Screen for MicroRNA and Drug Interactions in Breast Cancer Cell Lines Points to miR-126 as a Modulator of CDK4/6 and PIK3CA Inhibitors

Background: Breast cancer (BC) represents the most common cancer in women worldwide. Due to its heterogeneous nature, breast cancer management might benefit from differential treatments toward personalized medicine. Additionally, drug resistance is a common phenomenon. We systematically investigated the effect of 14 different drugs administered on BC cell lines in combination with microRNAs (miRNA, miR). Methods: Thirty-eight miRNAs, all associated with BC by clinical and molecular parameters including progression, prognosis and subtypes, were tested for their effects on the viability of 12 different BC cell lines. Four miRNAs with the strongest impact on viability were further assayed in combination with 14 BC drugs. Mann–Whitney U-test with Bonferroni correction was used for statistical analysis. Results: In a miRNA only pre-screen we observed effects on BC cell lines' viability for 34 out of 38 candidate miRNAs. We then identified 14 miRNA/drug combinations for which the combination IC50 was lower than that of both miRNA and drug as single agents. miR-181a, paired with GSK1070916, Doxorubicin, XL765 and AMG511, was the only miRNA active on the triple negative (TNBC) MDA-MB-468 cell line. miR-126 was the only miRNA (in combination with CDK4/6 or PIK3CA inhibitors) with significant effects on cell lines from different subtypes: MCF7 (Luminal) and MDA-MB-453 (HER2+). Because of its activity on different BC subtypes, we investigated the genome wide effects of miR-126 using transcriptomics and confirmed that expression of miR-126 in BC cell lines affected cell cycle and mitosis. Conclusion: Our results show that a combination treatment with miRNAs, in particular miR-181a, miR-326, miR-9 and miR-126, enhance the activity of specific BC drugs in vitro, even on the most aggressive BC subtypes, HER2+ and TNBC. Finally, as expected from its drug interactions, based on a whole transcriptome study we could confirm a role for miR-126 in cell cycle regulation.

[1]  Yate-Ching Yuan,et al.  Bone Marrow Niche Trafficking of miR-126 Controls Self-Renewal of Leukemia Stem Cells in Chronic Myelogenous Leukemia , 2018, Nature Medicine.

[2]  S. Loi,et al.  Combined CDK4/6 and PI3Kα Inhibition Is Synergistic and Immunogenic in Triple-Negative Breast Cancer. , 2017, Cancer research.

[3]  R. Scott,et al.  The potential role of miRNAs in therapy of breast and ovarian cancers associated with BRCA1 mutation , 2017, Hereditary Cancer in Clinical Practice.

[4]  A. Najafi,et al.  Identification of direct target genes of miR-7, miR-9, miR-96, and miR-182 in the human breast cancer cell lines MCF-7 and MDA-MB-231. , 2017, Molecular and cellular probes.

[5]  Chuan-yu Gao,et al.  Protective Effects of MicroRNA-126 on Human Cardiac Microvascular Endothelial Cells Against Hypoxia/Reoxygenation-Induced Injury and Inflammatory Response by Activating PI3K/Akt/eNOS Signaling Pathway , 2017, Cellular Physiology and Biochemistry.

[6]  J. Vandesompele,et al.  Influence of microRNAs and Long Non-Coding RNAs in Cancer Chemoresistance , 2017, Genes.

[7]  Yan-ru Ge,et al.  Simultaneous delivery of anti-miR21 with doxorubicin prodrug by mimetic lipoprotein nanoparticles for synergistic effect against drug resistance in cancer cells , 2016, International journal of nanomedicine.

[8]  Jingwen Liu,et al.  MicroRNA-200c delivered by solid lipid nanoparticles enhances the effect of paclitaxel on breast cancer stem cell , 2016, International journal of nanomedicine.

[9]  Ming Sun,et al.  Long non-coding RNAs in anti-cancer drug resistance , 2016, Oncotarget.

