A Risk Variant in an miR-125b Binding Site in BMPR1B Is Associated with Breast Cancer Pathogenesis
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Abstract
MicroRNAs regulate diverse cellular processes and play an integral role in cancer pathogenesis. Genomic variation within miRNA target sites may therefore be important sources for genetic differences in cancer risk. To investigate this possibility, we mapped HapMap single nucleotide polymorphisms (SNP) to putative miRNA recognition sites within genes dysregulated in estrogen receptor-stratified breast tumors and used local linkage disequilibrium patterns to identify high-ranking SNPs in the Cancer Genetic Markers of Susceptibility (CGEMS) breast cancer genome-wide association study for further testing. Two SNPs, rs1970801 and rs11097457, scoring in the top 100 from the CGEMS study, were in strong linkage disequilibrium with rs1434536, an SNP that resides within a miR-125b target site in the 3' untranslated region of the bone morphogenic receptor type 1B (BMPR1B) gene encoding a transmembrane serine/threonine kinase. We validated the CGEMS association findings for rs1970801 in an independent cohort of admixture-corrected cases identified from families with multiple case histories. Subsequent association testing of rs1434536 for these cases and CGEMS controls with imputed genotypes supported the association. Furthermore, luciferase reporter assays and overexpression of miR-125b-mimics combined with quantitative reverse transcription-PCR showed that BMPR1B transcript is a direct target of miR-125b and that miR-125b differentially regulates the C and T alleles of rs1434536. These results suggest that allele-specific regulation of BMPR1B by miR-125b explains the observed disease risk. Our approach is general and can help identify and explain the mechanisms behind disease association for alleles that affect miRNA regulation.
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Current target prediction algorithms often identify many false positive target genes and there is no strong overlap in predicted target gene list among prediction algorithms.
“current target prediction algorithms often identify many false positive target genes and there is no strong overlap in the predicted target gene list among prediction algorithms [138-141].”
From MicroRNAs in brain cholesterol metabolism and their implications for Alzheimer's disease (2016) · cites this paper as [141]
The Results section (‘Multiple HapMap SNPs map to putative miRNA target sites’; page unavailable) acknowledges false-positive target-site predictions when explaining the choice of 7mer seed sites. It does not establish that algorithms often predict many false-positive target genes, and our copy does not report how strongly target lists from different algorithms overlap. (LLM, conf=0.83)
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- Authors
- Sætrom, P., Biesinger, J., Li, S. M., Smith, D., Thomas, L. F., Majzoub, K., Rivas, G. E., Alluin, J., Rossi, J. J., Krontiris, T. G., Weitzel, J., Daly, M. B., Benson, A. B., Kirkwood, J. M., O'Dwyer, P. J., Sutphen, R., Stewart, J. A., Johnson, D., & Larson, G. P.
- Affiliations
- 1Cancer Research and Molecular Medicine and Departments of
- Brigham Young University (US)
- City Of Hope National Medical Center (US)
- 6Division of Molecular Biology, and Departments of
- 7Molecular Medicine and
- Beckman Research Institute (US)
- Fox Chase Cancer Center (US)
- Northwestern University (US)
- University of Pittsburgh (US)
- University of Pennsylvania (US)
- University of South Florida (US)
- University of Wisconsin–Madison (US)
- Vanderbilt University (US)
- Corresponding author
- Larson, Garrett P.
- ORCID
- Venue
- Cancer Research
- Published
- 2009-09-14
- Volume
- 69
- Issue
- 18
- Pages
- 7459-7465
- ISSN
- 0008-5472 (ISSN-L)
- 1538-7445
- PMC
- PMC2747041
- OpenAlex
- W2109029126
- Cited by
- 138
- References
- 41
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 2 · 2023: 2 · 2022: 3 · 2021: 5 · 2020: 5 · 2019: 6 · 2018: 6 · 2017: 8 · 2016: 12 · 2015: 10 · 2014: 12 · 2013: 12 · 2012: 19
- FWCI
- 5.93
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cancer Research (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation (0609454)
- Norges Forskningsråd
- National Institutes of Health (1rc4ca153828-01)
- National Heart, Lung, and Blood Institute (R01HL074704, HL074704)
- National Cancer Institute (R01CA106414, RC4-CA153828, U24CA114737)
- National Institute of Allergy and Infectious Diseases (P01AI046030)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- breast cancer susceptibility, miR-125b, BMPR1B, microRNA binding sites, single nucleotide polymorphisms, 3' untranslated region, allele-specific gene regulation, linkage disequilibrium, estrogen receptor-positive breast cancer, microRNA target regulation
- MeSH terms
- Adolescent, Adult, Aged, Aged, 80 and over, Alleles, Binding Sites, Breast Neoplasms, Cell Transformation, Neoplastic, Female, Humans, Middle Aged, Receptors, Estrogen, Transfection, Gene Expression Regulation, Neoplastic, Polymorphism, Single Nucleotide, MicroRNAs, Cell Line, Tumor, Bone Morphogenetic Protein Receptors, Type I, Young Adult
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