Quantitative proteomic strategies for the identification of microRNA targets

Abstract

Keywords: 2D difference gel electrophoresis • isobaric tags for relative and absolute quantification• isotope-coded affinity tags • microRNAs • pulsed stable-isotope labeling by amino acids in cell culture • quantitative proteomics • stable-isotope labeling by amino acids in cell cultureFor reprint orders, please contact reprints@expert-reviews.com

Post-transcriptional Regulation of Human Breast Cancer Cell Proteome by Unliganded Estrogen Receptor β via microRNAs

“…Among the miRNAs down-regulated by ER␤, miR-221 and miR-222 were identified as basal-like cell-specific miRNAs and were shown to function as regulators of epithelial-to-mesenchymal transition, with high expression in luminal-like BC cells resulting in increased cell migration and invasion due to the regulation of mesenchymal-specific genes (71), whereas low miR-9 expression has been associated with a less aggressive BC phenotype (72). The up-regulated miR-125b, in contrast, has been found down-regulated in HER2-overexpressing BCs (73) and is able to suppress HER2 and HER3 mRNA and protein levels, leading to a reduction in anchorage-dependent cell growth, motility, and invasiveness (74). The effect of ER␤ on these miRNAs correlates with the potential role of this nuclear receptor as a tumor suppressor, a conclusion further supported by the up-regulation of miR-30a-5p, known to be involved in epithelial-to-mesenchymal transition, leading to inhibited cell migration and invasion and tumor-initiating cell self-renewal (60,61).…”

“…This complexity, along with the uncertainties it raises, emphasizes the need for experimental validation of hypotheses derived from quantitative analysis of miRNA expression changes. In this respect, quantitative proteomics represents a suitable approach for miRNA target identification under controlled experimental conditions (74). Based on this assumption, and to search for an experimental validation of the hypothesis stated above, we focused our attention on miR-30a-5p, whose expression is affected by the presence of ER␤ both in BC MCF-7 and ZR75.1 cells in vitro and in tumor biopsies (Fig.…”

Quantitative proteomics and protein network analysis of A549 lung cancer cells affected by miR-206

“…For most targets may be repressed by a miRNA at the protein level without being affected at the mRNA level, proteomic tools represent powerful approaches in revealing the full spectrum of miRNA targets (7,8). However, most of the differently proteins found in proteomic studies belong to high or middle abundant proteins.…”

Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development

“…By knocking down endogenous miR-21 in U266 myeloma cells, they employed a stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative proteomic strategy to systematically identify potential targets of miR-21. Because miRNAs may regulate many of their targets at the translational level without affecting mRNA abundance, proteomic methods are best suited for revealing the full spectrum of miRNA targets [61,62]. In addition, Zeng Rong and her colleagues [63] firstly used the SILAC mouse strategy to screen diagnostic markers in the serum and urine of immunoglobulin A nephropathy patients, and then found related novel candidates, such as complement C3, albumin, vitamin D binding protein (VDBP), ApoA1, and insulin-like growth factor binding protein 7 (IGFBP7), which might provide potential disease-related biomarkers for evaluation of treatment Besides, Zhang LinJun's group [64] also discovered that the expression of protein disulfide-isomerase associated protein 3 (PDIA3) was decreased in non-parenchymal cells of their rat liver fibrosis models by 2D-gel combined LC-MS/MS.…”