Stem Cell Features and Accumulation of Genetic Alterations Define Anaplastic Thyroid Carcinomas

Background: Stem cell features and genetic definition of tumor grade is not available for follicular cell-derived thyroid carcinomas. We aim to assess whole exome sequencing and stem cell markers in high-stage high-grade thyroid carcinomas. Design: We selected stage IV thyroid carcinomas (TC): widely invasive follicular (WIFTC, 15), papillary (PTC, 21), poorly differentiated thyroid carcinoma (PDTC, 19), and anaplastic carcinomas (ATC, 14 with differentiated component and 15 without). Whole-exome sequencing was performed on tumor and normal tissue samples, using a Random Forest machine learning approach to compare ATC with and without differentiated component, and differentiated part vs. stage IV differentiated TC vs. PDTC. Predictive Model Analysis Pipeline and Methods ► Functional somatic mutations unique to tumors were identified and represented as a samples x genes mutation matrix (mutated=1, non-mutated=0). ► Pairwise Random Forest models were built for each diagnostic category ► Variable selection was conducted using Fisher's Exact test with 5x10 fold cross-validation design. Random Forest models were based on the training set using the caret package in R, and predictive accuracy measured in an independent test set. Telomerase immunostaining and FISH-PNA of telomere were also analyzed. Results: The grade-predictive genes included ARID1A (P=2.46E-09), MAPK10 (P=4.35E-08), CTNNB1 (P=3.19E-16), PIK3CA (P=2.12E-07), PIK3R1 (P=1.67E-11), PTEN (P=5.19E-25), and TP53 (P=8.65E-45). ATC–PDTC distinction was mainly dependent on the average number of target mutated genes (7 vs. 3), with no significant differences between ATC differentiated component and stage IV differentiated TC. Telomerase was significantly higher in PDTC-ATC (p<0.001), correlating with PNA-FISH detectable telomeres. PNA-FISH detectable telomere in more than 20% tumor cells was observed in high-grade lesions (PDTC-ATC), in particular at tumor periphery. Conclusions: Stem cell features and accumulation of cooperative genetic mutations defined poorly differentiated thyroid carcinomas. Maintained stem cell features in peripheral tumor cells would contribute to higher metastatic potential.