Non-coding RNAs play major roles in the translational control of gene expression. In order to identify disease-associated miRNAs in precursor lesions of lung cancer, RNA extracts from lungs of either c-Raf transgenic or wild-type (WT) mice were hybridized to the Agilent and Affymetrix miRNA microarray platforms, respectively. This resulted in the detection of a range of miRNAs varying between 111 and 267, depending on the presence or absence of the transgene, on the gender, and on the platform used. Importantly, when the two platforms were compared, only 11–16% of the 586 overlapping genes were commonly detected. With the Agilent microarray, seven miRNAs were identified as significantly regulated, of which three were selectively up-regulated in male transgenic mice. Much to our surprise, when the same samples were analyzed with the Affymetrix platform, only two miRNAs were identified as significantly regulated. Quantitative PCR performed with lung RNA extracts from WT and transgenic mice confirmed only partially the differential expression of significant regulated miRNAs and established that the Agilent platform failed to detect miR-433. Finally, bioinformatic analyses predicted a total of 152 mouse genes as targets of the regulated miRNAs of which 4 and 11 genes were significantly regulated at the mRNA level, respectively in laser micro-dissected lung dysplasia and lung adenocarcinomas of c-Raf transgenic mice. Furthermore, for many of the predicted mouse target genes expression of the coded protein was also repressed in human lung cancer when the publically available database of the Human Protein Atlas was analyzed, thus supporting the clinical significance of our findings. In conclusion, a significant difference in a cross-platform comparison was observed that will have important implications for research into miRNAs.
References
[1]
Carthew RW, Sontheimer EJ (2009) Origins and Mechanisms of miRNAs and siRNAs. Cell 136: 642–655.
[2]
Pillai RS, Bhattacharyya SN, Filipowicz W (2007) Repression of protein synthesis by miRNAs: how many mechanisms? Trends Cell Biol 17: 118–126.
[3]
Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNA are conserved targets of microRNAs. Genome Res 19: 92–105.
[4]
Stefani G, Slack FJ (2008) Small noncoding RNAs in animal development. Nat Rev Mol Cell Biol 9: 219–230.
[5]
He X, Eberhart JK, Postlethwait JH (2009) MicroRNAs and micromanaging the skeleton in disease, development, and evolution. J Cell Mol Med 13: 608–618.
[6]
Bueno MJ, de Castro IP, Malumbres M (2008) Control of cell proliferation pathways by microRNAs. Cell Cycle 7: 3143–3148.
[7]
Jovanovic M, Hengartner MO (2006) miRNAs and apoptosis: RNAs to die for. Oncogene 25: 6176–6187.
[8]
Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, et al. (2002) Frequent deletions and down-regulation of micro-RNA genes miRNA15 and miRNA16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99: 15524–15529.
[9]
Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, et al. (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65: 7065–7070.
[10]
Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, et al. (2004) Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 64: 3753–3756.
[11]
He H, Jazdewski K, Li W, Liyanarachchi S, Nagy R, et al. (2005) The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci USA 102: 19075–19080.
[12]
Denti MA, Barbareschi M, Grasso M, Cantaloni C (2013) Small RNA molecules of great utility as diagnostic biomarkers in lung cancer. Eur Pharmaceut Rev 18: 35–37.
[13]
Croce CM (2008) Oncogenes and cancer. N Engl J Med 358: 502–511.
[14]
Pritchard CC, Cheng HH, Tewari M (2012) microRNA profiling: approaches and considerations. Nature Rev Genet 13: 358–369.
[15]
Ach RA, Wang H, Curry B (2008) Measuring microRNAs: comparison of microarray and quantitative PCR measurements, and of different total RNA prep methods. BMC Biotechnol 8: 69.
[16]
Chen Y, Gelfond JAL, McManus L, Shireman PK (2009) Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis. BMC Genomics 10: 407.
Sato F, Tscuchiya S, Terasawa K, Tsujimoto G (2009) Intra-platform repeatability and inter-platform comparability of microRNA microarray technology. PLoS One 4: e5540.
[19]
Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, et al. (2011) Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 16: 991–1006.
[20]
Sah S, McNall MN, Eveleigh D, Wilson M, Irizarry RA (2010) Performance evaluations of commercial miRNA expression array platforms. BMC Res Notes 3: 80.
[21]
Pradervand S, Weber J, Lemoine F, Consales F, Paillusson A, et al. (2010) Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs. BioTechniques 48: 219–222.
