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| Status |
Public on Jul 02, 2013 |
| Title |
MIRnome Profiling of Hereditary Pheochromocytoma and Paraganglioma Reveals Specific Signatures According to Primary Mutation: Possible Implications in the Differentiation Status of Tumor Cells |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
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.
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| Overall design |
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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| Contributor(s) |
Robledo M, de Cubas AA, López-Jiménez E |
| Citation(s) |
23660872 |
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| Submission date |
Jun 03, 2011 |
| Last update date |
May 07, 2014 |
| Contact name |
Mercedes Robledo |
| E-mail(s) |
mrobledo@cnio.es
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| Organization name |
Spanish National Cancer Research Centre (CNIO)
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| Department |
Human Cancer Genetics Program
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| Lab |
Hereditary Endocrine Cancer Group
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| Street address |
C/ Melchor Fernández Almagro, 3
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| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
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| Platforms (1) |
| GPL8227 |
Agilent-019118 Human miRNA Microarray 2.0 G4470B (miRNA ID version) |
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| Samples (54)
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| Relations |
| BioProject |
PRJNA141171 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE29742_RAW.tar |
98.2 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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