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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 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]
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miR-125a-5p expression is associated with the age of breast cancer patients
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Lee, A.-R., Park, J., Jung, K. J., Jee, S. H., & Yoon, S. K. (2016) · OncoTargets and Therapy · doi:10.2147/ott.s108787 · Cited by 23
Wang, T., Huang, B., Guo, R., Ma, J., Peng, C., Zu, X., Tang, H., & Lei, X. (2015) · Oncology Letters · doi:10.3892/ol.2015.2938 · Cited by 23
“Previous studies have indicated that single nucleotide polymorphisms (SNPs) occurring in or near miRNA binding sites may be associated with tumor susceptibility and chemotherapeutic response in humans (6,17-19).”
BackgroundSato, A., Omi, T., Yamamoto, A., Satake, A., Hiramoto, A., Masutani, M., Tanuma, S.-I., Wataya, Y., & Kim, H. (2016) · PLoS ONE · doi:10.1371/journal.pone.0153130 · Cited by 22
Multiple testing under dependence via graphical models
Liu, J., Zhang, C., & Page, D. (2016) · The Annals of Applied Statistics · doi:10.1214/16-aoas956 · Cited by 22
“Storey, Taylor and Siegmund (2004) showed that the BH procedure coupled with p̂0(λ) maintains strong control of FDR under mild conditions.”
BackgroundManikandan, M., Raksha, G., & Munirajan, A. K. (2012) · Cancer Informatics · doi:10.4137/cin.s10176 · Cited by 20
A functional single nucleotide polymorphism of SET8 is prognostic for breast cancer
Liu, B., Zhang, X., Song, F., Liu, Q., Dai, H., Zheng, H., Cui, P., Zhang, L., Zhang, W., & Chen, K. (2016) · Oncotarget · doi:10.18632/oncotarget.9099 · Cited by 20
“Afterward numerous investigations have revealed the SNPs within miRNA-binding region may contribute to cancer risk and outcomes by altering miRNA-mRNA binding affinities and miRNA-targeted gene expression [7, 8].”
BackgroundNarouie, B., Ziaee, S. A. M., Basiri, A., & Hashemi, M. M. (2017) · Gene · doi:10.1016/j.gene.2017.05.060 · Cited by 19
Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome
Bhattacharya, A., Ziebarth, J. D., & Cui, Y. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046176 · Cited by 19
“Over the last several years, several association studies have identified polymorphisms in miRNA genes and their target sites that are linked with risk for several diseases, including schizophrenia [6], nonsyndromic progressive hearing loss [7], cancer [8,9,10,11,12,13,14,15], Parkinson’s disease [16], and stroke [17].”
BackgroundLncRNA SNHG6/miR-125b-5p/BMPR1B Axis: A New Therapeutic Target for Triple-Negative Breast Cancer
Lv, Y., Lv, X., Yang, H., Qi, X., Wang, X., Li, C., Shang, X., Guo, H., Zhang, J., & Zhang, Y. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.678474 · Cited by 17
“Moreover, the specific genetic variant involving the miR-125b—BMPR1B binding site has been found to contribute to breast cancer pathogenesis (34).”
BackgroundFeng, N., Xu, B., Tao, J., Li, P., Cheng, G., Min, Z.-C., Mi, Y., Wang, M., Tong, N., Tang, J., et al. (2011) · Molecular Biology Reports · doi:10.1007/s11033-011-0747-9 · Cited by 18
MicroRNA Binding-Site Polymorphisms as Potential Biomarkers of Cancer Risk
Blitzblau, R. C., & Weidhaas, J. B. (2010) · Molecular Diagnosis & Therapy · doi:10.1007/bf03256390 · Cited by 17
Emerging roles of microRNAs as extracellular vesicle cargo secreted from osteoblasts
Yoshiko, Y., & Minamizaki, T. (2020) · Journal of Oral Biosciences · doi:10.1016/j.job.2020.05.006 · Cited by 15
Liu, J., Huang, J., He, Y., Liu, J., Liao, B., & Liao, G. (2012) · Molecular Carcinogenesis · doi:10.1002/mc.21973 · Cited by 15
“Such SNPs are also associated with a variety of cancers namely, sporadic colorectal cancer [21], breast cancer [22,23] and non-small cell lung cancer [24].”
BackgroundWang, S., Liu, J., Li, X., Ji, X., Zhang, J., Wang, Y., & Cui, S. (2016) · Biology of Reproduction · doi:10.1095/biolreprod.115.131128 · Cited by 14
Jamalvandi, M., Motovali-Bashi, M., Amirmahani, F., Darvishi, P., & Goharrizi, K. J. (2018) · Molecular Biology Reports · doi:10.1007/s11033-018-4176-x · Cited by 14
MicroRNA signature for interpretable breast cancer classification with subtype clue
Andreini, P., Bonechi, S., Bianchini, M., & Geraci, F. (2022) · Journal of Computational Mathematics and Data Science · doi:10.1016/j.jcmds.2022.100042 · Cited by 13
MicroRNA-205 Mediates Proteinase-Activated Receptor 2 (PAR 2 ) -Promoted Cancer Cell Migration
Yang, X., Yang, L., Ma, Y., Zhao, X., & Wang, H. (2017) · Cancer Investigation · doi:10.1080/07357907.2017.1378671 · Cited by 13
“BMPR1B transcript is a direct target of miR-125b; interestingly, a risk variant in this miR-125b binding site in BMPR1B is associated with breast cancer pathogenesis (39).”
