New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer

Abstract

BackgroundPapillary Thyroid Cancer (PTC) is the most prevalent type of endocrine cancer. Its incidence has rapidly increased in recent decades but little is known regarding its complete microRNA transcriptome (miRNome). In addition, there is a need for molecular biomarkers allowing improved PTC diagnosis.MethodsWe performed small RNA deep-sequencing of 3 PTC, their matching normal tissues and lymph node metastases (LNM). We designed a new bioinformatics framework to handle each aspect of the miRNome: whole expression profiles, isomiRs distribution, non-templated additions distributions, RNA-editing or mutation. Results were validated experimentally by qRT-PCR on normal samples, tumors and LNM from 14 independent patients and in silico using the dataset from The Cancer Genome Atlas (small RNA deepsequencing of 59 normal samples, 495 PTC, and 8 LNM).ResultsWe performed small RNA deep-sequencing of 3 PTC, their matching normal tissues and lymph node metastases (LNM). We designed a new bioinformatics framework to handle each aspect of the miRNome: whole expression profiles, isomiRs distribution, non-templated additions distributions, RNA-editing or mutation. Results were validated experimentally by qRT-PCR on normal samples, tumors and LNM from 14 independent patients and in silico using the dataset from The Cancer Genome Atlas (small RNA deep-sequencing of 59 normal samples, 495 PTC, and 8 LNM). We confirmed already described up-regulations of microRNAs in PTC, such as miR-146b-5p or miR-222-3p, but we also identified down-regulated microRNAs, such as miR-7-5p or miR-30c-2-3p. We showed that these down-regulations are linked to the tumorigenesis process of thyrocytes. We selected the 14 most down-regulated microRNAs in PTC and we showed that they are potential biomarkers of PTC samples. Nevertheless, they can distinguish histological classical variants and follicular variants of PTC in the TCGA dataset. In addition, 12 of the 14 down-regulated microRNAs are significantly less expressed in aggressive PTC compared to non-aggressive PTC. We showed that the associated aggressive expression profile is mainly due to the presence of the BRAF V600E mutation. In general, primary tumors and LNM presented similar microRNA expression profiles but specific variations like the down-regulation of miR-7-2-3p and miR-30c-2-3p in LNM were observed. Investigations of the 5p-to-3p arm expression ratios, non-templated additions or isomiRs distributions revealed no major implication in PTC tumorigenesis process or LNM appearance.ConclusionsOur results showed that down-regulated microRNAs can be used as new potential common biomarkers of PTC and to distinguish main subtypes of PTC. MicroRNA expressions can be linked to the development of LNM of PTC. The bioinformatics framework that we have developed can be used as a starting point for the global analysis of any microRNA deep-sequencing data in an unbiased way.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2082-3) contains supplementary materia...

Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers

“…To ensure the quality of these RNA editing hotspots, we further ruled out the possibility of any unreported SNPs and somatic mutations or cross-mapping (Methods). Among these editing hotspots, 18 (95%) are located at the position 1-8 of mature miRNAs, 12 (63%) have been reported in previous studies (Blow et al 2006;Kawahara et al 2007aKawahara et al ,b, 2008Alon et al 2012;Choudhury et al 2012;Gong et al 2014;Warnefors et al 2014;Saiselet et al 2015;Tomaselli et al 2015;Nishikura 2016), and two editing sites (miR-151a and miR-376a) have been functionally characterized (Kawahara et al 2007a;Choudhury et al 2012). To further characterize these miRNA editing hotspots, we calculated their editing frequency (defined as the fraction of the tumor samples with detectable editing signals), the edited miRNA expression amount (defined as the RPM), and the editing level across cancer types.…”

miRNA expression and function in thyroid carcinomas: a comparative and critical analysis and a model for other cancers

“…Consequently, the discrepant results between studies could be due to the absence of specific miRNAs in some profiling platforms. miR-204-3p and miR-7-3p are examples of such miRNAs: their expressions have been reported as decreased in PTC in recent small RNA deep sequencing studies [18, 19] but these miRNAs are absent from the microarray platform used in a study using similar samples in 2011 [22]. Actually, miR-204-3p is still missing in more recent microarrays platforms [29, 30].…”

“…Since then, the field has been improved by the release of new miRNA functional and expression profiling studies. Next generation sequencing (small RNA deep sequencing technologies) gives a new reading of miRNA differential expression profiles of PTC and FTC [13–19]. …”

The Stature of Human Thyroid Cancer Related to Over Expressed mir-221 and mir-146b

“…Many publications have reported that PTC samples with different degrees of aggressiveness present different microRNA expression profiles, on the basis of microarrays and qRT-PCR analyses. These studies revealed the common up-regulation of the wellcharacterized miR-146b-5p, miR-221-3p and miR-222-3p in aggressive PTC compared to non-aggressive samples but no commonly down regulated microRNAs [24]. Through to investigations, it was revealed that miRNAs found in the exosomes are associated with a variety of specific diseases such as cancer, for example, research has shown that exosomes in blood circulation are similar to exosomes in the origin of their cancer cells.…”

“…Four were down-regulated (miR-122, miR-183, miR-149, and miR514a) and seven were up-regulated (miR-146b, miR-222, miR-221, miR-10b, miR-199a/miR-199b, miR-203 and miR-32) [23,24]. MiR-221, miR-222 and miR-146b were also up-regulated in experimental models of thyroid tumorigenesis [16,25].…”