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Mathias C, Marin AM, Kohler AF, Sanchuki HBS, Sukow N, Beltrame MH, Baal SCS, Sebastião APM, de Souza Fonseca Ribeiro EM, Gradia DF, Aoki MN, Carvalho de Oliveira J. LncRNA-SNPs in a Brazilian Breast Cancer Cohort: A Case-Control Study. Genes (Basel) 2023; 14:genes14050971. [PMID: 37239331 DOI: 10.3390/genes14050971] [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: 03/02/2023] [Revised: 04/18/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of non-coding RNAs that contain more than 200 nucleotides and exhibit a versatile regulatory capacity. Genomic alterations in lncRNAs have already been investigated in several complex diseases, including breast cancer (BC). BC is a highly heterogeneous disease and is the most prevalent cancer type among women worldwide. Single nucleotide polymorphisms (SNPs) in lncRNA regions appear to have an important role in BC susceptibility; however, little is known about lncRNA-SNPs in the Brazilian population. This study used Brazilian tumor samples to identify lncRNA-SNPs with a biological role in BC development. We applied a bioinformatic approach intersecting lncRNAs that are differentially expressed in BC tumor samples using The Cancer Genome Atlas (TCGA) cohort data and looked for lncRNAs with SNPs associated with BC in the Genome Wide Association Studies (GWAS) catalog. We highlight four lncRNA-SNPs-rs3803662, rs4415084, rs4784227, and rs7716600-which were genotyped in Brazilian BC samples in a case-control study. The SNPs rs4415084 and rs7716600 were associated with BC development at higher risk. These SNPs were also associated with progesterone status and lymph node status, respectively. The rs3803662/rs4784227 haplotype GT was associated with BC risk. These genomic alterations were also evaluated in light of the lncRNA's secondary structure and gain/loss of miRNA binding sites to better understand its biological functions. We emphasize that our bioinformatics approach could find lncRNA-SNPs with a potential biological role in BC development and that lncRNA-SNPs should be more deeply investigated in a highly heterogeneous disease population.
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Affiliation(s)
- Carolina Mathias
- Department of Genetics, Federal University of Parana, Graduate Program in Genetics, Curitiba 81310-020, Brazil
| | - Anelis Maria Marin
- Laboratory of Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81310-020, Brazil
| | - Ana Flávia Kohler
- Department of Genetics, Federal University of Parana, Graduate Program in Genetics, Curitiba 81310-020, Brazil
| | - Heloisa Bruna Soligo Sanchuki
- Laboratory of Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81310-020, Brazil
| | - Natalie Sukow
- Department of Genetics, Federal University of Parana, Graduate Program in Genetics, Curitiba 81310-020, Brazil
| | - Marcia Holsbach Beltrame
- Department of Genetics, Federal University of Parana, Graduate Program in Genetics, Curitiba 81310-020, Brazil
| | - Suelen Cristina Soares Baal
- Department of Genetics, Federal University of Parana, Graduate Program in Genetics, Curitiba 81310-020, Brazil
| | | | | | - Daniela Fiori Gradia
- Department of Genetics, Federal University of Parana, Graduate Program in Genetics, Curitiba 81310-020, Brazil
| | - Mateus Nóbrega Aoki
- Laboratory of Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81310-020, Brazil
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Hsieh YC, Tu SH, Su CT, Cho EC, Wu CH, Hsieh MC, Lin SY, Liu YR, Hung CS, Chiou HY. A polygenic risk score for breast cancer risk in a Taiwanese population. Breast Cancer Res Treat 2017; 163:131-138. [PMID: 28205043 DOI: 10.1007/s10549-017-4144-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/06/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Multiple common variants identified by genome-wide association studies showed limited evidence of the risk of breast cancer in Taiwan. In this study, we analyzed the breast cancer risk in relation to 13 individual single-nucleotide polymorphisms (SNPs) identified by a GWAS in an Asian population. METHODS In total, 446 breast cancer patients and 514 healthy controls were recruited for this case-control study. In addition, we developed a polygenic risk score (PRS) including those variants significantly associated with breast cancer risk, and also evaluated the contribution of PRS and clinical risk factors to breast cancer using receiver operating characteristic curve (AUC). RESULTS Logistic regression results showed that nine individual SNPs were significantly associated with breast cancer risk after multiple testing. Among all SNPs, six variants, namely FGFR2 (rs2981582), HCN1 (rs981782), MAP3K1 (rs889312), TOX3 (rs3803662), ZNF365 (rs10822013), and RAD51B (rs3784099), were selected to create PRS model. A dose-response association was observed between breast cancer risk and the PRS. Women in the highest quartile of PRS had a significantly increased risk compared to women in the lowest quartile (odds ratio 2.26; 95% confidence interval 1.51-3.38). The AUC for a model which contained the PRS in addition to clinical risk factors was 66.52%, whereas that for a model which with established risk factors only was 63.38%. CONCLUSIONS Our data identified a genetic risk predictor of breast cancer in Taiwanese population and suggest that risk models including PRS and clinical risk factors are useful in discriminating women at high risk of breast cancer from those at low risk.
