JS08.4.A LINEAR GRADING COEFFICIENT REVEALS EMBRYONIC DEVELOPMENT GENE SIGNATURE AS TREATMENT-INDEPENDENT PROGNOSTIC FACTOR IN IDH-MUTANT ASTROCYTOMA

Abstract

Abstract BACKGROUND Diffuse gliomas are classified into grade II/III and grade IV IDH-mutant (IDHmt) astrocytoma based on histology and homozygous deletion of the CDKN2AB locus, according to the 2021 WHO classification. There is considerable variation in prognosis within these classification groups and we therefore sought to identify features that might aid further tumor grading. MATERIAL AND METHODS RNA sequencing was performed on IDHmt astrocytomas included in the CATNON trial and overlaid with previously generated genome-wide methylation data. This dataset was extended by multi-omics data from the TCGA and GLASS-NL studies, where the latter was used for validation. For all datasets, only IDHmt astrocytomas were selected. We defined a linear grading coefficient (LGC) based on calibrated DNA methylation-based probability scores and performed differential gene expression (DGE) regression analysis on the LGC. Statistical analyses were intersected across the CATNON and TCGA cohorts ("discovery set") and validated on the primary-recurrent GLASS-NL dataset. Single-nucleus RNA-sequencing (snRNAseq) data of high-grade IDHmt astrocytomas was used to explore the source of expression signals. RESULTS DGE regression analysis revealed that higher-grade IDHmt tumors (high LGC) exhibited mRNA upregulation of key embryonic developmental transcription factors (HOXA/C/D, NKX, PAX, and TBX). Although the vast majority of CpG sites in LGC high tumors were hypomethylated, homeobox genes were strongly hypermethylated in our discovery set. All HOX gene clusters showed gene-ordered (differential) expression where e.g. HOXD10>D9>D8>D4>D1 and HOXA3>A7>A9>A13 suggesting derepression of enhancer sequences up/downstream of the gene cluster. Our expression-based gene signature was positively correlated with, but not limited to, the G-CIMP-low subtype and homozygous CDKN2AB deletion. More than half of the genes from the HOX gene family were part of our signature. Our embryonic development signature was prognostic (log-rank test) on both the discovery (CATNON: p < 0.0005, TCGA: p < 0.0005) and validation set (GLASS-NL: p < 0.005). As our signature was developed on molecular data from the first resection its prognostic value is treatment-independent. SnRNAseq on high-grade IDHmt astrocytomas indicated expression of embryonic development genes from tumor cells, which was not restricted to cells from the stemness program. CONCLUSION Our study highlights upregulation of embryonic development genes as potential molecular mechanism associated with the malignant progression of IDH-mutant astrocytomas.