[10]  K. Ghaedi,et al.  Aberrant expression of miR-9 in benign and malignant breast tumors. , 2016, Molecular and cellular probes.

[11]  Gary D Bader,et al.  miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells , 2016, Cancer cell.

[12]  R. Kong,et al.  microRNA-126 targeting PIK3R2 promotes rheumatoid arthritis synovial fibro-blasts proliferation and resistance to apoptosis by regulating PI3K/AKT pathway. , 2016, Experimental and molecular pathology.

[13]  B. Wang,et al.  MiR-126 inhibits vascular endothelial cell apoptosis through targeting PI3K/Akt signaling , 2016, Annals of Hematology.

[14]  A. Arance,et al.  Clinical implications of the intrinsic molecular subtypes of breast cancer. , 2015, Breast.

[15]  B. Han,et al.  The Role of MicroRNAs in the Chemoresistance of Breast Cancer , 2015, Drug development research.

[16]  Samira Mohammadi-Yeganeh,et al.  Targeting Of miR9/NOTCH1 Interaction Reduces Metastatic Behavior in Triple‐negative Breast Cancer , 2015, Chemical biology & drug design.

[17]  Isabella Castiglioni,et al.  MicroRNAs: New Biomarkers for Diagnosis, Prognosis, Therapy Prediction and Therapeutic Tools for Breast Cancer , 2015, Theranostics.

[18]  Yin Li,et al.  MiR-126 regulated breast cancer cell invasion by targeting ADAM9. , 2015, International journal of clinical and experimental pathology.

[19]  J. Ferlay,et al.  Recent trends in incidence of five common cancers in 26 European countries since 1988: Analysis of the European Cancer Observatory. , 2015, European journal of cancer.

[20]  Monilola A. Olayioye,et al.  A global microRNA screen identifies regulators of the ErbB receptor signaling network , 2015, Cell Communication and Signaling.

[21]  C. Croce,et al.  Pluripotent stem cell miRNAs and metastasis in invasive breast cancer. , 2014, Journal of the National Cancer Institute.

[22]  Yul Ri Chung,et al.  MicroRNA-9 is associated with epithelial-mesenchymal transition, breast cancer stem cell phenotype, and tumor progression in breast cancer , 2014, Breast Cancer Research and Treatment.

[23]  J. Lehár,et al.  CDK 4/6 inhibitors sensitize PIK3CA mutant breast cancer to PI3K inhibitors. , 2014, Cancer cell.

[24]  A. Haholu,et al.  miR-205 and miR-200c: Predictive Micro RNAs for Lymph Node Metastasis in Triple Negative Breast Cancer , 2014, Journal of breast cancer.

[25]  Jin-hai Tang,et al.  The Function Role of miR-181a in Chemosensitivity to Adriamycin by Targeting Bcl-2 in Low-Invasive Breast Cancer Cells , 2013, Cellular Physiology and Biochemistry.

[26]  Lin Zhao,et al.  MiR-181a enhances drug sensitivity in mitoxantone-resistant breast cancer cells by targeting breast cancer resistance protein (BCRP/ABCG2) , 2013, Breast Cancer Research and Treatment.

[27]  Jing Wang,et al.  WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 , 2013, Nucleic Acids Res..

[28]  Jincai Wang,et al.  Overexpressions of microRNA-9 and microRNA-200c in human breast cancers are associated with lymph node metastasis. , 2013, Cancer biotherapy & radiopharmaceuticals.

[29]  Andrea Sottoriva,et al.  The shaping and functional consequences of the microRNA landscape in breast cancer , 2013, Nature.

[30]  R. Agami,et al.  Oncogenic miR-181a/b affect the DNA damage response in aggressive breast cancer , 2013, Cell cycle.

[31]  Stefano Volinia,et al.  Prognostic microRNA/mRNA signature from the integrated analysis of patients with invasive breast cancer , 2013, Proceedings of the National Academy of Sciences.

[32]  William P Schiemann,et al.  TGF-β upregulates miR-181a expression to promote breast cancer metastasis. , 2013, The Journal of clinical investigation.

