Identifying targets of miR-143 using a SILAC-based proteomic approach

Yi Yang, Raghothama Chaerkady, Kumaran Kandasamy, Tai Chung Huang, Lakshmi Dhevi N Selvan, Sutopa B. Dwivedi, Oliver A. Kent, Joshua T. Mendell, Akhilesh Pandey

Research output: Contribution to journalArticle

49 Citations (Scopus)

Abstract

Although the targets of most miRNAs have not been experimentally identified, microRNAs (miRNAs) have begun to be extensively characterized in physiological, developmental and disease-related contexts in recent years. Thus far, mainly computational approaches have been employed to predict potential targets for the large majority of miRNAs. Although miRNAs exert a major influence on the efficiency of translation of their targets in animals, most studies describing experimental identification of miRNA target genes are based on detection of altered mRNA levels. miR-143 is a miRNA involved in tumorigenesis in multiple types of cancer, smooth muscle cell fate and adipocyte differentiation. Only a few miR-143 targets are experimentally verified, so we employed a SILAC-based quantitative proteomic strategy to systematically identify potential targets of miR-143. In total, we identified >1200 proteins from MiaPaCa2 pancreatic cancer cells, of which 93 proteins were downregulated >2-fold in miR-143 mimic transfected cells as compared to controls. Validation of 34 of these candidate targets in luciferase assays showed that 10 of them were likely direct targets of miR-143. Importantly, we also carried out gene expression profiling of the same cells and observed that the majority of the candidate targets identified by proteomics did not show a concomitant decrease in mRNA levels confirming that miRNAs affect the expression of most targets through translational inhibition. Our study clearly demonstrates that quantitative proteomic approaches are important and necessary for identifying miRNA targets.

Original languageEnglish (US)
Pages (from-to)1873-1882
Number of pages10
JournalMolecular BioSystems
Volume6
Issue number10
DOIs
StatePublished - Oct 1 2010
Externally publishedYes

Fingerprint

MicroRNAs
Proteomics
Muscle Neoplasms
Messenger RNA
Gene Expression Profiling
Luciferases
Pancreatic Neoplasms
Adipocytes
Smooth Muscle Myocytes
Carcinogenesis
Proteins
Down-Regulation
Genes

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology

Cite this

Yang, Y., Chaerkady, R., Kandasamy, K., Huang, T. C., Selvan, L. D. N., Dwivedi, S. B., ... Pandey, A. (2010). Identifying targets of miR-143 using a SILAC-based proteomic approach. Molecular BioSystems, 6(10), 1873-1882. https://doi.org/10.1039/c004401f

Identifying targets of miR-143 using a SILAC-based proteomic approach. / Yang, Yi; Chaerkady, Raghothama; Kandasamy, Kumaran; Huang, Tai Chung; Selvan, Lakshmi Dhevi N; Dwivedi, Sutopa B.; Kent, Oliver A.; Mendell, Joshua T.; Pandey, Akhilesh.

In: Molecular BioSystems, Vol. 6, No. 10, 01.10.2010, p. 1873-1882.

Research output: Contribution to journalArticle

Yang, Y, Chaerkady, R, Kandasamy, K, Huang, TC, Selvan, LDN, Dwivedi, SB, Kent, OA, Mendell, JT & Pandey, A 2010, 'Identifying targets of miR-143 using a SILAC-based proteomic approach', Molecular BioSystems, vol. 6, no. 10, pp. 1873-1882. https://doi.org/10.1039/c004401f
Yang Y, Chaerkady R, Kandasamy K, Huang TC, Selvan LDN, Dwivedi SB et al. Identifying targets of miR-143 using a SILAC-based proteomic approach. Molecular BioSystems. 2010 Oct 1;6(10):1873-1882. https://doi.org/10.1039/c004401f
Yang, Yi ; Chaerkady, Raghothama ; Kandasamy, Kumaran ; Huang, Tai Chung ; Selvan, Lakshmi Dhevi N ; Dwivedi, Sutopa B. ; Kent, Oliver A. ; Mendell, Joshua T. ; Pandey, Akhilesh. / Identifying targets of miR-143 using a SILAC-based proteomic approach. In: Molecular BioSystems. 2010 ; Vol. 6, No. 10. pp. 1873-1882.
@article{0da15994ea2c4ffc9420773abf22b13b,
title = "Identifying targets of miR-143 using a SILAC-based proteomic approach",
abstract = "Although the targets of most miRNAs have not been experimentally identified, microRNAs (miRNAs) have begun to be extensively characterized in physiological, developmental and disease-related contexts in recent years. Thus far, mainly computational approaches have been employed to predict potential targets for the large majority of miRNAs. Although miRNAs exert a major influence on the efficiency of translation of their targets in animals, most studies describing experimental identification of miRNA target genes are based on detection of altered mRNA levels. miR-143 is a miRNA involved in tumorigenesis in multiple types of cancer, smooth muscle cell fate and adipocyte differentiation. Only a few miR-143 targets are experimentally verified, so we employed a SILAC-based quantitative proteomic strategy to systematically identify potential targets of miR-143. In total, we identified >1200 proteins from MiaPaCa2 pancreatic cancer cells, of which 93 proteins were downregulated >2-fold in miR-143 mimic transfected cells as compared to controls. Validation of 34 of these candidate targets in luciferase assays showed that 10 of them were likely direct targets of miR-143. Importantly, we also carried out gene expression profiling of the same cells and observed that the majority of the candidate targets identified by proteomics did not show a concomitant decrease in mRNA levels confirming that miRNAs affect the expression of most targets through translational inhibition. Our study clearly demonstrates that quantitative proteomic approaches are important and necessary for identifying miRNA targets.",
author = "Yi Yang and Raghothama Chaerkady and Kumaran Kandasamy and Huang, {Tai Chung} and Selvan, {Lakshmi Dhevi N} and Dwivedi, {Sutopa B.} and Kent, {Oliver A.} and Mendell, {Joshua T.} and Akhilesh Pandey",
year = "2010",
month = "10",
day = "1",
doi = "10.1039/c004401f",
language = "English (US)",
volume = "6",
pages = "1873--1882",
journal = "Molecular BioSystems",
issn = "1742-206X",
publisher = "Royal Society of Chemistry",
number = "10",