[22]
Yauk CL, Rowan Carroll A, Stead JDH, Williams A (2010) Cross-platform analysis of global microRNA expression technologies. BMC Genomics 11: 330.
[23]
Wang H, Ach RA, Curry B (2007) Direct and sensitive miRNA profiling from low-input total RNA. RNA 13: 151–159.
[24]
Callari M, Dugo M, Musella V, Marchesi E, Chiorino G, et al. (2012) Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues. PLoS One 7: e45105.
[25]
Leshkowitz D, Horn-Saban S, Parmet Y, Feldmesser E (2013) Differences in microRNA detection levels are technology and sequence dependent. RNA 19: 527–538.
[26]
Kolbert CP, Feddersen RM, Rakhshan F, Grill DE, Simon G, et al. (2013) Multi-platform analysis of microRNA expression measurements in RNA from fresh-frozen and FFPE tissues. PLoS One 8: e52517.
[27]
Rohrbeck A, Mueller VS, Borlak J (2009) Molecular characterization of lung dysplasia induced by c-Raf-1. PloS One 4: e5637.
[28]
Rohrbeck A, Borlak J (2009) Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1. PLoS One 4: e7315.
[29]
Morrison DK, Cutler RE (1997) The complexity of Raf-1 regulation. Curr Opin Cell Biol 9: 174–179.
[30]
Alessi DR, Saito Y, Campbell DG, Cohen P, Sithanandam G, et al. (1994) Identification of the sites in MAP kinase kinase-1 phosphorylated by p74raf-1. EMBO 13: 1610–1619.
[31]
Payne DM, Rossomando AJ, Martino P, Erickson AK, Her JH, et al. (1991) Identification of the regulatory phosphorylation sites in pp42/mitogen-activated protein kinase (MAP kinase). EMBO 10: 885–892.
[32]
Inoue A, Nukiwa T (2005) Gene Mutations in Lung Cancer: Promising Predictive Factors for the Success of Molecular Therapy. PLoS Medicine 2: 5–13.
[33]
Rütters H, Zürbig P, Halter R, Borlak J (2006) Towards a lung adenocarcinoma proteome map: studies with SP-C/c-raf transgenic mice. Proteomics 6: 3127–3137.
[34]
Chatterji B, Borlak J (2007) Serum proteomics of lung adenocarcinomas induced by targeted overexpression of c-raf in alveolar epithelium identifies candidate biomarkers. Proteomics 7: 3980–3991.
[35]
Lewis BP, Burge CB, Bartel DP (2005) Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets. Cell 120: 15–20.
[36]
Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91–105.
[37]
Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278–1284.
[38]
Dong J, Jiang G, Asmann YW, Tomaszek S, Jen J, et al. (2010) MicroRNA networks in mouse lung organogenesis. PloS One 5: e10854.
[39]
Peltier HJ, Latham GJ (2008) Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues. RNA 14: 844–852.
[40]
Mascaux C, Laes JF, Anthoine G, Haller A, Ninane V, et al. (2009) Evolution of microRNA expression during human bronchial squamous carcinogenesis. Eur Respir J 33: 352–359.
[41]
Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, et al. (2004) Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 64: 3753–3756.
[42]
Fabbri M, Garzon R, Cimmino A, Liu Z, Zanesi N, et al. (2007) MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc Natl Acad Sci USA 104: 15805–15810.
[43]
Nasser MW, Datta J, Nuovo G, Kutay H, Motiwala T, et al. (2008) Down-regulation of micro-RNA-1 (miR-1) in lung cancer. Suppression of tumorigenic property of lung cancer cells and their sensitization to doxorubicin-induced apoptosis by miR-1. J Biol Chem 283: 33394–33405.
[44]
Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, et al. (2006) Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9: 189–198.
[45]
Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, et al. [2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA 103: 2257–2261.
[46]
Raponi M, Dossey L, Jatkoe T, Wu X, Chen G, et al. (2009) MicroRNA classifiers for predicting prognosis of squamous cell lung cancer. Cancer Res 69: 5776–5783.
[47]
Boeri M, Verri C, Conte D, Roz L, Modena P, et al. (2011) MicroRNA signatures in tissues and plasma predict development and prognosis of computed tomography detected lung cancer. Proc Natl Acad Sci USA 108: 3713–3718.
[48]
Seike M, Goto A, Okano T, Bowman ED, Schetter AJ, et al. (2009) MiR-21 is an EGFR-regulated anti-apoptotic factor in lung cancer in never-smokers. Proc Natl Acad Sci USA 106: 12085–12090.
