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Jayasekera LP, Ranasinghe R, Senathilake KS, Kotelawala JT, de Silva K, Abeygunasekara PH, Goonesinghe R, Tennekoon KH. Mitochondrial genome in sporadic breast cancer: A case control study and a proteomic analysis in a Sinhalese cohort from Sri Lanka. PLoS One 2023; 18:e0281620. [PMID: 36758048 PMCID: PMC9910733 DOI: 10.1371/journal.pone.0281620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/27/2023] [Indexed: 02/10/2023] Open
Abstract
Breast cancer is the commonest malignancy in women and the majority occurs sporadically with no hereditary predisposition. However, sporadic breast cancer has been studied less intensively than the hereditary form and to date hardly any predictive biomarkers exist for the former. Furthermore, although mitochondrial DNA variants have been reported to be associated with breast cancer, findings have been inconsistent across populations. Thus we carried out a case control study on sporadic breast cancer patients and healthy controls of Sinhalese ethnicity (N = 60 matched pairs) in order to characterize coding region variants associated with the disease and to identify any potential biomarkers. Mitochondrial genome was fully sequenced in 30 pairs and selected regions were sequenced in the remaining 30 pairs. Several in-silico tools were used to assess functional significance of the variants observed. A number of variants were identified among the patients and the controls. Missense variants identified were either polymorphisms or rare variants. Their prevalence did not significantly differ between patients and the healthy controls (matched for age, body mass index and menopausal status). MT-CYB, MT-ATP6 and MT-ND2 genes showed a higher mutation rate. A higher proportion of pre-menopausal patients carried missense and pathogenic variants. Unique combinations of missense variants were seen within genes and these occurred mostly in MT-ATP6 and MT-CYB genes. Such unique combinations that occurred exclusively among the patients were common in obese patients. Mitochondrial DNA variants may have a role in breast carcinogenesis in obesity and pre-menopause. Molecular dynamic simulations suggested the mutants, G78S in MT-CO3 gene and T146A in MT-ATP6 gene are likely to be more stable than their wild type counterparts.
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Affiliation(s)
- Lakshika P. Jayasekera
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - Ruwandi Ranasinghe
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - Kanishka S. Senathilake
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - Joanne T. Kotelawala
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | | | | | | | - Kamani H. Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
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Sirisena ND, Adeyemo A, Kuruppu AI, Neththikumara N, Samaranayake N, Dissanayake VHW. Genetic determinants of sporadic breast cancer in Sri Lankan women. BMC Cancer 2018; 18:180. [PMID: 29433565 PMCID: PMC5809862 DOI: 10.1186/s12885-018-4112-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 02/09/2018] [Indexed: 11/25/2022] Open
Abstract
Background While a range of common genetic variants have been identified to be associated with risk of sporadic breast cancer in several Western studies, little is known about their role in South Asian populations. Our objective was to examine the association between common genetic variants in breast cancer related genes and risk of breast cancer in a cohort of Sri Lankan women. Methods A case-control study of 350 postmenopausal women with breast cancer and 350 healthy postmenopausal women was conducted. Genotyping using the iPLEX GOLD assay was done for 56 haplotype-tagging single nucleotide polymorphisms (SNPs) in 36 breast cancer related genes. Testing for association was done using an additive genetic model. Odds ratios and 95% confidence intervals were calculated using adjusted logistic regression models. Results Four SNPs [rs3218550 (XRCC2), rs6917 (PHB), rs1801516 (ATM), and rs13689 (CDH1)] were significantly associated with risk of breast cancer. The rs3218550 T allele and rs6917 A allele increased breast cancer risk by 1.5-fold and 1.4-fold, respectively. The CTC haplotype defined by the SNPs rs3218552|rs3218550|rs3218536 on chromosome 7 (P = 0.0088) and the CA haplotype defined by the SNPs rs1049620|rs6917 on chromosome 17 (P = 0.0067) were significantly associated with increased risk of breast cancer. The rs1801516 A allele and the rs13689 C allele decreased breast cancer risk by 0.6-fold and 0.7-fold, respectively. Conclusions These findings suggest that common genetic polymorphisms in the XRCC2, PHB, CDH1 and ATM genes are associated with risk of breast cancer among Sri Lankan postmenopausal women. The exact biological mechanisms of how these variants regulate overall breast cancer risk need further evaluation using functional studies. Electronic supplementary material The online version of this article (10.1186/s12885-018-4112-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Anchala I Kuruppu
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo 8, Sri Lanka
