MicroRNA expression profiles of seminoma from paraffin-embedded formalin-fixed tissue

Abstract

In this study, we used microRNA (miRNA) microarrays in an unbiased screen for aberrantly expressed miRNAs in seminoma, a primitive type of germ cell tumor. Formalin-fixed and paraffin-embedded (FFPE) surgical samples from 11 cases of normal testicular tissue resected for nonneoplastic causes and from 11 cases of seminoma were assessed for miRNA expression. Normal testicular tissue and seminoma were paired by race. We found 112 miRNAs to be differentially expressed between seminoma and normal testicular tissue; 52 miRNAs were overexpressed, and 60, downregulated in seminoma. We did not observe significant differences between black and white populations in our race-paired study. The upregulation of the expression of hsa-mir-21, hsa-mir-372, hsa-mir-373, has-mir-221, and hsa-mir-222 was validated by reverse transcription and real-time PCR. Hsa-mir-372 was upregulated around 1,270-fold (95 % confidence interval (CI) 525.2-3,064.8; p = 8.1e-5 by Mann-Whitney U test). Hsa-mir-373 was upregulated around 1,530-fold (95 % CI 620.5-3,785.6; p = 8.0e-5 by Mann-Whitney U test), consistent with previous reports, indicating that the miRNAs in FFPE are well preserved, and FFPE can be a valuable source for the miRNA study of seminoma. In addition, expression of hsa-mir-21 (12.2-fold, 0.0095), hsa-mir-221 (3.8-fold, 0.014) and hsa-mir-222 (3.8-fold, 0.019) was found elevated in seminoma compared to normal testicular tissue.

MicroRNA miR-371a-3p - A Novel Serum Biomarker of Testicular Germ Cell Tumors: Evidence for Specificity from Measurements in Testicular Vein Blood and in Neoplastic Hydrocele Fluid

“…They can be measured there by quantitative real time polymerase chain reaction (qPCR). miRs-371-3 and miR-302 have been detected in GCT tissue [14,21,22,23] and elevated serum levels have been documented in several pilot studies [15,16], [24]. miR-371a-3p appears to be the most sensitive marker because it showed the greatest decrease of levels in response to treatment [16,17].…”

Graded expression of microRNA-371a-3p in tumor tissues, contralateral testes, and in serum of patients with testicular germ cell tumor

“…Early experiments had provided evidence for the presence of miRs 372-373 in GCT tissue [19]. Later, highthroughput screening and microarray expression profiling documented miRs 371-373 to be present in tissue of GCTs [20][21][22][23][24]. A study using RNA extraction from formalinfixed paraffin embedded GCT tissue again demonstrated the presence of miR-371a-3p in tumor tissue with different expression levels in the various histological subtypes of GCT [25].…”

Fit for genomic and proteomic purposes: Sampling the fitness of nucleic acid and protein derivatives from formalin fixed paraffin embedded tissue

“…The fitness of miRNA contrasted clearly with the fitness of co-extracted RNA (Table 3). These are non-coding RNAs of approximately 20–22 nucleotides in length, making them less prone to degradation and modification than total RNA due to their already short length and their close association with large protein aggregates [15, 16, 25, 26]. There are several studies that have directly compared miRNA and RNA fitness from paired FFPE blocks and frozen tissue samples, which demonstrated the better fitness of miRNA compared to RNA [15, 16, 25, 26].…”