Epco-39. clarifying the molecular consequences of oncogenic mutations through multiscale and multiomic analysis of individual tumors

Understanding the molecular consequences of oncogenic mutations is an important goal that may reveal essential features of malignant cells and new therapeutic targets for diverse cancers. However, this task is complicated by substantial inter- and intra-tumoral heterogeneity, which obscure the molecular consequences of oncogenic mutations in malignant cells. Although single-cell methods hold promise for this task, it remains non-trivial to isolate DNA and RNA from the same cell at scale. Here we describe a statistically motivated strategy that controls for inter-tumoral heterogeneity and exploits intra-tumoral heterogeneity to reveal the most consistent molecular phenotypes of malignant cells. By combining deep, multiscale sampling of IDH-mutant astrocytomas with integrative, multiomic analysis, we reconstruct and validate the phylogenies, spatial distributions, and molecular profiles of distinct malignant clones. Importantly, by genotyping nuclei for driver mutations, we show that existing strategies for inferring malignancy from gene expression profiles of single cells may be inaccurate. We identify genes that are consistently upregulated in the truncal clone of IDH-mutant astrocytomas, which are significantly enriched with genes involved in RNA splicing, mRNA transport and the nuclear pore, and WNT / MYC signaling. Furthermore, we find that expression phenotypes of malignancy persist despite loss of the mutant IDH1 protein following chr2q deletion in a subset of malignant cells. More broadly, our work provides a generalizable strategy for precisely deconstructing intra-tumoral heterogeneity and determining the most robust molecular consequences of oncogenic mutations in any kind of solid tumor.