization” is a classical theory to elaborate the malignant progression of MPCs. Apart from environmental and immune factors, genetic factors may have great potential as molecular markers for MPCs risk prediction. This review focuses on inherited and acquired gene mutations in MPCs, including germ-line mutation, single-nucleotide polymorphism, chromosomal instability, microsatellite instability and DNA methylation. And definition and prognosis of MPCs have also been discussed. These may pave the way for the early detection, prevention and effective treatment of MPCs in HNSCC.
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Affiliation(s)
- Wei-Long Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhuo-Li Zhu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mei-Chang Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ya-Ling Tang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin-Hua Liang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Situ Y, Chung L, Lee CS, Ho V. MRN (MRE11-RAD50-NBS1) Complex in Human Cancer and Prognostic Implications in Colorectal Cancer. Int J Mol Sci 2019; 20:E816. [PMID: 30769804 PMCID: PMC6413120 DOI: 10.3390/ijms20040816] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
The MRE11-RAD50-NBS1 (MRN) complex has been studied in multiple cancers. The identification of MRN complex mutations in mismatch repair (MMR)-defective cancers has sparked interest in its role in colorectal cancer (CRC). To date, there is evidence indicating a relationship of MRN expression with reduced progression-free survival, although the significance of the MRN complex in the clinical setting remains controversial. In this review, we present an overview of the function of the MRN complex, its role in cancer progression, and current evidence in colorectal cancer. The evidence indicates that the MRN complex has potential utilisation as a biomarker and as a putative treatment target to improve outcomes of colorectal cancer.
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Affiliation(s)
- Yiling Situ
- School of Medicine, Western Sydney University, Penrith, NSW 2751, Australia.
| | - Liping Chung
- School of Medicine, Western Sydney University, Penrith, NSW 2751, Australia.
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia.
| | - Cheok Soon Lee
- School of Medicine, Western Sydney University, Penrith, NSW 2751, Australia.
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia.
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia.
- Discipline of Pathology, School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia.
- Faculty of Medicine, South Western Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia.
- Faculty of Medicine and Health, Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia.
| | - Vincent Ho
- School of Medicine, Western Sydney University, Penrith, NSW 2751, Australia.
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Podralska M, Ziółkowska-Suchanek I, Żurawek M, Dzikiewicz-Krawczyk A, Słomski R, Nowak J, Stembalska A, Pesz K, Mosor M. Genetic variants in ATM, H2AFX and MRE11 genes and susceptibility to breast cancer in the polish population. BMC Cancer 2018; 18:452. [PMID: 29678143 PMCID: PMC5910560 DOI: 10.1186/s12885-018-4360-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/11/2018] [Indexed: 11/10/2022] Open
Abstract
Background DNA damage repair is a complex process, which can trigger the development of cancer if disturbed. In this study, we hypothesize a role of variants in the ATM, H2AFX and MRE11 genes in determining breast cancer (BC) susceptibility. Methods We examined the whole sequence of the ATM kinase domain and estimated the frequency of founder mutations in the ATM gene (c.5932G > T, c.6095G > A, and c.7630-2A > C) and single nucleotide polymorphisms (SNPs) in H2AFX (rs643788, rs8551, rs7759, and rs2509049) and MRE11 (rs1061956 and rs2155209) among 315 breast cancer patients and 515 controls. The analysis was performed using high-resolution melting for new variants and the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for recurrent ATM mutations. H2AFX and MRE11 polymorphisms were analyzed using TaqMan assays. The cumulative genetic risk scores (CGRS) were calculated using unweighted and weighted approaches. Results We identified four mutations (c.6067G > A, c.8314G > A, c.8187A > T, and c.6095G > A) in the ATM gene in three BC cases and two control subjects. We observed a statistically significant association of H2AFX variants with BC. Risk alleles (the G of rs7759 and the T of rs8551 and rs2509049) were observed more frequently in BC cases compared to the control group, with P values, odds ratios (OR) and 95% confidence intervals (CIs) of 0.0018, 1.47 (1.19 to 1.82); 0.018, 1.33 (1.09 to 1.64); and 0.024, 1.3 (1.06 to 1.59), respectively. Haplotype-based tests identified a significant association of the H2AFX CACT haplotype with BC (P < 0.0001, OR = 27.29, 95% CI 3.56 to 209.5). The risk of BC increased with the growing number of risk alleles. The OR (95% CI) for carriers of ≥ four risk alleles was 1.71 (1.11 to 2.62) for the CGRS. Conclusions This study confirms that H2AFX variants are associated with an increased risk of BC. The above-reported sequence variants of MRE11 genes may not constitute a risk factor of breast cancer in the Polish population. The contribution of mutations detected in the ATM gene to the development of breast cancer needs further detailed study.
