Unknown,Transcriptomics,Genomics,Proteomics

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Development of micoRNA expression signatures for invasive ductal breast carcinoma

ABSTRACT: To further develop gene expression approach to miRNA biomarker discovery, we have employed miRNA microarray expression profiling as a discovery platform to identify miRNA with the potential to regulated the gene expression signatures in the process of tumor development. Human FFPE tissues from grade 1, 2 and 3 were used to profile miRNA. The miRNA targeted genes were also studied for expression along with the selected miRNA, from this signature in the same RNA samples by real-time PCR, confirming the selected miRNA has regulatory action on the target gene expression. miRNA were profiled with less number of samples from each grade using miRNa microarray hybridization. Confirmation of the expression was carried out with more (20 from each grade)number of samples and targetted gene expression regulation was confirmed using RT PCR.

ORGANISM(S): Homo sapiens

SUBMITTER: Parvathi MVS

PROVIDER: E-GEOD-51233 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Pheochromocytoma (PCC) and paraganglioma (PGL) are rare neuroendocrine neoplasias of neural crest origin. They can be part of several syndromes, and their mRNA profile is dependent on genetic background, but questions related to clinical behavior or even main location remain unanswered. MicroRNAs are key modulators of target genes through translational repression, mRNA degradation, or both, and therefore they could resolve some of these issues. To determine the role microRNAs play in tumorigenesis and progression of PCC/PGL, as well as to identify microRNA biomarkers specifically related to different PCC/PGL genetic classes known so far, we characterized microRNA profiles in a large series of frozen tumors with germline mutations in SDHD, SDHB, VHL, RET, NF1, and TMEM127 genes through microarray analysis. We identified microRNA signatures specific to, as well as common among, the genetic classes of PCC/PGLs, and the best candidate microRNAs (miR-122, miR-126*, miR-129*, miR-133b, miR-137, miR-183, miR-210, miR-382, miR-488, miR-885-5p, and miR-96) were validated in an independent series of formalin-fixed paraffin-embedded PCC/PGL samples by qRT-PCR. MicroRNA-137, -96/183, and -143/145 expression in PCC/PGLs correlated inversely with the differentiation status of tumor cells. MicroRNA-210, -382, and -380 could modulate pseudohypoxic cellular response in VHL-deficient PCC/PGL. MicroRNA-193b, -365, and -424 were commonly downregulated among all genetic classes, suggesting their involvement in cell cycle control and differentiation. Herein, we demonstrate that PCC/PGLs have different microRNA profiles according to the underlying primary mutation, suggesting they could be used as specific biomarkers and add information on the etiology of these tumors. For this study, we employed the Agilent-019118 Human miRNA Microarray 2.0 G4470B (with Labeling kit: Agilent miRNA labeling reagent and Hybridization Kit, Cat # 5190-0408) to perform microRNA expression profiling on a large series of 54 fresh-frozen tissue samples, including a total of 48 genetically characterized pheochromocytomas (n=37) and paragangliomas (n=11) (8 SDHB-related tumors, 4 SDHD-related tumors, 14 Ret-related tumors, 12 VHL-related tumors, 4 NF1-related tumors, 3 TMEM127-related tumors, and 3 familial pheochromocytoma (FPCC) samples), and 6 normal adrenal medulla. Normalization of array data was performed applying the robust multiarray average (RMA) method using the AgiMicroRna package in Bioconductor. RMA normalization, by default, merges replicates of each probe and produces an Eset with a single value for each microRNA.

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Development of micoRNA expression signatures for invasive ductal breast carcinoma

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