| | - Nilaksha Neththikumara
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo 8, Sri Lanka
| | - Nilakshi Samaranayake
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Vajira H W Dissanayake
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo 8, Sri Lanka
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De Silva S, Tennekoon KH, Dissanayake A, De Silva K, Jayasekara L. Novel and reported pathogenic variants in exon 11 of BRCA2 gene in a cohort of Sri Lankan young breast cancer patients. Fam Cancer 2018; 16:329-338. [PMID: 28039656 DOI: 10.1007/s10689-016-9962-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Women with breast carcinoma diagnosed before 40 years of age with a strong familial risk have a greater prevalence of germline BRCA1 or BRCA2 variants than late onset breast cancer. Previously germline variants in BRCA1 and BRCA2 genes were characterized in a cohort of Sri Lankan breast cancer patients unselected for age of onset. This study focused on young breast cancer patients who were screened for previously identified hotspot regions in BRCA2 gene. A total of 48 young breast cancer patients with family history of cancer and 25 healthy controls were studied. Direct sequencing was used to detect pathogenic and other sequence variants in the hotspot regions of BRCA2 gene. Thirty-six sequence variants including seven pathogenic (c.2411_2412delAA/p.Glu804Valfs*2, c.2500_2501insG/p.Leu834Cysfs*4, c.3881T>G/p.Leu1294*, c.4768A>T/p.Lys1590*, c.5645C>G/p.Ser1882*, c.5747delC/p.His1916Phefs*3, c.6728C>T/p.Ser2243Phe) and two likely pathogenic (c.1922C>T and c.3378A>T) variants, two intronic variants of unknown significance (c.1910-74T>C, c.1910-51G>T), two variants of uncertain significance (c.2324C>T c.5104C>T) and 23 benign variants were detected. Among them, seven were novel (pathogenic 5 and likely pathogenic 2). Prevalence of pathogenic and likely pathogenic variants in the hotspots regions of BRCA2 was 23 and 6.3 % respectively in this cohort. This justifies BRCA2 variant testing in young breast cancer patients with family history of cancer in Sri Lanka.
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Affiliation(s)
- Sumadee De Silva
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, 90, Cumaratunga Munidasa Mawatha, Colombo, 00300, Sri Lanka.
| | - Kamani Hemamala Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, 90, Cumaratunga Munidasa Mawatha, Colombo, 00300, Sri Lanka
| | - Aravinda Dissanayake
- National Cancer Research, Maharagama, Sri Lanka.,Teaching Hospital Jaffna, Jaffna, Sri Lanka
| | | | - Lakshika Jayasekara
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, 90, Cumaratunga Munidasa Mawatha, Colombo, 00300, Sri Lanka
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Kwong A, Shin VY, Ho JCW, Kang E, Nakamura S, Teo SH, Lee ASG, Sng JH, Ginsburg OM, Kurian AW, Weitzel JN, Siu MT, Law FBF, Chan TL, Narod SA, Ford JM, Ma ESK, Kim SW. Comprehensive spectrum of BRCA1 and BRCA2 deleterious mutations in breast cancer in Asian countries. J Med Genet 2015; 53:15-23. [PMID: 26187060 DOI: 10.1136/jmedgenet-2015-103132] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/02/2015] [Indexed: 12/20/2022]
Abstract
Approximately 5%-10% of breast cancers are due to genetic predisposition caused by germline mutations; the most commonly tested genes are BRCA1 and BRCA2 mutations. Some mutations are unique to one family and others are recurrent; the spectrum of BRCA1/BRCA2 mutations varies depending on the geographical origins, populations or ethnic groups. In this review, we compiled data from 11 participating Asian countries (Bangladesh, Mainland China, Hong Kong SAR, Indonesia, Japan, Korea, Malaysia, Philippines, Singapore, Thailand and Vietnam), and from ethnic Asians residing in Canada and the USA. We have additionally conducted a literature review to include other Asian countries mainly in Central and Western Asia. We present the current pathogenic mutation spectrum of BRCA1/BRCA2 genes in patients with breast cancer in various Asian populations. Understanding BRCA1/BRCA2 mutations in Asians will help provide better risk assessment and clinical management of breast cancer.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, Hong Kong Departments of Medicine (Oncology) and Genetics, Stanford University School of Medicine, Stanford, California, USA Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong, Hong Kong
| | - Vivian Y Shin
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - John C W Ho
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, Hong Kong
| | - Eunyoung Kang
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Seigo Nakamura
- Department of Surgery, Division of Breast Surgical Oncology, Showa University School of Medicine, Tokyo, Japan
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Selangor, Malaysia Faculty of Medicine, University Malaya Cancer Research Institute, University Malaya, Subang Jaya, Malaysia
| | - Ann S G Lee
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore Office of Clinical & Academic Faculty Affairs, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Jen-Hwei Sng
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ophira M Ginsburg
