Characterization of the mutational landscape of anaplastic thyroid cancer via whole-exome sequencing

Abstract

Anaplastic thyroid carcinoma (ATC) is a frequently lethal malignancy that is often unresponsive to available therapeutic strategies. The tumorigenesis of ATC and its relationship to the widely prevalent well-differentiated thyroid carcinomas are unclear. We have analyzed 22 cases of ATC as well as 4 established ATC cell lines using whole-exome sequencing. A total of 2674 somatic mutations (121/sample) were detected. Ontology analysis revealed that the majority of variants aggregated in the MAPK, ErbB and RAS signaling pathways. Mutations in genes related to malignancy not previously associated with thyroid tumorigenesis were observed, including mTOR, NF1, NF2, MLH1, MLH3, MSH5, MSH6, ERBB2, EIF1AX and USH2A; some of which were recurrent and were investigated in 24 additional ATC cases and 8 ATC cell lines. Somatic mutations in established thyroid cancer genes were detected in 14 of 22 (64%) tumors and included recurrent mutations in BRAF, TP53 and RAS-family genes (6 cases each), as well as PIK3CA (2 cases) and single cases of CDKN1B, CDKN2C, CTNNB1 and RET mutations. BRAF V600E and RAS mutations were mutually exclusive; all ATC cell lines exhibited a combination of mutations in either BRAF and TP53 or NRAS and TP53. A hypermutator phenotype in two cases with >8 times higher mutational burden than the remaining mean was identified; both cases harbored unique somatic mutations in MLH mismatch-repair genes. This first comprehensive exome-wide analysis of the mutational landscape of ATC identifies novel genes potentially associated with ATC tumorigenesis, some of which may be targets for future therapeutic intervention.

Figure 1.

Overall mutational profile of the 22 ATCs studied by exome sequencing. All panels are aligned with vertical tracks representing 22 individuals with ATC (left) and 4 established ATC cell lines (right). The underlying heatmap shows the distribution of somatic coding mutations in thyroid malignancy-related genes, novel ATC gene variants [established driver genes as suggested by Vogelstein et al. (24) or recurrently mutated COSMIC genes found in ≥3 samples], and finally mutated Mut homolog genes in which a correlation to the amount of mutational rate was observed.

Figure 2.

Simplistic overview of the top two mutation-enriched transduction signaling pathways in ATC as according to the Genomatix Pathway System. The ErbB (top) and MAPK/Erk (bottom) signaling pathways are illustrated with each mutated gene depicted. Gene products are drawn as rounded rectangles, snip-sided rectangles denote proteins with kinase properties and star-shaped symbols denote co-factors. The top right number denotes the number of sources for a chemical association with established molecules (for therapeutic purposes), the lower right number refers to the number of established interactions within the pathway in addition to the drawn association. Filled lines with arrows denote an activating effect; filled lines with stop line and circle denote inhibitory effect. Dotted lines indicate evidence at the level of co-citation, in contrast to filled lines which indicate evidence at expert-curation level.

Figure 3.

LOH profile for the exome cohort. The graph depicts the overall LOH profile of the 22 ATC cases. Chromosome numbers are annotated on the x-axis and frequency of LOH on the y-axis. LOH events were most frequently identified in chromosomes 9p, 13p and 22q, averaging 40% of the cases.