Targeted RNA sequencing of thyroid tumors from individuals with PTEN hamartoma tumor syndrome reveals a unique transcriptome with a predominantly RAS-like expression profile.

Background: Differentiated thyroid cancer is typically caused by a single oncogenic driver alteration. In PTEN hamartoma tumor syndrome, a pathogenic germline PTEN alteration results in a predisposition to thyroid cancer and adenomatous thyroid nodules. This provides a unique model to study thyroid carcinogenesis in the setting of a baseline "hit" to the PI3K/AKT/mTOR pathway, implicated in RAS-like thyroid tumors.

Methods: RNA sequencing and differential expression analysis were performed on thyroid cancers, adenomatous nodules, and background thyroid tissue in patients with PTEN hamartoma tumor syndrome. BRAF^V600E-RAS scores were calculated and compared across histologic subtypes. RNA sequencing data were then integrated with previously published paired exome sequencing data.

Results: RNA sequencing was performed on 26 cancers, 27 adenomatous nodules, and 15 background thyroid samples from 20 patients with PTEN hamartoma tumor syndrome. This demonstrated 3 expression clusters: papillary architecture tumors, follicular architecture tumors, and background thyroid tissue. The majority (17, 65.4%) of cancers were RAS-like. Follicular architecture cancers were primarily RAS-like (BRAF^V600E-RAS score +0.67) and frequently associated with biallelic PTEN alterations. Papillary architecture cancers were BRAF-like (BRAF^V600E-RAS score -0.77), often in absence of biallelic PTEN alterations. Adenomatous nodules had indistinguishable expression profiles from follicular architecture cancers.

Conclusions: PTEN hamartoma tumor syndrome-associated thyroid tumors most frequently have RAS-like expression profiles. This appears to be caused by baseline dysregulation of the PI3K/AKT/mTOR pathway, with predisposition to biallelic PTEN inactivation promoting follicular adenomatous growth and subsequent malignant transformation to follicular architecture cancers. Better understanding malignant potential and tumor progression in PTEN hamartoma tumor syndrome thyroid tissue is essential for optimizing diagnosis, enhanced surveillance, and treatment in this population.