PATH-15. HOX-Associated Differences between IDH-mutant Astrocytoma and Oligodendroglioma are Independent of 1p/19q-Codeletion

Abstract IDH-mutant adult-type diffuse gliomas show variable clinical outcomes influenced by patient age. Recent studies have linked HOX gene activity to age, survival, and tumor aggressiveness in both IDH-mutant astrocytoma (IDH-A) and oligodendroglioma (IDH-O), but the extent to which HOX activity defines shared biology across these entities remains unclear. To address this, we assembled a large DNA methylation dataset of IDH-O (N=1,445) and IDH-A (N=2,232), integrating published cohorts, TCGA, and an in-house NIH collection. Multi-omic analyses included DNA methylation (450K, EPIC, EPICv2), RNA-Seq, somatic copy number alterations (SCNA), mutation, pathology, and clinical features, enabling a comprehensive characterization of HOX-associated biology. Unsupervised clustering of HOX gene body methylation consistently identified two subgroups—HOX-High and HOX-Low—in both IDH-O and IDH-A across all platforms. HOX High tumors were associated with older age, higher tumor grade, increased Ki-67%, shorter survival, and higher SCNA and mutation burdens. Differential methylation analyses revealed that most probes distinguishing HOX High and HOX Low subgroups in IDH-O were also differentially methylated in IDH-A, with similar effect sizes, and vice versa. Notably, probes within the HOXD locus showed the greatest differences in both tumor types. RNA-Seq data revealed congruent differences in HOXD gene expression. Gene ontology analyses showed highly correlated enrichment scores between IDH-O and IDH-A, even after excluding HOX-related genes, suggesting broader shared biology. Importantly, HOX-associated subgroups were observed in both tumor types regardless of 1p/19q-codeletion status, indicating that this signature is independent of the canonical molecular subclassification. Our results support the existence of a pan-IDH-mutant glioma biological program, transcending traditional molecular subtypes. Identification of these HOX-associated subgroups provides new opportunities for biologically informed risk stratification and may inform the development of targeted therapies for IDH-mutant gliomas. Further prospective studies are warranted to explore the clinical utility of HOX-based biomarkers.