1
|
Butkiewicz D, Krześniak M, Gdowicz-Kłosok A, Składowski K, Rutkowski T. DNA Double-Strand Break Response and Repair Gene Polymorphisms May Influence Therapy Results and Prognosis in Head and Neck Cancer Patients. Cancers (Basel) 2023; 15:4972. [PMID: 37894339 PMCID: PMC10605140 DOI: 10.3390/cancers15204972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Radiotherapy and cisplatin-based chemotherapy belong to the main treatment modalities for head and neck squamous cell carcinoma (HNSCC) and induce cancer cell death by generating DNA damage, including the most severe double-strand breaks (DSBs). Alterations in DSB response and repair genes may affect individual DNA repair capacity and treatment sensitivity, contributing to the therapy resistance and poor prognosis often observed in HNSCC. In this study, we investigated the association of a panel of single-nucleotide polymorphisms (SNPs) in 20 DSB signaling and repair genes with therapy results and prognosis in 505 HNSCC patients treated non-surgically with DNA damage-inducing therapies. In the multivariate analysis, there were a total of 14 variants associated with overall, locoregional recurrence-free or metastasis-free survival. Moreover, we identified 10 of these SNPs as independent predictors of therapy failure and unfavorable prognosis in the whole group or in two treatment subgroups. These were MRE11 rs2155209, XRCC5 rs828907, RAD51 rs1801321, rs12593359, LIG4 rs1805388, CHEK1 rs558351, TP53 rs1042522, ATM rs1801516, XRCC6 rs2267437 and NBN rs2735383. Only CHEK1 rs558351 remained statistically significant after correcting for multiple testing. These results suggest that specific germline variants related to DSB response and repair may be potential genetic modifiers of therapy effects and disease progression in HNSCC treated with radiotherapy and cisplatin-based chemoradiation.
Collapse
Affiliation(s)
- Dorota Butkiewicz
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Małgorzata Krześniak
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Agnieszka Gdowicz-Kłosok
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Krzysztof Składowski
- I Radiation and Clinical Oncology Department, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Tomasz Rutkowski
- I Radiation and Clinical Oncology Department, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
- Radiotherapy Department, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| |
Collapse
|
2
|
Liu D, Gao Y, Li L, Chen H, Bai L, Qu Y, Zhou B, Yan Y, Zhao Y. Single nucleotide polymorphisms in breast cancer susceptibility gene 1 are associated with susceptibility to lung cancer. Oncol Lett 2021; 21:424. [PMID: 33850565 DOI: 10.3892/ol.2021.12685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 02/10/2021] [Indexed: 12/24/2022] Open
Abstract
BRCA1 is a tumor suppressor that has been found to be involved DNA synthesis during cell replication. In a recent study, the single nucleotide polymorphism (SNP), rs799917, in BRCA1 was found to be associated with the development and progression of various types of tumor. In the present study, the association between rs799917 and susceptibility to lung cancer was evaluated in a Han Chinese population in the Liaoning Province of China. The BRCA1 rs799917 genotypes (C/C, C/T and T/T) were analyzed using TaqMan quantitative PCR in 682 patients with lung cancer and 694 healthy controls, and the results were analyzed using a Student's t-test, a χ2 test and logistic regression analysis. Individuals carrying the C/T or T/T genotype had a lower risk of lung cancer compared with those carrying the C/C genotype [odds ratio (OR), 0.741; P=0.021; and OR, 0.610; P=0.011, respectively). The C/T + T/T genotype group had an even lower risk (OR, 0.709; P=0.005) compared with that in the C/C genotype group. In the stratified analyses of non-smokers, individuals with the C/T or T/T genotype had a lower risk of developing lung cancer compared with that in those carrying the C/C genotype (OR, 0.681; P=0.013; and OR, 0.569; P=0.021, respectively). The stratified analyses of the BRCA1 rs799917 polymorphism based on pathological type, chemotherapy and radiotherapy, showed that in the squamous cell carcinoma, non-chemotherapy and non-radiotherapy subgroups, individuals with the T/T genotype had a lower risk of lung cancer compared with that in those carrying the C/C genotype (OR, 0.454; P=0.007; OR, 0.485; P=0.002; and OR, 0.599; P=0.020, respectively). In conclusion, the T allele of the rs799917 SNP in BRCA1 was associated with a lower risk of lung cancer in the ethnic Han Chinese population in Liaoning Province and may represent a protective factor against lung cancer.
