Comparing ERK signaling and tumor microenvironment in BRAF-altered gliomas.

Abstract

2063 Background: Many patients with BRAF-altered glioma (V600E mutations, fusions) respond to BRAF inhibitors (BRAFi), but some—particularly those with high-grade gliomas (HGG)—progress on treatment. Here, we aim to assess MAPK/ERK activation associated with various BRAF alterations in a large dataset of adult and pediatric patients with low-grade (LGG) and HGG using previously validated transcriptomic signatures. Methods: Samples underwent next-generation sequencing and whole transcriptome sequencing at Caris Life Sciences (Phoenix, AZ). The MAPK Pathway Activity Score (MPAS, Wagle 2018, NPJPO) and two MEK inhibitor sensitivity signatures (Dry 2019, Cancer Res & Pratilas 2009, PNAS) were calculated from RNA-seq data. Tumor immune microenvironment was assessed using immune deconvolution (quanTIseq) and the Tumor Inflammation Signature (TIS). Results were compared for HGG in two age groups (AYA: 0-39y; adult: > 39y) in V600E mutation, fusions, or controls (BRAF-WT/IDH-WT/NF1-WT). For LGG 0-39y, V600E were compared to fusion, but not to BRAF-WT due to near-universal enrichment of MAPK alterations in LGG. There were insufficient LGG > 39y for analysis. Mann-Whiney U tests were used at α = 0.05. Results: In adult HGG (V600E: n = 35, fusions: n = 11, WT: n = 3235), both V600E and fusions showed significantly higher MAPK/ERK signatures than WT (all p < 0.01), with no significant difference between V600E and fusions. In AYA HGG (V600E: n = 32, fusions: n = 11, WT: n = 235), all three MAPK/ERK signatures were significantly higher in V600E compared to WT (all p < 0.01), while fusions fell in between BRAF V600E and WT (p > 0.05). In both AYA and adult HGG, B cells were higher in WT compared to V600E, while among infiltrated cells only M1 and M2 macrophages were elevated in fusions compared to WT (p < 0.05). Comparison of MAPK/ERK signatures in LGG (V600E: n = 28, fusions: n = 54) revealed no significant difference between V600E and fusions. TIS did not differ among BRAF alterations in any groups. Pathway analysis revealed RAS signaling and inflammation were enriched in BRAF V600E compared to WT in both HGG and LGG (NES > 2; FDR < 0.005), regardless of age. When comparing all V600E HGG patients (0-90y) previously treated with BRAFi (n = 21) to those who were not (n = 46), no difference in MAPK/ERK signatures were seen. Pathway analysis revealed samples with prior BRAFi had upregulated complement activation, B-cell activation, and opsonization (NES > 3.5; FDR < 10e-5), while treatment-naïve samples had higher BRAF/MAPK signaling (NES > 2, FDR < 0.03). Conclusions: These data confirm higher MAPK/ERK dependence signatures and RAS signaling in BRAF-altered HGG (V600E, fusion) compared to BRAF-WT controls. Differences in immune cell infiltration were observed between BRAF alteration classes. Changes in humoral immunity may be correlated with acquired resistance to BRAFi, in line with previous reports of increased B-cell infiltration in BRAFi-resistant melanomas.