[49]
Hatley ME, Patrick DM, Garcia MR, Richardson JA, Bassel-Duby R, et al. (2010) Modulation of K-Ras-dependent lung tumorigenesis by MicroRNA-21. Cancer Cell 18: 282–293.
[50]
Patnaik SK, Kannisto E, Mallick R, Yendamuri S (2011) Overexpression of the Lung Cancer-Prognostic miR-146b MicroRNAs Has a Minimal and Negative Effect on the Malignant Phenotype of A549 Lung Cancer Cells. PLoS ONE 6: e22379.
[51]
Tsitsiou E, Williams AE, Moschos SA, Patel K, Rossios C, et al. (2012) Transcriptome analysis shows activation of circulating CD8(+) T cells in patients with severe asthma. J Allergy Clin Immunol 129: 95–103.
[52]
Taganov KD, Boldin MP, Chang KJ, Baltimore D (2006) NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci USA 103: 12481–12486.
[53]
Perry MM, Moschos SA, Williams AE, Shepherd NJ, Larner-Svensson HM, et al. (2008) Rapid changes in microRNA-146a expression negatively regulate the IL-1beta-induced inflammatory response in human lung alveolar epithelial cells. J Immunol 180: 5689–5698.
[54]
Lu TX, Munitz A, Rothenberg ME (2009) MicroRNA-21 is up-regulated in allergic airway inflammation and regulates IL-12p35 expression. J Immunol 182: 4994–5002.
[55]
Del Vescovo V, Cantaloni C, Cucino A, Girlando S, Silvestri M, et al. (2011) miR-205 Expression levels in nonsmall cell lung cancer do not always distinguish adenocarcinomas from squamous cell carcinomas. Am J Surg Pathol 35: 268–275.
[56]
Bhaskaran M, Wang Y, Zhang H, Weng T, Baviskar P, et al. (2009) MicroRNA-127 modulates fetal lung development. Physiol Genomics 37: 268–278.
[57]
Mujahid S, Logvinenko T, Volpe MV, Nielsen HC (2013) miRNA regulated pathways in late stage murine lung development. BMC Dev Biol 13: 13.
[58]
Song G, Wang L (2009) A conserved gene structure and expression regulation of miR-433 and miR-127 in mammals. PLoS One. 4: e7829.
[59]
Yang CH, Yue J, Pfeffer SR, Handorf CR, Pfeffer LM (2011) MicroRNA miR-21 Regulates the Metastatic Behavior of B16 Melanoma Cells. J Biol Chem 286: 39172–39178.
[60]
Iliopoulos D, Jaeger SA, Hirsch HA, Bulyk ML, Struhl K (2010) STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer. Mol Cell 39: 493–506.
[61]
Ceresa BP, Horvath CM, Pessin JE (1997) Signal transducer and activator of transcription-3 serine phosphorylation by insulin is mediated by a Ras/Raf/MEK-dependent pathway. Endocrinology 138: 4131–4137.
[62]
Frezzetti D, De Menna M, Zoppoli P, Guerra C, Ferraro A, et al. (2011) Upregulation of miR-21 by Ras in vivo and its role in tumor growth. Oncogene 30: 275–286.
[63]
Yoshida Y, Ninomiya K, Hamada H, Noda M (2012) Involvement of the SKP2-p27(KIP1) pathway in suppression of cancer cell proliferation by RECK. Oncogene 31: 4128–4138.
[64]
Fang H, Harris SC, Su Z, Chen M, Qian F, et al. (2009) ArrayTrack: an FDA and public genomic tool. Methods Mol Biol 563: 379–398.
[65]
Saeed AI, Sharov V, White J, Li J, Liang W, et al. (2003) TM4: a free, open-source system for microarray data management and analysis. BioTechniques 34: 374–378.
[66]
Pontén F, Schwenk JM, Asplund A, Edqvist PH (2011) The Human Protein Atlas as a proteomic resource for biomarker discovery. J Intern Med 70: 428–446.
[67]
Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, et al. (2010) Towards a knowledge-based Human Protein Atlas. Nat Biotechnol 28: 1248–1250.
[68]
Al-Shahrour F, Minguez P, Tarraga J, Medina I, Alloza E, et al. (2007) FatiGO : a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res 35: W91–W96.
[69]
Sugimoto N, Nakano S, Katoh M, Matsumura A, Nakamuta H, et al. (1995) Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34: 11211–11216.
[70]
Wei H, Kuan P-F, Tian S, Yang C, Nie J, et al. (2008) A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucl Acids Res 36: 2926–2938.