Collapse
Affiliation(s)
- Dan Liu
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Ya Gao
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China.,Department of Oncology, Kailuan Hospital, Tangshan, Hebei 063000, P.R. China
| | - Lingling Li
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - He Chen
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Lu Bai
- Department of Radiation Oncology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yanli Qu
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Baosen Zhou
- Department of Epidemiology, China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Ying Yan
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China.,Department of Radiation Oncology, The General Hospital of Shenyang Military Region, Shenyang, Liaoning 110016, P.R. China
| | - Yuxia Zhao
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| |
Collapse
|
3
|
Lin J, Chen Y, Zhang Y, Ouyang Z. Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB. NAR Genom Bioinform 2020; 2:lqaa057. [PMID: 33575608 PMCID: PMC7671322 DOI: 10.1093/nargab/lqaa057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 06/22/2020] [Accepted: 08/11/2020] [Indexed: 11/27/2022] Open
Abstract
RNA conformational alteration has significant impacts on cellular processes and phenotypic variations. An emerging genetic factor of RNA conformational alteration is a new class of single nucleotide variant (SNV) named riboSNitch. RiboSNitches have been demonstrated to be involved in many genetic diseases. However, identifying riboSNitches is notably difficult as the signals of RNA structural disruption are often subtle. Here, we introduce a novel computational framework–RIboSNitch Predictor based on Robust Analysis of Pairing probabilities (Riprap). Riprap identifies structurally disrupted regions around any given SNVs based on robust analysis of local structural configurations between wild-type and mutant RNA sequences. Compared to previous approaches, Riprap shows higher accuracy when assessed on hundreds of known riboSNitches captured by various experimental RNA structure probing methods including the parallel analysis of RNA structure (PARS) and the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). Further, Riprap detects the experimentally validated riboSNitch that regulates human catechol-O-methyltransferase haplotypes and outputs structurally disrupted regions precisely at base resolution. Riprap provides a new approach to interpreting disease-related genetic variants. In addition, we construct a database (RiboSNitchDB) that includes the annotation and visualization of all presented riboSNitches in this study as well as 24 629 predicted riboSNitches from human expression quantitative trait loci.
Collapse
Affiliation(s)
- Jianan Lin
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Yang Chen
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Yuping Zhang
- Department of Statistics, University of Connecticut, Storrs, CT 06269, USA
| | - Zhengqing Ouyang
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003, USA
| |
Collapse
|
4
|
Yang M, Du X, Zhang F, Yuan S. Association between BRCA1 polymorphisms rs799917 and rs1799966 and breast cancer risk: a meta-analysis. J Int Med Res 2019; 47:1409-1416. [PMID: 30832521 PMCID: PMC6460623 DOI: 10.1177/0300060519826819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Background Several studies have reported correlations between BRCA1 polymorphisms rs799917 and rs1799966 with the risk of breast cancer (BC). However, this relationship remains controversial. Methods We conducted a meta-analysis of seven studies to assess the associations between BRCA1 rs799917 and rs1799966 and BC risk, with the aim of more accurately determining the potential correlation. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated to evaluate the correlation of rs799917 and rs1799966 with BC risk. Results There was no overall correlation between BRCA1 rs799917 and BC risk (TT vs CC: OR = 0.87, 95% CI = 0.66–1.16; CT vs CC: OR = 1.02, 95% CI = 0.89–1.15; dominant model: OR = 0.99, 95% CI = 0.88–1.11; recessive model: OR = 0.87, 95% CI = 0.65–1.16). Subgroup analysis by ethnicity also revealed no significant correlation between rs799917 and BC risk in either Asians or Caucasians. There was also no significant association between BRCA1 rs1799966 and BC risk (GG vs AA: OR = 0.70, 95% CI = 0.33–1.47; AG vs AA: OR = 0.68, 95% CI = 0.35–1.30; dominant model: OR = 0.76, 95% CI = 0.49–1.06; recessive model: OR = 0.82, 95% CI = 0.49–1.36). Conclusion BRCA1polymorphisms rs799917 and rs1799966 were not significantly associated with BC risk in this meta-analysis.