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Affiliation(s)
- Yi-Chen Hsieh
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Shih-Hsin Tu
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, 252 Wu-Hsing St., Taipei, Taiwan.,Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan.,Breast Medical Center, Taipei Medical University Hospital, Taipei, Taiwan
| | - Chien-Tien Su
- School of Public Health, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan.,Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Er-Chieh Cho
- Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Chih-Hsiung Wu
- Department of Surgery, Taipei Medical University-Shuang Ho Hospital, Taipei, Taiwan
| | - Mao-Chih Hsieh
- Department of Surgery, Taipei Medical University-Wan Fang Hospital, Taipei, Taiwan
| | - Shiyng-Yu Lin
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yun-Ru Liu
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Chin-Sheng Hung
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, 252 Wu-Hsing St., Taipei, Taiwan. .,Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan. .,Breast Medical Center, Taipei Medical University Hospital, Taipei, Taiwan.
| | - Hung-Yi Chiou
- School of Public Health, College of Public Health and Nutrition, Taipei Medical University, 250 Wu-Hsing St., Taipei, Taiwan.
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Identification of novel susceptibility markers for the risk of overall breast cancer as well as subtypes defined by hormone receptor status in the Chinese population. J Hum Genet 2016; 61:1027-1034. [DOI: 10.1038/jhg.2016.97] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/02/2016] [Accepted: 07/04/2016] [Indexed: 02/03/2023]
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Associations of Genetic Variants at Nongenic Susceptibility Loci with Breast Cancer Risk and Heterogeneity by Tumor Subtype in Southern Han Chinese Women. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3065493. [PMID: 27022606 PMCID: PMC4789034 DOI: 10.1155/2016/3065493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/06/2016] [Accepted: 02/04/2016] [Indexed: 12/05/2022]
Abstract
Current understanding of cancer genomes is mainly “gene centric.” However, GWAS have identified some nongenic breast cancer susceptibility loci. Validation studies showed inconsistent results among different populations. To further explore this inconsistency and to investigate associations by intrinsic subtype (Luminal-A, Luminal-B, ER−&PR−&HER2+, and triple negative) among Southern Han Chinese women, we genotyped five nongenic polymorphisms (2q35: rs13387042, 5p12: rs981782 and rs4415084, and 8q24: rs1562430 and rs13281615) using MassARRAY IPLEX platform in 609 patients and 882 controls. Significant associations with breast cancer were observed for rs13387042 and rs4415084 with OR (95% CI) per-allele 1.29 (1.00–1.66) and 0.83 (0.71–0.97), respectively. In subtype specific analysis, rs13387042 (per-allele adjusted OR = 1.36, 95% CI = 1.00–1.87) and rs4415084 (per-allele adjusted OR = 0.82, 95% CI = 0.66–1.00) showed slightly significant association with Luminal-A subtype; however, only rs13387042 was associated with ER−&PR−&HER2+ tumors (per-allele adjusted OR = 1.55, 95% CI = 1.00–2.40), and none of them were linked to Luminal-B and triple negative subtype. Collectively, nongenic SNPs were heterogeneous according to the intrinsic subtype. Further studies with larger datasets along with intrinsic subtype categorization should explore and confirm the role of these variants in increasing breast cancer risk.
