A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women

Breast Cancer Research

卷:20

Elisa V. Bandera¹  Praveen Sethupathy²  Song Yao³  Kathryn L. Lunetta⁴  Qianqian Zhu⁵  Song Liu⁵  Christine B. Ambrosone⁵  Chi-Chen Hong⁵  Lara E. Sucheston-Campbell⁵  Jeannette T. Bensen⁶  Melissa A. Troester⁶  Andrew F. Olshan⁶  Kristin L. Young⁶  Mariaelisa Graff⁶  Kevin Currin⁷  Joel Parker⁷  Chad V. Pecot⁸  Edward A. Ruiz-Narváez⁹  Christopher A. Haiman¹⁰  Julie R. Palmer¹¹  Stephen A. Haddad¹¹  Lynn Rosenberg¹¹ 

[1] Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey;

[2] Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University;

[3] Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute;

[4] Department of Biostatistics, Boston University School of Public Health;

[5] Department of Cancer Prevention and Control, Roswell Park Cancer Institute;

[6] Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill;

[7] Department of Genetics, University of North Carolina at Chapel Hill;

[8] Department of Medicine, Division of Oncology, School of Medicine, University of North Carolina at Chapel Hill;

[9] Department of Nutritional Sciences, University of Michigan School of Public Health;

[10] Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center;

[11] Slone Epidemiology Center at Boston University;

关键词: microRNA;    miRNA;    SNP;    Breast cancer;    African American;    Case-control;   

DOI  :  10.1186/s13058-018-0964-4

来源: DOAJ

【 摘 要 】

Abstract Background MicroRNAs (miRNAs) regulate gene expression and influence cancer. Primary transcripts of miRNAs (pri-miRNAs) are poorly annotated and little is known about the role of germline variation in miRNA genes and breast cancer (BC). We sought to identify germline miRNA variants associated with BC risk and tumor subtype among African-American (AA) women. Methods Under the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, genotyping and imputed data from four studies on BC in AA women were combined into a final dataset containing 224,188 miRNA gene single nucleotide polymorphisms (SNPs) for 8350 women: 3663 cases and 4687 controls. The primary miRNA sequence was identified for 566 miRNA genes expressed in Encyclopedia of DNA Elements (ENCODE) Tier 1 cell types and human pancreatic islets. Association analysis was conducted using logistic regression for BC status overall and by tumor subtype. Results A novel BC signal was localized to an 8.6-kb region of 17q25.3 by four SNPs (rs9913477, rs1428882938, rs28585511, and rs7502931) and remained statistically significant after multiple test correction (odds ratio (OR) = 1.44, 95% confidence interval (CI) = 1.26–1.65; p = 3.15 × 10−7; false discovery rate (FDR) = 0.03). These SNPs reside in a genomic location that includes both the predicted primary transcript of the noncoding miRNA gene MIR3065 and the first intron of the gene for brain-specific angiogenesis inhibitor 1-associated protein 2 (BAIAP2). Furthermore, miRNA-associated SNPs on chromosomes 1p32.3, 5q32, and 3p25.1 were the strongest signals for hormone receptor, luminal versus basal-like, and HER2 enrichment status, respectively. A second phase of genotyping (1397 BC cases, 2418 controls) that included two SNPs in the 8.6-kb region was used for validation and meta-analysis. While neither rs4969239 nor rs9913477 was validated, when meta-analyzed with the original dataset their association with BC remained directionally consistent (OR = 1.29, 95% CI = 1.16–1.44 (p = 4.18 × 10–6) and OR = 1.33, 95% CI = 1.17–1.51 (p = 1.6 × 10–5), respectively). Conclusion Germline genetic variation indicates that MIR3065 may play an important role in BC development and heterogeneity among AA women. Further investigation to determine the potential functional effects of these SNPs is warranted. This study contributes to our understanding of BC risk in AA women and highlights the complexity in evaluating variation in gene-dense regions of the human genome.

【 授权许可】

Unknown