Collapse
Affiliation(s)
- Meiming Yang
- 1 Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaoli Du
- 2 Department of Nursing, Fourth Military Medical University, Xi'an, China
| | - Feng Zhang
- 2 Department of Nursing, Fourth Military Medical University, Xi'an, China
| | - Shifang Yuan
- 1 Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| |
Collapse
|
5
|
Solodskikh SA, Panevina AV, Gryaznova MV, Gureev AP, Serzhantova OV, Mikhailov AA, Maslov AY, Popov VN. Targeted sequencing to discover germline variants in the BRCA1 and BRCA2 genes in a Russian population and their association with breast cancer risk. Mutat Res 2018; 813:51-57. [PMID: 30611917 DOI: 10.1016/j.mrfmmm.2018.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 02/08/2023]
Abstract
BRCA1 and BRCA2 are tumor suppressor genes involved in the repair of DNA damage and transcriptional regulation of the cell cycle. Alterations in BRCA1/2 lead to production of functionally defective proteins that impair DNA repair. Certain mutant variants of BRCA1/2 are strongly associated with increased risk of breast and ovarian cancers, with emerging data on association with other types of cancer. However, variability of BRCA1/2 in Russian populations remains understudied. In this study, we performed targeted sequencing of BRCA1/2 in 145 breast cancer (BC) patients with a family history of BRCA-associated cancers and 47 age-matched cancer-free control individuals with or without a family history of cancer. Subjects for this study were recruited in the Voronezh region of the Russian Federation. We found that two polymorphic variants, rs1799967 (BRCA1) and rs4987117 (BRCA2), were strongly associated with the risk of BC. Both variants have not been previously reported as associated with risk of breast cancer. Presence of the rs4987117 variant increases risk of breast cancer onset (OR = 2.76, p-value = 0.022). Notably, although variant rs80357906 (5382InsC) has been reported as a risk factor for hereditary BC, it was not significantly associated with breast cancer risk in our population (p = 0.192). We also found 12 novel polymorphic variants in BRCA1/2 genes (2 in BRCA1 and 10 in BRCA2). However, none of these variants demonstrated association with the disease. Five germline variants were observed at high frequency (mean AF = 67.14%) and therefore can be considered as a common haplotype in the Voronezh region of the Russian Federation. In summary, our study demonstrates that known pathological variants of BRCA1/2 genes may not be reflective of breast cancer risk assessment when applied to the Russian population. Further, more extended population-specific studies are needed to reveal the reliable list of BRCA1/2 polymorphisms associated with risk of breast cancer in the Russian population.
Collapse
Affiliation(s)
- Sergei A Solodskikh
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russian Federation.
| | - Anna V Panevina
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russian Federation; Department of Surgery, Voronezh Regional Clinical Oncological Dispensary, Voronezh, Russian Federation
| | - Maria V Gryaznova
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russian Federation
| | - Artem P Gureev
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russian Federation
| | - Olga V Serzhantova
- Department of Surgery, Voronezh Regional Clinical Oncological Dispensary, Voronezh, Russian Federation
| | - Andrei A Mikhailov
- Department of Surgery, Voronezh Regional Clinical Oncological Dispensary, Voronezh, Russian Federation
| | - Alexander Y Maslov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russian Federation; Department of Genetics, Albert Einstein College of Medicine of Yeshiva University, New-York, USA
| | - Vasily N Popov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russian Federation.