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McCarthy AM, Keller B, Kontos D, Boghossian L, McGuire E, Bristol M, Chen J, Domchek S, Armstrong K. The use of the Gail model, body mass index and SNPs to predict breast cancer among women with abnormal (BI-RADS 4) mammograms. Breast Cancer Res 2015; 17:1. [PMID: 25567532 PMCID: PMC4311477 DOI: 10.1186/s13058-014-0509-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 12/18/2014] [Indexed: 11/10/2022] Open
Abstract
Introduction Mammography screening results in a significant number of false-positives. The use of pretest breast cancer risk factors to guide follow-up of abnormal mammograms could improve the positive predictive value of screening. We evaluated the use of the Gail model, body mass index (BMI), and genetic markers to predict cancer diagnosis among women with abnormal mammograms. We also examined the extent to which pretest risk factors could reclassify women without cancer below the biopsy threshold. Methods We recruited a prospective cohort of women referred for biopsy with abnormal (BI-RADS 4) mammograms according to the American College of Radiology’s Breast Imaging-Reporting and Data System (BI-RADS). Breast cancer risk factors were assessed prior to biopsy. A validated panel of 12 single-nucleotide polymorphisms (SNPs) associated with breast cancer were measured. Logistic regression was used to assess the association of Gail risk factors, BMI and SNPs with cancer diagnosis (invasive or ductal carcinoma in situ). Model discrimination was assessed using the area under the receiver operating characteristic curve, and calibration was assessed using the Hosmer-Lemeshow goodness-of-fit test. The distribution of predicted probabilities of a cancer diagnosis were compared for women with or without breast cancer. Results In the multivariate model, age (odds ratio (OR) = 1.05; 95% confidence interval (CI), 1.03 to 1.08; P < 0.001), SNP panel relative risk (OR = 2.30; 95% CI, 1.06 to 4.99, P = 0.035) and BMI (≥30 kg/m2 versus <25 kg/m2; OR = 2.20; 95% CI, 1.05 to 4.58; P = 0.036) were significantly associated with breast cancer diagnosis. Older women were more likely than younger women to be diagnosed with breast cancer. The SNP panel relative risk remained strongly associated with breast cancer diagnosis after multivariable adjustment. Higher BMI was also strongly associated with increased odds of a breast cancer diagnosis. Obese women (OR = 2.20; 95% CI, 1.05 to 4.58; P = 0.036) had more than twice the odds of cancer diagnosis compared to women with a BMI <25 kg/m2. The SNP panel appeared to have predictive ability among both white and black women. Conclusions Breast cancer risk factors, including BMI and genetic markers, are predictive of cancer diagnosis among women with BI-RADS 4 mammograms. Using pretest risk factors to guide follow-up of abnormal mammograms could reduce the burden of false-positive mammograms. Electronic supplementary material The online version of this article (doi:10.1186/s13058-014-0509-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne Marie McCarthy
- Department of Medicine, Massachusetts General Hospital, 50 Staniford Street, 940F, Boston, MA, 02114, USA.
| | - Brad Keller
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Despina Kontos
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Leigh Boghossian
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
| | - Erin McGuire
- Department of General Internal Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Mirar Bristol
- Department of Medicine, Massachusetts General Hospital, 50 Staniford Street, 940F, Boston, MA, 02114, USA.
| | - Jinbo Chen
- Department of Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Susan Domchek
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
| | - Katrina Armstrong
- Department of Medicine, Massachusetts General Hospital, 50 Staniford Street, 940F, Boston, MA, 02114, USA.
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