Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

MiR-148b modulates the expression of multiple genes

ABSTRACT: To identify which miR-148b targets were involved in tumorigenesis, a microarray analysis was performed for miR-148b over-expressing cells versus controls and 129 (49 up and 80 down) modulated genes were revealed. The effects of miR-148b on cancer progression depend on the direct and indirect regulation of multiple target genes. To identify miR-148b modulated genes, MDA-MB-231 cells were transfected with miR-148b precursors or negative controls (pre-miR-148b or control) and used 48h later for microarray and western blot (WB) analyses. When a âWhole Human Genome Oligo Microarrayâ (Agilent) platform was employed, 129 differentially expressed genes (49 upregulated, 80 downmodulated) were found at 48h, considering a fold change (FC) cut of 1.5 and a false discovery rate (FDR) of 16% (Table S4). Crossing these results with the list of putative miR-148b targets (3642) obtained by the miRecords System, we observed that 33 of the modulated genes were also miR-148b predicted targets and interestingly, 26 out of these 33 genes were downmodulated.

ORGANISM(S): Homo sapiens

SUBMITTER: Gerolamo Lanfranchi

PROVIDER: E-GEOD-26662 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

miR148b is a major coordinator of breast cancer progression in a relapse-associated microRNA signature by targeting ITGA5, ROCK1, PIK3CA, NRAS, and CSF1.

Cimino Daniela D De Pittà Cristiano C Orso Francesca F Zampini Matteo M Casara Silvia S Penna Elisa E Quaglino Elena E Forni Marco M Damasco Christian C Pinatel Eva E Ponzone Riccardo R Romualdi Chiara C Brisken Cathrin C De Bortoli Michele M Biglia Nicoletta N Provero Paolo P Lanfranchi Gerolamo G Taverna Daniela D

FASEB journal : official publication of the Federation of American Societies for Experimental Biology 20121211 3

Breast cancer is often fatal during its metastatic dissemination. To unravel the role of microRNAs (miRs) during malignancy, we analyzed miR expression in 77 primary breast carcinomas and identified 16 relapse-associated miRs that correlate with survival and/or distinguish tumor subtypes in different datasets. Among them, miR-148b, down-regulated in aggressive breast tumors, was found to be a major coordinator of malignancy. In fact, it is able to oppose various steps of tumor progression when o ...[more]

PMID: 23233531

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Project description:Background/Objective: Quantitative real-time PCR (RT-qPCR) is widely used in miRNA expression studies on cancer. To compensate for the analytical variability produced by the multiple steps of the method, relative quantification of the measured miRNAs is required, which is based on normalization to endogenous reference genes. A literature search in PubMed revealed that no study has been performed so far on reference miRNAs for normalization of miRNA expression in urothelial carcinoma. The aim of this study was to identify suitable reference genes for miRNA expression studies by RT-qPCR in urothelial carcinoma. Methods: Candidate reference miRNAs were selected from 24 papillary urothelial carcinoma and normal bladder tissue samples by miRNA microarrays. The usefulness of these candidate reference miRNAs together with the commonly for normalization purposes used small nuclear RNAs RNU6B, RNU48, and Z30 were thereafter validated by RT-qPCR in 58 tissue samples and analyzed by the algorithms geNorm, NormFinder, and BestKeeper. Principal Findings: Based on the miRNA microarray data, a total of 16 miRNAs were identified as putative reference genes. After validation by RT-qPCR, miR-101, miR-125a-5p, miR-148b, miR-151-3p, miR-151-5p, miR-181a, miR-181b miR-29c, miR-324-3p, miR-424, miR-874, RNU6B, RNU48, and Z30 were used for geNorm, NormFinder, and BestKeeper analyses that gave different combinations of recommended reference genes for normalization. Conclusions: The present study provided the first systematic analysis for identifying suitable reference miRNAs for miRNA expression studies of urothelial carcinoma by RT-qPCR. Different combinations of reference genes resulted in reliable expression data for both strongly and less strongly altered miRNAs. Notably, RNU6B, which is the most frequently used reference gene for miRNA studies, gave inaccurate normalization. The combination of four (miR-125a-5p, miR-148b, miR-151-3p, and miR-151-5p) or three (miR-148b, miR-874, miR-181b) miRNA reference genes is recommended for normalization. Candidate reference miRNAs (for RT-qPCR analysis) were selected from 24 papillary urothelial carcinoma and normal bladder tissue samples by miRNA microarrays.

Project description:A common experimental setup to investigate the function of a microRNA is a â??gain-of-functionâ?? approach, in which the microRNA of interest is overexpressed to analyze its impact on a given process. However, a major drawback of this technique is that microRNAs, when expressed significantly above endogenous levels, may target genes that are not affected under physiological conditions. To circumvent this problem, we have generated a retroviral microRNA-knockdown library encompassing the majority of the microRNA families expressed throughout lymphocyte development. MicroRNA knockdown is mediated by sponges, mRNAs that possess multiple binding sites for a certain microRNA family in their 3â??-UTR region. MiRNA sponges function as competitive inhibitors that sequester all specific microRNA/RISC complexes, thereby de-repressing the endogenous target genes. Using this library in pre-B cells as a model system, we have characterized all microRNAs expressed in early B cells development according to their impact on processes such as apoptosis and differentiation. In doing so, we show that functional knockdown of the known tumor-suppressive miR-15 family has only slight effects under cellular steady-state conditions. Upon withdrawal of the growth factor IL-7, however, loss of miR-15 function almost completely inhibits pre-B to immature B cell differentiation, partially protects from apoptosis and enables prolonged proliferation. In correspondence with that, knockdown of the miR-15 family confers a competitive advantage in suboptimal IL-7 concentrations, indicating that levels of miR-15 determine the sensitivity of cells towards growth factor receptor signaling. Moreover, IL-7 withdrawal seems to increase the activity of endogenous miR-15 family members in pre-B cells. Using microarray analysis, we have identified cyclin E1 as a direct and cyclin D3 as an indirect putative target gene of the miR-15 family in B cell precursors. Exogenous expression of cyclin E1 or cyclin D3 recapitulates the miR-15 loss-of-function phenotype in B cell precursors, validating their biological importance. Together, this suggests that the miR-15 family functions as a central element in a positive feedback loop that reinforces cell-cycle arrest at low growth factor concentrations, which is considered a prerequisite for light chain gene recombination and differentiation. Gene expression in cells expressing a scrambled sponge as a control vector or a sponge designed to sequester all members of the miR-15 family (miR-15a, miR-15b, miR-16, miR-497, miR-195, miR-322) was measured either in the presence or 36 hours after withdrawal of the growth factor IL-7. Two independent experiments were performed, using independently generated cell clones for each repetition.

Dataset Information

MiR-148b modulates the expression of multiple genes

Publications

miR148b is a major coordinator of breast cancer progression in a relapse-associated microRNA signature by targeting ITGA5, ROCK1, PIK3CA, NRAS, and CSF1.

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