| |
Collapse
|
6
|
Faramarzi S, Dianatpour A, Ghafouri-Fard S. Association of BRCA2 variants with breast cancer risk: A meta-analysis. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
|
7
|
Xu GP, Zhao Q, Wang D, Xie WY, Zhang LJ, Zhou H, Chen SZ, Wu LF. The association between BRCA1 gene polymorphism and cancer risk: a meta-analysis. Oncotarget 2018; 9:8681-8694. [PMID: 29492227 PMCID: PMC5823592 DOI: 10.18632/oncotarget.24064] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 11/17/2017] [Indexed: 12/20/2022] Open
Abstract
Many studies have reported that BRCA1 polymorphisms are associated with cancer risk, but the results remain controversial. The purpose of this meta-analysis is to evaluate the relationship between BRCA1 polymorphisms (rs799917, rs1799950, rs1799966, or rs16941) and cancer risk. Relevant studies were identified via a systematic search of the PubMed, Embase, and Web of Science databases up to July 31, 2017. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to examine the strength of the associations. Thirty-five studies published in 19 publications involving 28,094 cases and 50,657 controls were included in this meta-analysis. There was no obvious association between rs799917, rs1799966, or rs16941 polymorphisms and overall cancer risk in any genetic models. However, subgroup analyses revealed that the rs799917 polymorphism could decrease the risk of cervical cancer, esophageal squamous cell carcinoma (ESCC), gastric cancer, and non-Hodgkin lymphoma (NHL) among Asian populations in one or more genetic models and that rs16941 could increase overall cancer risk among Caucasian populations in the homozygote and recessive models. Our meta-analysis also indicated that rs1799950 could decrease the breast cancer (BC) risk among Caucasian populations in the homozygote and recessive models. In summary, our results suggest that BRCA1 polymorphisms may play an important role in the etiology of cancer. However, due to the limited number of studies, these findings should be confirmed by new studies with larger sample sizes that address various types of cancer.
Collapse
Affiliation(s)
- Gui-Ping Xu
- Transfusion Department, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qing Zhao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ding Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wen-Yue Xie
- Department of Oncology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li-Jun Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hua Zhou
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shi-Zhi Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li-Fang Wu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
8
|
Terry MB, Keegan THM, Houghton LC, Goldberg M, Andrulis IL, Daly MB, Buys SS, Wei Y, Whittemore AS, Protacio A, Bradbury AR, Chung WK, Knight JA, John EM. Pubertal development in girls by breast cancer family history: the LEGACY girls cohort. Breast Cancer Res 2017; 19:69. [PMID: 28595647 PMCID: PMC5465536 DOI: 10.1186/s13058-017-0849-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 05/03/2017] [Indexed: 01/29/2023] Open
Abstract
Background Pubertal milestones, such as onset of breast development and menstruation, play an important role in breast cancer etiology. It is unclear if these milestones are different in girls with a first- or second-degree breast cancer family history (BCFH). Methods In the LEGACY Girls Study (n = 1040), we examined whether three mother/guardian-reported pubertal milestones (having reached Tanner Stage 2 or higher (T2+) for breast and pubic hair development, and having started menstruation) differed by BCFH. We also examined whether associations between body size and race/ethnicity and pubertal milestones were modified by BCFH. We used mother/guardian reports as the primary measure of pubertal milestones, but also conducted sensitivity analyses using clinical Tanner measurements available for a subcohort (n = 204). We analyzed cross-sectional baseline data with logistic regression models for the entire cohort, and longitudinal data with Weibull survival models for the subcohort of girls that were aged 5–7 years at baseline (n = 258). Results BCFH was modestly, but not statistically significantly, associated with Breast T2+ (odds ratio (OR) = 1.36, 95% confidence interval (CI) = 0.88–2.10), with a stronger association seen in the subcohort of girls with clinical breast Tanner staging (OR = 2.20, 95% CI = 0.91–5.32). In a longitudinal analysis of girls who were aged 5–7 years at baseline, BCFH was associated with a 50% increased rate of having early breast development (hazard ratio (HR) = 1.49, 95% CI = 1.0–2.21). This association increased to twofold in girls who were not overweight at baseline (HR = 2.04, 95% CI = 1.29–3.21). BCFH was not associated with pubic hair development and post-menarche status. The median interval between onset of breast development and menarche was longer for BCFH+ than BCFH– girls (2.3 versus 1.7 years), suggesting a slower developmental tempo for BCFH+ girls. Associations between pubertal milestones and body size and race/ethnicity were similar in girls with or without a BCFH. For example, weight was positively associated with Breast T2+ in both girls with (OR = 1.06 per 1 kg, 95% CI = 1.03–1.10) and without (OR = 1.14 per 1 kg, 95% CI = 1.04–1.24) a BCFH. Conclusions These results suggest that BCFH may be related to earlier breast development and slower pubertal tempo independent of body size and race/ethnicity. Electronic supplementary material The online version of this article (doi:10.1186/s13058-017-0849-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.
