Objectives: The identification of novel causing genes in thyroid carcinoma is very important in diagnosis and prognosis of the disease. Recently, The Cancer Genome Atlas (TCGA) study found EIF1AX, CHEK2 and PPM1D genes as new minor causing genes in the papillary thyroid cancer (PTC) development. The goal of this study was to detect variants in these genes in PTC, follicular thyroid carcinoma (FTC) and anaplastic thyroid carcinoma (ATC) cohorts.
Methods: DNAs were isolated from 324 fresh-frozen thyroid tissues of the patients 316 with PTC, 2 with FTC and 6 with ATC. Exons 1, 2, 5 and 6 of the EIF1AX gene, exons 3, 4, 7, 11, 13 of the CHEK2 gene and exons 1, 4, 5 and 6 of the PPM1D gene were analyzed by next generation sequencing (NGS) using Nextera XT kit for the preparation of library and sequenced on MisDefault (Illumina). These exons were selected based on the TCGA study results.
Results: In summary, 5 variants in the EIF1AX gene were detected - 2 in PTC (0.6%), 1 in FTC (50%) and 2 in ATC (33.3%). A113_splice variant in the exon 6 with TERT C250T and TP53 P153Afs*28 mutations in the first ATC tissue and G9V variant in the exon 2 with TERT C228T and TP53 S215G mutations in the second ATC were detected. c.429+1 G>A splice variant affecting donor site with HRAS Q61K mutation in FTC was found. K3N variant in the exon 1 with BRAF V600E and TERT C250T mutations in one PTC and P2L variant in the exon 1 with KRAS Q61R mutation in the other PTC were detected. Only germline variants in CHEK2 and PPM1D genes in 21 PTC (6.6%) and 10 PTC (3.2%) were revealed, respectively. Eight different variants with main I157T variant in the CHEK2 gene and seven different variants with the most frequent A152A variant in the PPM1D gene were recognized.
Conclusions: Totally, five different somatic variants in the EIF1AX gene in 5 cases (in ATC, FTC and PTC) were identified. All these variants co-occurred with other known mutations and contribute to cancer behaviour. Only germline variants in the other two genes were detected. Thus, EIF1AX gene is verified as a minor causing gene, but CHEK2 and PPM1D genes have predisposition function. However, it is necessary to enlarge the studied cohorts, because the detection rates of variations are low. This work was supported by AZV 16-32665A and MZ ČR-RVO (EÚ, 00023761) grants.
18 May 2019 - 21 May 2019