Integrated analysis of miRNA and mRNA profiles enables target acquisition in human cancers

References

• Buffa FM, Camps C, Winchester L et al. microRNA associated progression pathways and potential therapeutic targets identified by integrated mRNA and microRNA expression profiling in breast cancer. Cancer Res.71(17), 5635–45 (2011).
   PubMed Web of Science ®Google Scholar
• Finak G, Bertos N, Pepin F et al. Stromal gene expression predicts clinical outcome in breast cancer. Nat. Med.14(5), 518–527 (2008).
   PubMed Web of Science ®Google Scholar
• Liu H, Brannon AR, Reddy AR et al. Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell renal cell carcinoma. BMC Syst. Biol.4, 51 (2010).
   PubMed Web of Science ®Google Scholar
• Jayaswal V, Lutherborrow M, Ma DD, Yang YH. Identification of microRNA–mRNA modules using microarray data. BMC Genomics12, 138 (2011).
   PubMedGoogle Scholar
• Foekens JA, Sieuwerts AM, Smid M et al. Four miRNAs associated with aggressiveness of lymph node-negative, estrogen receptor-positive human breast cancer. Proc. Natl Acad. Sci. USA105(35), 13021–13026 (2008).
   PubMed Web of Science ®Google Scholar
• van Kouwenhove M, Kedde M, Agami R. MicroRNA regulation by RNA-binding proteins and its implications for cancer. Nat. Rev. Cancer11(9), 644–656 (2011).
   PubMedGoogle Scholar
• Bahubeshi A, Tischkowitz M, Foulkes WD. miRNA processing and human cancer: DICER1 cuts the mustard. Sci. Transl. Med.3(111), 111ps46 (2011).
   Google Scholar
• Kumar MS, Lu J, Mercer KL, Golub TR, Jacks T. Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat. Genet.39(5), 673–677 (2007).
   PubMed Web of Science ®Google Scholar
• Martello G, Rosato A, Ferrari F et al. A microRNA targeting dicer for metastasis control. Cell141(7), 1195–1207 (2010).
   PubMed Web of Science ®Google Scholar
• Li L, Yu C, Gao H, Li Y. Argonaute proteins: potential biomarkers for human colon cancer. BMC Cancer10(1), 38 (2010).
   PubMedGoogle Scholar
• Bader AG, Brown D, Stoudemire J, Lammers P. Developing therapeutic microRNAs for cancer. Gene Ther.18(12), 1121–1126 (2011).
   PubMed Web of Science ®Google Scholar
• Gunaratne PH, Creighton CJ, Watson M, Tennakoon JB. Large-scale integration of microRNA and gene expression data for identification of enriched microRNA–mRNA associations in biological systems. Methods Mol. Biol.667, 297–315 (2010).
   PubMedGoogle Scholar
• Tang G, Shak S, Paik S et al. Comparison of the prognostic and predictive utilities of the 21-gene recurrence score assay and Adjuvant! for women with node-negative, ER-positive breast cancer: results from NSABP B-14 and NSABP B-20. Breast Cancer Res. Treat.127(1), 133–142 (2011).
   PubMed Web of Science ®Google Scholar
• Hajage D, de Rycke Y, Bollet M et al. External validation of Adjuvant! online breast cancer prognosis tool. Prioritising recommendations for improvement. PLoS One6(11), e27446 (2011).
   Google Scholar
• Enerly E, Steinfeld I, Kleivi K et al. miRNA–mRNA integrated analysis reveals roles for miRNAs in primary breast tumors. PLoS One6(2), e16915 (2011).
   PubMedGoogle Scholar
• Ma Y, Zhang P, Wang F et al. miR-150 as a potential biomarker associated with prognosis and therapeutic outcome in colorectal cancer. Gut doi:gutjnl-2011-301122 (2011) (Epub ahead of print).
   Google Scholar
• Bezman NA, Chakraborty T, Bender T, Lanier LL. miR-150 regulates the development of NK and iNKT cells. J. Exp. Med.208(13), 2717–2731 (2011).
   PubMed Web of Science ®Google Scholar
• Zhang Z, Sun H, Dai H et al. MicroRNA miR-210 modulates cellular response to hypoxia through the MYC antagonist MNT. Cell Cycle8(17), 2756–2768 (2009).
   PubMed Web of Science ®Google Scholar
• Huang X, Ding L, Bennewith KL et al. Hypoxia-inducible mir-210 regulates normoxic gene expression involved in tumor initiation. Mol. Cell35(6), 856–867 (2009).