| | - Theresa H M Keegan
- Division of Hematology and Oncology, University of California (UC) Davis School of Medicine, and UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Lauren C Houghton
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Mandy Goldberg
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Irene L Andrulis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Saundra S Buys
- Department of Medicine, University of Utah Health Sciences Center, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Ying Wei
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Alice S Whittemore
- Departments of Biomedical Data Sciences and Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Angeline Protacio
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Angela R Bradbury
- Departments of Medicine, Hematology/Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Medical Ethics and Health Policy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wendy K Chung
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.,Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Julia A Knight
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA.,Department of Health Research and Policy (Epidemiology), and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
9
|
Miao L, Yu Y, Ji Y, Zhang B, Yuan Z, Du Y, Zhu L, Wang R, Chen N, Yuan H. Association between BRCA1 P871L polymorphism and cancer risk: evidence from a meta-analysis. Oncotarget 2017; 8:30587-30594. [PMID: 28427168 PMCID: PMC5444767 DOI: 10.18632/oncotarget.15739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/13/2017] [Indexed: 01/23/2023] Open
Abstract
Breast cancer 1 (BRCA1) gene makes great contributions to the repair of DNA. The association between BRCA1 P871L polymorphism and cancer risk has been investigated in a growing number of studies, but the conclusions are not conclusive. To obtain a comprehensive conclusion, we performed a meta-analysis of 24 studies with 13762 cases and 22388 controls. The pooled results indicated that BRCA1 gene P871L variant decreased risk of overall cancer (homozygous model: odds ratio (OR) = 0.89, 95%confidence interval (CI) = 0.79-1.00; recessive model: OR = 0.89, 95% CI = 0.80-0.99). The stratified analysis observed decreased risk associated with BRCA1 P871L in subgroups among Asians and high score studies, but not Caucasians or low score studies. In conclusion, despite several limitations, this meta-analysis suggested that BRCA1 P871L genetic variation may be associated with decreased susceptibility to cancer.
Collapse
Affiliation(s)
- Limin Miao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yang Yu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yefeng Ji
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Bo Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Zhiyao Yuan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yifei Du
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Longbiao Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Ruixia Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Ning Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Hua Yuan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| |
Collapse
|
10
|
Wu HC, Southey MC, Hibshoosh H, Santella RM, Terry MB. DNA Methylation in Breast Tumor from High-risk Women in the Breast Cancer Family Registry. Anticancer Res 2017; 37:659-664. [PMID: 28179314 DOI: 10.21873/anticanres.11361] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 01/13/2017] [Accepted: 01/17/2017] [Indexed: 01/22/2023]
Abstract
To examine DNA methylation profiles in breast tumors of women with a strong breast cancer family history, we measured methylation by bisulfite sequencing in 40 genes in 40 breast tumor tissues from women in the Breast Cancer Family Registry. We selected candidate genes from analysis of the Cancer Genome Atlas project (TCGA) breast data. Compared to TCGA breast cancer, BCFR cases are younger and more likely to be ER-negative. Overall, we found that many of the methylation differences between BCFR tumor and normal adjacent tissues were smaller than that in TCGA samples. We found only 32% of tested genes were hypermethylated in BCFR; the largest difference was 36.1% for SEPW1, and the smallest difference was 10% for RYR2. These data suggest the importance of examining breast cancer cases including familial cases enriched with early-onset cancers to identify methylation markers that can be examined in blood as biomarkers for early detection.
