Papillary 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.
METHODS: We 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).
RESULTS: We 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.
CONCLUSIONS: Our 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.