BackgroundEvidence for a link between TNFRSF11A and risk of breast cancer
Bonifaci, N., Palafox, M., Pellegrini, P., Osório, A., Benitez, J. J., Peterlongo, P., Manoukian, S., Peissel, B., Zaffaroni, D., Roversi, G., et al. (2011) · Breast Cancer Research and Treatment · doi:10.1007/s10549-011-1546-7 · Cited by 13
“Similarly, BMP-2 (bone morphogenetic protein 2) can induce RANKL-mediated signaling [26, 27], and its receptor, BMPR1B, has recently been identified as a potential breast cancer susceptibility gene product [28].”
BackgroundUncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity
Alsamarah, A., LaCuran, A. E., Oelschlaeger, P., Hao, J., & Luo, Y. (2015) · PLoS ONE · doi:10.1371/journal.pone.0132221 · Cited by 14
Three functional polymorphisms in CCDC170 were associated with osteoporosis phenotype
Liu, X., Li, Y.-G., Tan, F., Liu, J., Yi, R., & Zhao, X. (2021) · Biology Open · doi:10.1242/bio.050930 · Cited by 11
“DISCUSSION Identifying target genes is pivotal to understanding the roles of miRNAs in various diseases including osteoporosis (Saetrom et al., 2009; Liu et al., 2015; Juz_ enas et al., 2015).”
BackgroundThe Butterfly Effect of RNA Alterations on Transcriptomic Equilibrium
Desi, N., & Tay, Y. (2019) · Cells · doi:10.3390/cells8121634 · Cited by 12
“For example, a SNP (rs1434536) on the 3′UTR of bone morphogenic receptor type 1B (BMPR1B) creates C and T alleles that are differentially targeted by miR-125b in breast cancer [58].”
BackgroundWang, Y., Long, L., Li, T., Zhou, Y. J., Jiang, L., Zeng, X. Y., Dan, H., Liao, G., Luo, G., Wang, H., et al. (2014) · The Tohoku Journal of Experimental Medicine · doi:10.1620/tjem.233.33 · Cited by 11
“Similar associations were also observed in other cancers, such as non-small cell lung cancer (Chin et al. 2008), papillary thyroid carcinoma (Jazdzewski et al. 2008), gastric adenocarcinoma (Wang et al. 2013) and breast cancer (Saetrom et al. 2009).”
ResultValidation of micro RNA pathway polymorphisms in esophageal adenocarcinoma survival
Faluyi, O. O., Eng, L., Qiu, X., Che, J., Zhang, Q., Cheng, D., Ying, N., Tse, A., Kuang, Q., Dodbiba, L., et al. (2017) · Cancer Medicine · doi:10.1002/cam4.989 · Cited by 11
He, B., Pan, Y., Kang, L., Ying, H., Wang, F., Deng, Q.-W., Sun, H., Gao, T., & Wang, S.-K. (2015) · Gene · doi:10.1016/j.gene.2015.07.052 · Cited by 11
Zhang, W., Lin, W., Cao, H.-F., Li, C.-Y., & Li, F. (2015) · Genetics and Molecular Research · doi:10.4238/2015.october.9.8 · Cited by 11
“Many studies have revealed that genetic variances in microRNA genes and their TSs are associated with complex genetic diseases (Sethupathy et al., 2007; Saetrom et al., 2009).”
BackgroundAssociation Between Single Nucleotide Polymorphisms of miRNAs and Gastric Cancer: A Scoping Review
Pan, L., Shi, Y., Zhang, J., & Luo, G. (2022) · Genetic Testing and Molecular Biomarkers · doi:10.1089/gtmb.2021.0258 · Cited by 10
“A growing body of evidence suggests that miRNA-associated SNPs can be used as surrogate markers to predict tumor prognosis (Moriyama et al, 2009; Saetrom et al, 2009; Wang et al, 2019).”
Gorący, I., Safranow, K., Dawid, G., Skonieczna‐Żydecka, K., Kaczmarczyk, M., Gorący, J., Łoniewska, B., & Ciechanowicz, A. (2012) · Genetic Testing and Molecular Biomarkers · doi:10.1089/gtmb.2012.0164 · Cited by 10
Siddiqui, S. S., Loganathan, S., El-Faskhany, F. M., Allaf, F. A., Siddiqui, Z. K., Lamfon, H. A., & Beyari, M. M. (2014) · Clinical Medicine and Diagnostics · Cited by 10
Profile of the breast cancer susceptibility marker rs4245739 identifies a role for miRNAs
Sumadi, L. A., Wulaningsih, W., & Watkins, J. A. (2017) · Cancer Biology and Medicine · doi:10.20892/j.issn.2095-3941.2017.0050 · Cited by 9
The screening of the functional microRNA binding site SNPs in sporadic colorectal cancer genes
He, H., Lei, L., Chen, E., Xu, X., Wang, L., Pan, J., Yang, F., Wang, M., Dong, J., & Yang, J. (2017) · Cancer Biology & Therapy · doi:10.1080/15384047.2017.1323584 · Cited by 8
“SNPs of miRNA target sites were reported to be associated with lung and breast cancers, etc..(6,8) The T allele of rs696 within the 30-UTR ofNFkBIAwas reported to increase CRC susceptibility.”
BackgroundModeling SNP mediated differential targeting of homologous 3′UTR by microRNA
Ahluwalia, J. K., Soni, K., Sivasubbu, S., & Brahmachari, V. (2012) · RNA Biology · doi:10.4161/rna.19318 · Cited by 8
“A significant effect of SNP in miRNAmediated regulation is demonstrated for BRCA1, XCCR1, TGFB1, BMPR1B in luciferase reporter assays on one hand, and correlation with population susceptibility to breast cancer on the other.(13,14) The role of SNP in miRNA mediated regulation has been widely acknowledged and allelic i…”
BackgroundFindlay, V. J. (2010) · The Open Cancer Journal · Cited by 7
Metadata
- 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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