Collapse
Affiliation(s)
- Hui-Chen Wu
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NY, U.S.A.
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, College of Physicians & Surgeons of Columbia University, New York, NY, U.S.A
| | - Regina M Santella
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NY, U.S.A.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, U.S.A
| | - Mary Beth Terry
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, U.S.A.,Department of Epidemiology, Mailman School of Public Health of Columbia University, New York, NY, U.S.A
| |
Collapse
|
11
|
Kappil M, Terry MB, Delgado-Cruzata L, Liao Y, Santella RM. Mismatch Repair Polymorphisms as Markers of Breast Cancer Prevalence in the Breast Cancer Family Registry. Anticancer Res 2017; 36:4437-41. [PMID: 27630279 DOI: 10.21873/anticanres.10987] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 07/20/2016] [Indexed: 01/17/2023]
Abstract
BACKGROUND Major breast cancer susceptibility genes involved in DNA repair, including BRCA1 and BRCA2, have been identified. However, mutations in these genes account for only 5-10% of identified breast cancer cases. Additional DNA repair pathway genes may also contribute to susceptibility. MATERIALS AND METHODS We investigated the association between 12 single nucleotide polymorphisms (SNPs) in mismatch repair (MMR) genes and breast cancer risk among 313 sister-sets enrolled in the New York site of the Breast Cancer Family Registry (BCFR) (n=744) using conditional logistic regression analysis. RESULTS An increase in breast cancer risk was observed for women with the MUTYH_rs3219489 variant allele (odds ratio (OR)=2.23, 95% confidence interval (CI)=1.10-4.52) and for women with the MSH2_rs2303428 variant allele (OR=1.73, 95% CI=1.00-2.99). CONCLUSION Deficiencies in DNA repair pathways, such as MMR, have implications for the onset of familial breast cancer.
Collapse
Affiliation(s)
- Maya Kappil
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, U.S.A.
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, U.S.A. Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, U.S.A
| | - Lissette Delgado-Cruzata
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, U.S.A
| | - Yuyan Liao
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, U.S.A
| | - Regina M Santella
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, U.S.A. Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, U.S.A
| |
Collapse
|
12
|
Association of genetic polymorphisms in PRKDC and XRCC4 with risk of ESCC in a high-incidence region of North China. TUMORI JOURNAL 2015; 102:131-4. [PMID: 26166223 DOI: 10.5301/tj.5000306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2015] [Indexed: 11/20/2022]
Abstract
BACKGROUND The nonhomologous end-joining (NHEJ) pathway is the main mechanism repairing DNA double-strand breaks (DSBs) in human cells. This research was designed to study the association between selected variants in NHEJ members and esophageal squamous cell carcinoma (ESCC). METHODS Two single nucleotide polymorphisms (SNPs), PRKDC (rs7003908) and X-ray repair cross complementing group 4 (XRCC4; rs1805377), were genotyped in a total of 189 patients with ESCC and 189 unrelated control individuals in a high-risk area for ESCC in North China, and the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was applied. RESULTS A significantly different distribution was found in the frequency of PRKDC (rs7003908) genotype between the ESCC group and controls. Individuals homozygous for the C allele had a significant (3.185-fold) increased risk of ESCC. As for XRCC4 (rs1805377) polymorphism, no difference was found in distribution between the ESCC and control groups. CONCLUSIONS Our results suggest that variation in DNA repair genes may be associated with risk of ESCC.