[33]  F. Yu,et al.  MiR-27 as a Prognostic Marker for Breast Cancer Progression and Patient Survival , 2012, PloS one.

[34]  Gary D Bader,et al.  Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion , 2012, Cell stem cell.

[35]  S. Volinia,et al.  MicroRNA Expression Signatures in Solid Malignancies , 2012, Cancer journal.

[36]  C. Croce,et al.  Breast cancer signatures for invasiveness and prognosis defined by deep sequencing of microRNA , 2012, Proceedings of the National Academy of Sciences.

[37]  C. Sotiriou,et al.  Global MicroRNA Expression Profiling Identifies MiR-210 Associated with Tumor Proliferation, Invasion and Poor Clinical Outcome in Breast Cancer , 2011, PloS one.

[38]  I. Pogribny,et al.  MicroRNA-mediated drug resistance in breast cancer , 2011, Clinical Epigenetics.

[39]  Yuan Shen,et al.  Endothelial-specific intron-derived miR-126 is down-regulated in human breast cancer and targets both VEGFA and PIK3R2 , 2011, Molecular and Cellular Biochemistry.

[40]  F. Ferrari,et al.  A MicroRNA Targeting Dicer for Metastasis Control , 2010, Cell.

[41]  Y. Pekarsky,et al.  Reprogramming of miRNA networks in cancer and leukemia. , 2010, Genome research.

[42]  M. Baker.  RNA interference: MicroRNAs as biomarkers , 2010, Nature.

[43]  Hyunsuk Shim,et al.  Involvement of miR-326 in chemotherapy resistance of breast cancer through modulating expression of multidrug resistance-associated protein 1. , 2010, Biochemical pharmacology.

[44]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[45]  Debra L Winkeljohn.  Triple-negative breast cancer. , 2008, Clinical journal of oncology nursing.

[46]  Duan Ma,et al.  The cell growth suppressor, mir-126, targets IRS-1. , 2008, Biochemical and biophysical research communications.

[47]  John W M Martens,et al.  Four miRNAs associated with aggressiveness of lymph node-negative, estrogen receptor-positive human breast cancer , 2008, Proceedings of the National Academy of Sciences.

[48]  U. Lehmann,et al.  Epigenetic inactivation of microRNA gene hsa‐mir‐9‐1 in human breast cancer , 2008, The Journal of pathology.

[49]  C. Benz,et al.  Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies , 2006, Molecular Cancer.

[50]  M. Barbacid,et al.  Mammalian cyclin-dependent kinases. , 2005, Trends in biochemical sciences.

[51]  C. Croce,et al.  MicroRNA gene expression deregulation in human breast cancer. , 2005, Cancer research.

[52]  Philip M. Long,et al.  Breast cancer classification and prognosis based on gene expression profiles from a population-based study , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[53]  T. Tuschl,et al.  Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.

[54]  R. Tibshirani,et al.  Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Christian A. Rees,et al.  Molecular portraits of human breast tumours , 2000, Nature.

[56]  M. Roussel,et al.  Glycogen synthase kinase-3beta regulates cyclin D1 proteolysis and subcellular localization. , 1998, Genes & development.

[57]  G. Landberg,et al.  Deregulation of cyclin E and D1 in breast cancer is associated with inactivation of the retinoblastoma protein , 1997, Oncogene.

[58]  D. Horsfall,et al.  Androgens induce divergent proliferative responses in human breast cancer cell lines , 1995, The Journal of Steroid Biochemistry and Molecular Biology.

[59]  M. Rocchi,et al.  Molecular cloning, cDNA sequence, and chromosomal localization of the human phosphatidylinositol 3-kinase p110 alpha (PIK3CA) gene. , 1994, Genomics.

[60]  Chunyan Yang,et al.  The expression of miR-25 is increased in colorectal cancer and is associated with patient prognosis , 2013, Medical Oncology.

[61]  P. Rothberg,et al.  Oncogenes and cancer. , 1983, Cancer investigation.