Identification of miR-145 targets through an integrated omics analysis

Tai Chung Huang, Santosh Renuse, Sneha Pinto, Praveen Kumar, Yi Yang, Raghothama Chaerkady, Brian Godsey, Joshua T. Mendell, Marc K. Halushka, Curt I. Civin, Luigi Marchionni, Akhilesh Pandey

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and protein synthesis. To characterize functions of miRNAs and to assess their potential applications, we carried out an integrated multi-omics analysis to study miR-145, a miRNA that has been shown to suppress tumor growth. We employed gene expression profiling, miRNA profiling and quantitative proteomic analysis of a pancreatic cancer cell line. In our transcriptomic analysis, overexpression of miR-145 was found to suppress the expression of genes that are implicated in development of cancer such as ITGA11 and MAGEA4 in addition to previously described targets such as FSCN1, YES1 and PODXL. Based on miRNA profiling, overexpression of miR-145 also upregulated other miRNAs including miR-124, miR-133b and miR-125a-3p, all of which are implicated in suppression of tumors and are generally co-regulated with miR-145 in other cancers. Using the SILAC system, we identified miR-145-induced downregulation of several oncoproteins/cancer biomarkers including SET, RPA1, MCM2, ABCC1, SPTBN1 and SPTLC1. Luciferase assay validation carried out on a subset of downregulated candidate targets confirmed them to be novel direct targets of miR-145. Overall, this multi-omics approach provided insights into miR-145-mediated tumor suppression and could be used as a general strategy to study the targets of individual miRNAs. This journal is

Original languageEnglish (US)
Pages (from-to)197-207
Number of pages11
JournalMolecular BioSystems
Volume11
Issue number1
DOIs
StatePublished - Jan 1 2015

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MicroRNAs
Neoplasms
Down-Regulation
Gene Expression
Small Untranslated RNA
Oncogene Proteins
Gene Expression Profiling
Tumor Biomarkers
Luciferases
Pancreatic Neoplasms
Proteomics
Cell Line
Growth
Proteins

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology

Cite this

Huang, T. C., Renuse, S., Pinto, S., Kumar, P., Yang, Y., Chaerkady, R., ... Pandey, A. (2015). Identification of miR-145 targets through an integrated omics analysis. Molecular BioSystems, 11(1), 197-207. https://doi.org/10.1039/c4mb00585f

Identification of miR-145 targets through an integrated omics analysis. / Huang, Tai Chung; Renuse, Santosh; Pinto, Sneha; Kumar, Praveen; Yang, Yi; Chaerkady, Raghothama; Godsey, Brian; Mendell, Joshua T.; Halushka, Marc K.; Civin, Curt I.; Marchionni, Luigi; Pandey, Akhilesh.

In: Molecular BioSystems, Vol. 11, No. 1, 01.01.2015, p. 197-207.

Research output: Contribution to journalArticle

Huang, TC, Renuse, S, Pinto, S, Kumar, P, Yang, Y, Chaerkady, R, Godsey, B, Mendell, JT, Halushka, MK, Civin, CI, Marchionni, L & Pandey, A 2015, 'Identification of miR-145 targets through an integrated omics analysis', Molecular BioSystems, vol. 11, no. 1, pp. 197-207. https://doi.org/10.1039/c4mb00585f
Huang TC, Renuse S, Pinto S, Kumar P, Yang Y, Chaerkady R et al. Identification of miR-145 targets through an integrated omics analysis. Molecular BioSystems. 2015 Jan 1;11(1):197-207. https://doi.org/10.1039/c4mb00585f
Huang, Tai Chung ; Renuse, Santosh ; Pinto, Sneha ; Kumar, Praveen ; Yang, Yi ; Chaerkady, Raghothama ; Godsey, Brian ; Mendell, Joshua T. ; Halushka, Marc K. ; Civin, Curt I. ; Marchionni, Luigi ; Pandey, Akhilesh. / Identification of miR-145 targets through an integrated omics analysis. In: Molecular BioSystems. 2015 ; Vol. 11, No. 1. pp. 197-207.
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