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Affiliation(s)
- Marta Podralska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.
| | | | - Magdalena Żurawek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,University of Life Sciences of Poznan, Poznan, Poland
| | - Jerzy Nowak
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Karolina Pesz
- Department of Genetics, Wrocław Medical University, Wroclaw, Poland
| | - Maria Mosor
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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Association of DNA repair genes polymorphisms and mutations with increased risk of head and neck cancer: a review. Med Oncol 2017; 34:197. [PMID: 29143133 PMCID: PMC5688183 DOI: 10.1007/s12032-017-1057-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 11/10/2017] [Indexed: 12/21/2022]
Abstract
DNA repair mechanisms allow maintain genomic stability and proper functioning within the cells. Any aberrations may cause an increased risk of many diseases such as cancer. The most crucial risk factors for head and neck squamous cell carcinoma are behavioral factors, predominantly chronic exposure to tobacco, alcohol addiction, and infection with human papillomavirus or Epstein–Barr virus. These agents can induce DNA damage; therefore, cells must activate appropriate mechanisms in order to function correctly. Cancer cells are marked with genomic instability, which is associated with a greater tendency for the accumulation of a DNA damage and increased chemo- and radioresistance. Multiple studies have assessed the correlation of increased head and neck cancer (HNC) risk with polymorphism in the DNA repair genes. However, they suggest that interaction of DNA repair genes mutations with susceptibility to HNC depends on a patient’s race and risk factors, especially tobacco smoking. Further identification of these sequence variations must be performed. In this review, we discuss the current knowledge about the DNA repair genes mutations and polymorphisms associated with the high risk of head and neck treatment.
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Studies of lncRNAs in DNA double strand break repair: what is new? Oncotarget 2017; 8:102690-102704. [PMID: 29254281 PMCID: PMC5731991 DOI: 10.18632/oncotarget.22090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 09/24/2017] [Indexed: 01/06/2023] Open
Abstract
The ‘junk DNA’ that has haunted human genetics for a long time now turns out to hold enormous hidden treasures. As species had their genomes and transcriptomes sequenced, there are an overwhelming number of lncRNA transcripts being reported, however, less than 100 of them have been functionally characterized. DNA damage is recognized and quickly repaired by the cell, with increased expression of numerous genes involved in DNA repair. Most of the time the studies have focused only on proteins involved in these signaling pathways. However, recent studies have implied that lncRNAs can be broadly induced by DNA damage and regulate DNA repair processes by various mechanisms. In this paper, we focus on recent advances in the identification and functional characterization of novel lncRNAs participating in DNA double strand break repair.
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Naccarati A, Rosa F, Vymetalkova V, Barone E, Jiraskova K, Di Gaetano C, Novotny J, Levy M, Vodickova L, Gemignani F, Buchler T, Landi S, Vodicka P, Pardini B. Double-strand break repair and colorectal cancer: gene variants within 3' UTRs and microRNAs binding as modulators of cancer risk and clinical outcome. Oncotarget 2016; 7:23156-69. [PMID: 26735576 PMCID: PMC5029617 DOI: 10.18632/oncotarget.6804] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/09/2015] [Indexed: 12/25/2022] Open
Abstract
Genetic variations in 3' untranslated regions of target genes may affect microRNA binding, resulting in differential protein expression. microRNAs regulate DNA repair, and single-nucleotide polymorphisms in miRNA binding sites (miRSNPs) may account for interindividual differences in the DNA repair capacity. Our hypothesis is that miRSNPs in relevant DNA repair genes may ultimately affect cancer susceptibility and impact prognosis.In the present study, we analysed the association of polymorphisms in predicted microRNA target sites of double-strand breaks (DSBs) repair genes with colorectal cancer (CRC) risk and clinical outcome. Twenty-one miRSNPs in non-homologous end-joining and homologous recombination pathways were assessed in 1111 cases and 1469 controls. The variant CC genotype of rs2155209 in MRE11A was strongly associated with decreased cancer risk when compared with the other genotypes (OR 0.54, 95% CI 0.38-0.76, p = 0.0004). A reduced expression of the reporter gene was observed for the C allele of this polymorphism by in vitro assay, suggesting a more efficient interaction with potentially binding miRNAs. In colon cancer patients, the rs2155209 CC genotype was associated with shorter survival while the TT genotype of RAD52 rs11226 with longer survival when both compared with their respective more frequent genotypes (HR 1.63, 95% CI 1.06-2.51, p = 0.03 HR 0.60, 95% CI 0.41-0.89, p = 0.01, respectively).miRSNPs in DSB repair genes involved in the maintenance of genomic stability may have a role on CRC susceptibility and clinical outcome.
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Affiliation(s)
- Alessio Naccarati
- Molecular and Genetic Epidemiology Research Unit, Human Genetics Foundation, Turin, Italy
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
| | - Fabio Rosa
- Genomic Variation in Human Populations and Complex Diseases Research Unit, Human Genetics Foundation, Turin, Italy
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Elisa Barone
- Department of Biology, University of Pisa, Pisa, Italy
| | - Katerina Jiraskova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Cornelia Di Gaetano
- Genomic Variation in Human Populations and Complex Diseases Research Unit, Human Genetics Foundation, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Jan Novotny
- Department of Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Miroslav Levy
- Department of Surgery, First Faculty of Medicine, Charles University and Thomayer University Hospital, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Tomas Buchler
- Department of Oncology, Thomayer Hospital and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Barbara Pardini
- Genomic Variation in Human Populations and Complex Diseases Research Unit, Human Genetics Foundation, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
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DNA Double-Strand Break Repair Inhibitors as Cancer Therapeutics. ACTA ACUST UNITED AC 2015; 22:17-29. [DOI: 10.1016/j.chembiol.2014.11.013] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/26/2014] [Accepted: 11/10/2014] [Indexed: 12/29/2022]
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