}

TY - JOUR

T1 - Identifying targets of miR-143 using a SILAC-based proteomic approach

AU - Yang, Yi

AU - Chaerkady, Raghothama

AU - Kandasamy, Kumaran

AU - Huang, Tai Chung

AU - Selvan, Lakshmi Dhevi N

AU - Dwivedi, Sutopa B.

AU - Kent, Oliver A.

AU - Mendell, Joshua T.

AU - Pandey, Akhilesh

PY - 2010/10/1

Y1 - 2010/10/1

N2 - Although the targets of most miRNAs have not been experimentally identified, microRNAs (miRNAs) have begun to be extensively characterized in physiological, developmental and disease-related contexts in recent years. Thus far, mainly computational approaches have been employed to predict potential targets for the large majority of miRNAs. Although miRNAs exert a major influence on the efficiency of translation of their targets in animals, most studies describing experimental identification of miRNA target genes are based on detection of altered mRNA levels. miR-143 is a miRNA involved in tumorigenesis in multiple types of cancer, smooth muscle cell fate and adipocyte differentiation. Only a few miR-143 targets are experimentally verified, so we employed a SILAC-based quantitative proteomic strategy to systematically identify potential targets of miR-143. In total, we identified >1200 proteins from MiaPaCa2 pancreatic cancer cells, of which 93 proteins were downregulated >2-fold in miR-143 mimic transfected cells as compared to controls. Validation of 34 of these candidate targets in luciferase assays showed that 10 of them were likely direct targets of miR-143. Importantly, we also carried out gene expression profiling of the same cells and observed that the majority of the candidate targets identified by proteomics did not show a concomitant decrease in mRNA levels confirming that miRNAs affect the expression of most targets through translational inhibition. Our study clearly demonstrates that quantitative proteomic approaches are important and necessary for identifying miRNA targets.

AB - Although the targets of most miRNAs have not been experimentally identified, microRNAs (miRNAs) have begun to be extensively characterized in physiological, developmental and disease-related contexts in recent years. Thus far, mainly computational approaches have been employed to predict potential targets for the large majority of miRNAs. Although miRNAs exert a major influence on the efficiency of translation of their targets in animals, most studies describing experimental identification of miRNA target genes are based on detection of altered mRNA levels. miR-143 is a miRNA involved in tumorigenesis in multiple types of cancer, smooth muscle cell fate and adipocyte differentiation. Only a few miR-143 targets are experimentally verified, so we employed a SILAC-based quantitative proteomic strategy to systematically identify potential targets of miR-143. In total, we identified >1200 proteins from MiaPaCa2 pancreatic cancer cells, of which 93 proteins were downregulated >2-fold in miR-143 mimic transfected cells as compared to controls. Validation of 34 of these candidate targets in luciferase assays showed that 10 of them were likely direct targets of miR-143. Importantly, we also carried out gene expression profiling of the same cells and observed that the majority of the candidate targets identified by proteomics did not show a concomitant decrease in mRNA levels confirming that miRNAs affect the expression of most targets through translational inhibition. Our study clearly demonstrates that quantitative proteomic approaches are important and necessary for identifying miRNA targets.

UR - http://www.scopus.com/inward/record.url?scp=77956550890&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77956550890&partnerID=8YFLogxK

U2 - 10.1039/c004401f

DO - 10.1039/c004401f

M3 - Article

C2 - 20544124

AN - SCOPUS:77956550890

VL - 6

SP - 1873

EP - 1882

JO - Molecular BioSystems

JF - Molecular BioSystems

SN - 1742-206X

IS - 10

ER -