DICER1 somatic mutations strongly impair miRNA processing even in benign thyroid lesions

Abstract

The alteration of miRNA processing is a driver event in several tumors including thyroid cancer. In particular, somatic DICER1 mutations, reported in follicular-patterned lesions, are shared by benign as well as malignant tumors. In the present study, we investigated the effects of alterations in the miRNA processing genes on the miRNA profile. The study included 19 follicular adenomas (FAs) and 22 follicular variant of papillary thyroid carcinomas (FVPTCs). The mutational status in the hot spot regions of DICER1 , DROSHA , TARBP2 , DGCR8 and the most commonly affected genes in thyroid tumors was investigated on both tumor and paired normal tissues. The miRNA profile and the mRNA expression levels of DICER1 , DROSHA , TARBP2 , DGCR8 and XPO5 were also evaluated. Two DICER1 RNase IIIb domain mutations were found in FAs. These lesions presented a considerable loss of 5p miRNAs. Fifteen miRNAs were specifically deregulated in DICER1 -mutant lesions compared to FAs and FVPTCs. These miRNAs regulate crucial pathways in cancer such as Hippo, p53 and TGF-beta signalling. DICER1 somatic mutations in the RNase IIIb domain are not specific for malignancy, but the miRNA imbalance that they cause is remarkable, especially with regard to the loss of 5p miRNAs. DICER1 -mutant lesions have a characteristic miRNA deregulation, which is different from that of FVPTCs; nevertheless, this impairment is consistent with malignant transformation. Further studies providing the real risk of malignancy associated with DICER1 mutations and the evolution of DICER1 -mutant lesions are needed to make them useful in the clinical practice.

A pan-cancer atlas of somatic mutations in miRNA biogenesis genes

“…As shown in Figure 5C, normalization against miR-451a in samples with hotspot mutations abolished the effects of neither 5p-miRNA decreases nor 3p-miRNA increases. This indicates that hotspot mutations, as reported previously [60][61][62]65,92], decrease 5p-miRNA levels, but contrary to previous reports, they also increase the levels of numerous 3p-miRNAs. KEGG pathway enrichment analysis performed with miRPath v3.0 ( Supplementary Table S6) showed that upregulated 3p-miRNAs, among others, are strongly associated with various cancer-related processes, such as 'TGF-beta signaling pathway', 'Pathways in cancer', 'ErbB signaling pathway' and 'Hippo signaling pathway', which were found among the top ten most significant associations (adjusted p<0.00001).…”

“…The miRNA profiling performed in our study showed a global decrease in 5p-miRNAs and a global increase in 3p-miRNAs in samples with both hotspot and deleterious DICER1 mutations. A similar effect has been observed before [61,62,65,92,126,127]. The global decrease in 5p-miRNAs has been interpreted as the result of inefficient 5-miRNA processing, but the increase in 3p-miRNAs was considered an artifact of miRNA level normalization (against the total number of miRNA reads) that, as a reflection of the global 5p-miRNA deficit, resulted in a relative increase in unaffected 3p-miRNAs [65].…”

“…These hotspots were previously detected and functionally characterized in various pediatric cancers, including cancers associated with DICER1 syndrome (e.g., pleuropulmonary blastoma) and Wilms' tumor, as summarized in [54,64]. More recently, they were also investigated in thyroid adenomas [92] and the TCGA cohort, mostly in UCEC samples [65]. It was shown that RIIIb hotspot mutations affect the RIIIb cleavage of the 5p-arm of pre-miRNAs, resulting in inefficient production of 5p-miRNAs [60][61][62]92].…”

“…Two other clusters of missense hotspot mutations are located in metal ion-binding residues of the RIIIa (S1344) and RIIIb (E1705, D1709, D1810, and E1813) domains of DICER1 ( Figure 2C). These hotspots were previously detected and functionally characterized in various pediatric cancers [54,64], thyroid adenomas [92], and the TCGA cohort, mostly in UCEC samples [65].…”

“…More recently, they were also investigated in thyroid adenomas [92] and the TCGA cohort, mostly in UCEC samples [65]. It was shown that RIIIb hotspot mutations affect the RIIIb cleavage of the 5p-arm of pre-miRNAs, resulting in inefficient production of 5p-miRNAs [60][61][62]92]. In a very recent study, it was also shown that the hotspot mutations of the S1344 residue, although located in RIIIa, spatially interfere with RIIIb, resulting in the same effect as that observed for the mutations in RIIIb [65].…”