Genomic profiling and outcomes of BRAF V600E mutated papillary thyroid cancer.
Authors: Shaikh Hira , McGrath Julie , Brodskiy Pavel , Xiu Joanne , Ikpeazu Chukwuemeka , Leddon Jennifer , Sukari Ammar , Zandberg Dan Paul , Abraham Jim , Wise-Draper Trisha Michel 
Published: June 2022

e18086

Background: BRAF (BRAF mut) is the most common mutation in PTC (45% prevalence). It is associated with a higher clinical stage, tumor recurrence, absence of tumor avidity, and treatment failure. Methods: BRAF WT or BRAF mut (n = 538) PTC tumors tested with NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS) by Caris Life Sciences (Phoenix, AZ) were analyzed. PD-L1 expression was tested by IHC (22c3 antibody, ≥1 combined positive score (CPS) being positive). Real world overall survival (rwOS) was obtained from insurance claims data, calculated from treatment start to last contact. Time-on-treatment (TOT) is calculated from start to end of treatment. Kaplan-Meier estimates were used for comparison. Statistical significance was determined using Fisher’s-Exact/Mann Whitney/X2 test with Benjamini-Hochberg correction. Differential gene expression was analyzed using the Limma R package (q < 0.001, logFC > 1.5, -log10 FDR > 20). Gene Set Enrichment Analysis (GSEA) was used with a p < 0.01 cutoff. Results: BRAF mut were found in PTC (69%, 369/538) but not in the follicular subtype (0/117). No gender difference was seen in BRAF mut PTC (F: 53%, 297/538). BRAF mut were more prevalent in metastases compared to primary/local tumors (42% vs. 30%) and BRAF mut was highest in metastatic lymph nodes (55%, 130/235). TERT promoter was the most common mutation in both BRAF mut and WT groups but higher in BRAF mut (64% vs 40%, q < 0.0001), while NRAS (0.2% vs 23%, q < 0001), HRAS (0% vs 8.8%, q < 0001), KRAS (0.4% vs 5.4%, q < 0001), and EIF1AX (0% vs 6.6%, q = 0.0005) mutations were more prevalent in BRAF WT PTC. PD-L1 expression was higher in the BRAF mut patients compared to WT (37% vs 22%, q < 0.01). BRAF mut PTCs were associated with higher immune cell infiltrate including M1 macrophages, and Treg cells, but lower M2 macrophages, NK cells, CD4+ T cells, and myeloid dendritic cells (all q < 0.01). GSEA analysis revealed enrichment in IL6, JAK, and STAT3 signaling, inflammatory response, apoptosis, and interferon gamma response (all NES = 1.5 - 1.8, p < 0.01) gene sets. DCSTAMP was the most differentially expressed gene in BRAF mut tumors relative to WT (logFC = 4.4). When comparing BRAF mut with WT, no significant difference in rwOS was seen (NR vs 50 mo, HR 0.73, P> 0.2). In BRAF mut patients, treatment with multikinase inhibitors (n = 32) was associated with longer rwOS compared to BRAF inhibitor treatment (n = 37) (61 mo vs 27 mo, HR 0.364, P< 0.05). Despite small patient number, data suggests BRAF mut patients may benefit from immunotherapy (n = 4) when compared to BRAF inhibitors (n = 31) (TOT, HR = 0.35, p = 0.07). Conclusions: Our data highlights new genomic signatures that indicate potential new, while also validating current targets for BRAF mut PTC: higher PD-L1 expression, immune infiltrate, and inflammatory gene signature. Clinical trials are needed to assess the best sequencing of therapies used in this group, particularly TKIs vs BRAF inhibitors and the role of immunotherapy.