Collapse
|
13
|
Nguyen-Dumont T, Hammet F, Mahmoodi M, Tsimiklis H, Teo ZL, Li R, Pope BJ, Terry MB, Buys SS, Daly M, Hopper JL, Winship I, Goldgar DE, Park DJ, Southey MC. Mutation screening of PALB2 in clinically ascertained families from the Breast Cancer Family Registry. Breast Cancer Res Treat 2015; 149:547-54. [PMID: 25575445 DOI: 10.1007/s10549-014-3260-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 12/22/2014] [Indexed: 11/28/2022]
Abstract
Loss-of-function mutations in PALB2 are associated with an increased risk of breast cancer, with recent data showing that female breast cancer risks for PALB2 mutation carriers are comparable in magnitude to those for BRCA2 mutation carriers. This study applied targeted massively parallel sequencing to characterize the mutation spectrum of PALB2 in probands attending breast cancer genetics clinics in the USA. The coding regions and proximal intron-exon junctions of PALB2 were screened in probands not known to carry a mutation in BRCA1 or BCRA2 from 1,250 families enrolled through familial cancer clinics by the Breast Cancer Family Registry. Mutation screening was performed using Hi-Plex, an amplicon-based targeted massively parallel sequencing platform. Screening of PALB2 was successful in 1,240/1,250 probands and identified nine women with protein-truncating mutations (three nonsense mutations and five frameshift mutations). Four of the 33 missense variants were predicted to be deleterious to protein function by in silico analysis using two different programs. Analysis of tumors from carriers of truncating mutations revealed that the majority were high histological grade, invasive ductal carcinomas. Young onset was apparent in most families, with 19 breast cancers under 50 years of age, including eight under the age of 40 years. Our data demonstrate the utility of Hi-Plex in the context of high-throughput testing for rare genetic mutations and provide additional timely information about the nature and prevalence of PALB2 mutations, to enhance risk assessment and risk management of women at high risk of cancer attending clinical genetic services.
Collapse
Affiliation(s)
- Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Qin TT, Chen T, Zhang Q, Du HN, Shu YQ, Luo K, Zhu LJ. Association between BRCA1 rs799917 polymorphism and breast cancer risk: A meta-analysis of 19,878 subjects. Biomed Pharmacother 2014; 68:905-10. [PMID: 25194442 DOI: 10.1016/j.biopha.2014.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 08/04/2014] [Indexed: 01/24/2023] Open
Abstract
Studies investigating the association between the BRCA1 rs799917 polymorphism and breast cancer risk have reported controversial results. In order to derive a more precise estimation of the relationship, we performed a comprehensive meta-analysis. A total of 8 articles comprising 19,878 subjects were included in this meta-analysis. Odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were calculated by Stata 11 software. Heterogeneity tests were conducted by Q test with I(2) value, and publication bias assessment was performed by Begg's funnel plot and Egger's test. The pooled results did not show any sufficient evidence approving the association between the BRCA1 rs799917 polymorphism and breast cancer risk in total population (T vs C: OR=1.01, 95% CI=0.97-1.06; TT vs CC: OR=1.03, 95% CI=0.93-1.13; CT vs CC: OR=1.04, 95% CI=0.92-1.16; TT+CT vs CC: OR=1.04, 95% CI=0.94-1.15; TT vs CT+CC: OR=1.03, 95% CI=0.94-1.12). In the further subgroup analyses, no significant associations were found in any comparison models according to ethnicity and source of controls. No publication bias was observed in this meta-analysis. In summary, based on the overall results, this meta-analysis strongly suggests that the BRCA1 rs799917 polymorphism is not associated with breast cancer risk.
Collapse
Affiliation(s)
- Ting-ting Qin
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Tao Chen
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Qian Zhang
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Hai-na Du
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Yong-qian Shu
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Kai Luo
- Department of Breast Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.
| | - Ling-jun Zhu
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.
| |
Collapse
|