BRAFV600E/pTERT double mutated papillary thyroid cancers exhibit immune gene suppression

BRAFV600E mutation (BRAF^mut) is common in papillary thyroid cancer (PTC), and most patients have an excellent outcome. However, a TERT-promoter mutation (pTERT^mut) in the presence of BRAF^mut (BRAF^mutpTERT^mut) has been demonstrated to confer a more aggressive behavior to PTC. Lymphocytic infiltration is often present in PTC. In this study, we sought to decipher the relationship between the BRAF and pTERT mutations and immune gene dysregulation in tumor samples from a cohort of 147 samples of PTC.

The abundance of 770 immune gene transcripts was determined by multiprex capture/detection and digital counting of mRNA transcripts using the NanoString nCounter^® PanCancer Immune Profiling Panel.

We identified 40 immune transcripts differentially expressed in BRAF^mutpTERT^mut vs BRAF^mutpTERT wildtype (pTERT^wt) (P<0.05). Transcripts induced by BRAF^mut alone were significantly repressed in BRAF^mutpTERT^mut samples, such as genes expressed by lymphoid cells, antigen-presenting cells, and cytotoxic cells, including chemokines, cytokines, checkpoint control proteins, interferon downstream markers, TNF superfamily proteins and BMP markers. A validation analysis using 444 samples from The Cancer Genome Atlas (TCGA) PTC dataset yielded similar results. Deconvolution analysis confirmed differences in the immune cell populations such as increased presence of M2 macrophages in the BRAF^mutpTERT^mut Mayo cohort and a lower abundance of M1 macrophages in the BRAF^mutpTERT^mut TCGA cohort compared to BRAF^mutpTERT^wt. Most of the immune gene pathways were enriched in the BRAF^mutpTERT^wt tumors in both Mayo and TCGA cohorts but not in BRAF^mutpTERT^mut. BRAF^mutpTERT^wt had higher stromal lymphocytes infiltration as compared to BRAF^wtpTERT^wt tumors, corroborating the transcriptomic findings.

To our knowledge this is the first report of a potential link between TERT and the immune microenvironment, offering an explanation for the aggressive nature of BRAF^mutpTERT^mut PTC.