Considering that (i) the three upregulated miRNAs targeting BRAF were associated with BRAF expression/mutation in previous studies [53,54,55], (ii) the downregulation of four miRNAs in PTC tissue (three targeting BRAF and one targeting HLA-G) conducts to a harmful role in thyroid tumorigenesis, and (iii) the genes targeted by downregulated miRNAs have higher expression and increased activity on miRNA-related pathways, these findings provide a more comprehensive understanding of the complex regulation of the BRAF and HLA-G genes in PTC. Here, HLA-G is linked to thyroiditis.