   PubMed Web of Science ®Google Scholar
• Wang Y, Rathinam R, Walch A, Alahari SK. ST14 (suppression of tumorigenicity 14) gene is a target for miR-27b, and the inhibitory effect of ST14 on cell growth is independent of miR-27b regulation. J. Biol. Chem.284(34), 23094–23106 (2009).
   PubMed Web of Science ®Google Scholar
• Chi SW, Zang JB, Mele A, Darnell RB. Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps. Nature460(7254), 479–486 (2009).
   PubMed Web of Science ®Google Scholar
• Davis ME, Zuckerman JE, Choi CH et al. Evidence of RNAi in humans from systemically administered siRNA via targeted nanoparticles. Nature464(7291), 1067–1070 (2010).
   PubMed Web of Science ®Google Scholar
• Borgan E, Navon R, Vollan HK et al. Ischemia caused by time to freezing induces systematic microRNA and mRNA responses in cancer tissue. Mol. Oncol.5(6), 564–576 (2011).
   Google Scholar
• Sieuwerts AM, Mostert B, Bolt-de Vries J et al. mRNA and microRNA expression profiles in circulating tumor cells and primary tumors of metastatic breast cancer patients. Clin. Cancer Res.17(11), 3600–3618 (2011).
   PubMed Web of Science ®Google Scholar
• Van der Auwera I, Limame R, van Dam P, Vermeulen PB, Dirix LY, Van Laere SJ. Integrated miRNA and mRNA expression profiling of the inflammatory breast cancer subtype. Br. J. Cancer103(4), 532–541 (2010).
   Google Scholar
• Blenkiron C, Goldstein L, Thorne N et al. MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biology8(10), R214 (2007).
   PubMed Web of Science ®Google Scholar
• Lionetti M, Biasiolo M, Agnelli L et al. Identification of microRNA expression patterns and definition of a microRNA/mRNA regulatory network in distinct molecular groups of multiple myeloma. Blood114(25), e20–e26 (2009).
   Web of Science ®Google Scholar
• Fulci V, Colombo T, Chiaretti S et al. Characterization of B- and T-lineage acute lymphoblastic leukemia by integrated analysis of microRNA and mRNA expression profiles. Genes Chromosomes Cancer48(12), 1069–1082 (2009).
   PubMed Web of Science ®Google Scholar
• Wu XM, Shao XQ, Meng XX et al. Genome-wide analysis of microRNA and mRNA expression signatures in hydroxycamptothecin-resistant gastric cancer cells. Acta. Pharmacol. Sin.32(2), 259–269 (2011).
   PubMed Web of Science ®Google Scholar
• Lanza G, Ferracin M, Gafa R et al. mRNA/microRNA gene expression profile in microsatellite unstable colorectal cancer. Mol. Cancer6, 54 (2007).
   PubMed Web of Science ®Google Scholar
• Li X, Gill R, Cooper NG, Yoo JK, Datta S. Modeling microRNA–mRNA interactions using PLS regression in human colon cancer. BMC Med. Genomics4, 44 (2011).
   Google Scholar
• Li X, Chen J, Hu X et al. Comparative mRNA and microRNA expression profiling of three genitourinary cancers reveals common hallmarks and cancer-specific molecular events. PloS One6(7), e22570 (2011).
   Google Scholar
• Zhu J, Jiang Z, Gao F et al. A systematic analysis on DNA methylation and the expression of both mRNA and microRNA in bladder cancer. PloS One6(11), e28223 (2011).
   PubMedGoogle Scholar
• Gmeiner WH, Reinhold WC, Pommier Y. Genome-wide mRNA and microRNA profiling of the NCI 60 cell-line screen and comparison of FdUMP[10] with fluorouracil, floxuridine, and topoisomerase 1 poisons. Mol. Cancer Ther.9(12), 3105–3114 (2010).
   PubMed Web of Science ®Google Scholar
• Blower PE, Verducci JS, Lin S et al. MicroRNA expression profiles for the NCI-60 cancer cell panel. Mol. Cancer Ther.6(5), 1483–1491 (2007).
   PubMed Web of Science ®Google Scholar
• Sokilde R, Kaczkowski B, Podolska A et al. Global microRNA analysis of the NCI-60 cancer cell panel. Mol. Cancer Ther.10(3), 375–384 (2011).
   Google Scholar