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Allison W Kurian
- Departments of Medicine (Oncology) and Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jeffrey N Weitzel
- Division of Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, California, USA
| | - Man-Ting Siu
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Fian B F Law
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, Hong Kong Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, Hong Kong
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, Hong Kong Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, Hong Kong
| | - Steven A Narod
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - James M Ford
- Departments of Medicine (Oncology) and Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, Hong Kong Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, Hong Kong
| | - Sung-Won Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
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Xue WQ, He YQ, Zhu JH, Ma JQ, He J, Jia WH. Association of BRCA2 N372H polymorphism with cancer susceptibility: a comprehensive review and meta-analysis. Sci Rep 2014; 4:6791. [PMID: 25348552 PMCID: PMC4210867 DOI: 10.1038/srep06791] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/07/2014] [Indexed: 02/07/2023] Open
Abstract
BRCA2 gene plays an important role in homologous recombination. Polymorphic variants in this gene has been suggested to confer cancer susceptibility. Numerous studies have investigated association between BRCA2 N372H polymorphism and risk of several cancers, especially breast cancer. However, the results were inconsistent. We performed a comprehensive meta-analysis to provide a more precise assessment of the association between N372H and cancer risk, following the latest meta-analysis guidelines (PRISMA). Forty six studies involving 36299 cases and 48483 controls were included in our meta-analysis. The crude ORs and the 95% CIs were used to evaluate the strength of the association. The results indicated that the BRCA2 N372H variant was significantly associated with an increased risk of overall cancer (dominant model: OR = 1.07, 95% CI = 1.01-1.13; recessive model: OR = 1.12, 95% CI = 1.02-1.23). Moreover, stratified analyses by the cancer type and source of control observed significantly increased risk associated with BRCA2 N372H in subgroups with ovarian cancer, non-Hodgkin lymphoma and population-based controls, but not breast cancer or hospital-based controls. We also found such association among Africans. Overall, the meta-analysis suggested that BRCA2 N372H may be a cancer susceptibility polymorphism. Well-designed and large-scale studies are needed to substantiate the association between BRCA2 N372H polymorphism and cancer risk.
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Affiliation(s)
- Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, China
| | - Jin-Hong Zhu
- Molecular Epidemiology Laboratory and Laboratory Medicine, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Jian-Qun Ma
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Jing He
- State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, China
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De Silva S, Tennekoon KH, Karunanayake EH, Amarasinghe I, Angunawela P. Analysis of BRCA1and BRCA2 large genomic rearrangements in Sri Lankan familial breast cancer patients and at risk individuals. BMC Res Notes 2014; 7:344. [PMID: 24906410 PMCID: PMC4057568 DOI: 10.1186/1756-0500-7-344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 05/29/2014] [Indexed: 11/10/2022] Open
Abstract
Background Majority of mutations found to date in the BRCA1/BRCA2 genes in breast and/or ovarian cancer families are point mutations or small insertions and deletions scattered over the coding sequence and splice junctions. Such mutations and sequence variants of BRCA1 and BRCA2 genes were previously identified in a group of Sri Lankan breast cancer patients. Large genomic rearrangements have been characterized in BRCA1 and BRCA2 genes in several populations but these have not been characterized in Sri Lankan breast cancer patients. Findings A cohort of familial breast cancer patients (N = 57), at risk individuals (N = 25) and healthy controls (N = 23) were analyzed using multiplex ligation-dependent probe amplification method to detect BRCA1 and BRCA2 large genomic rearrangements. One familial breast cancer patient showed an ambiguous deletion in exon 6 of BRCA1 gene. Full sequencing of the ambiguous region was used to confirm MLPA results. Ambiguous deletion detected by MLPA was found to be a false positive result confirming that BRCA1 large genomic rearrangements were absent in the subjects studied. No BRCA2 rearrangement was also identified in the cohort. Conclusion Thus this study demonstrates that BRCA1 and BRCA2 large genomic rearrangements are unlikely to make a significant contribution to aetiology of breast cancer in Sri Lanka.
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Affiliation(s)
| | - Kamani Hemamala Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka.
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