The lineage-defining transcription factors FOXA1 and POU2F3 as markers of poor prognosis across two large cohorts of thymic malignancies.

Abstract

e20172 Background: Thymic epithelial tumors (TETs) are rare neoplasms arising in the anterior mediastinum. TETs are stratified using the WHO classification system, which remains fundamental to prognostication and clinical decision-making. However, metastasis and aggressive tendencies are observed in all WHO subtypes, warranting further understanding of the pathobiology of TETs. Although the expression of some lineage-defining transcription factors (LTFs) in TETs has been reported previously, their clinical significance remains largely unexplored. We, herein, evaluate expression of 14 LTFs and the corresponding impact on patient outcomes across two large clinicogenomic cohorts. Methods: Expression of LTFs previously identified in thymic tissues ( AIRE , FOXA1 , FOXA2 , FOXA3 , FOXJ1 , GRHL1 , GRHL2 , GRHL3 , HNF4A , HNF4G , MYOG , POU2F3 , SOX8 and SPIB ) was evaluated in two cohorts (Caris and TCGA). The Caris cohort consisted of whole-transcriptome data from FFPE-preserved TETs using the Caris Life Sciences platform, which was also supplemented with clinicopathological data curated from the Caris data repository as well as insurance claims data. Blinded histology review with WHO subtype classification was performed by a pathologist with expertise in thymic tumors (S.S.B.). TCGA data was obtained from publicly available resources. Statistical methods employed included quantitative Cox regression and Log-Rank methods for analyses with overall survival (OS) as well as the Mann-Whitney U test for single gene expression comparisons. Results: After filtering out LTFs with low expression (median TPM<1) from the Caris dataset (n=107, 71% WHO type B3/C), seven LTFs were retained for further analysis including FOXA1 , GRHL1 , GRHL2 , GRHL3 , HNF4G , POU2F3 , and SPIB . Univariate survival analyses revealed positive associations with FOXA1 , HNF4G , and POU2F3 , while only FOXA1 and POU2F3 remained independent biomarkers in a multivariate model ( FOXA1 : HR = 1.02; p = 0.05; POU2F3 : HR = 1.01; p = 0.03). Multivariate analysis from the less aggressive TCGA cohort (n=117; 18% WHO type B3/C) also validated FOXA1 and POU2F3 associations with poor outcomes ( FOXA1 : HR = 1.14, p = 0.008; POU2F3 : HR = 1.04, p = 0.05). Tumors highly expressing both LTFs were associated with exceptionally poor outcomes as compared to tumors with low expression of both (median OS: 8 mos. vs 58 mos.; p<0.0001). Thymic carcinomas were associated with higher expression of both LTFs when compared to thymomas. Robust correlation between FOXA1 and POU2F3 was observed as well as with markers of tuft cell differentiation, KIT and GFI1B . Conclusions: FOXA1 and POU2F3 expression are markers of poor outcomes and likely related to tuft cell differentiation in thymic epithelial tumors. Testing these biomarkers prospectively may improve diagnostic resolution for previously established classification systems.