Long-read Spatial Transcriptomic Profiling of Patient-derived ccRCC Tumoroids Reveals Heterogeneity in Isoform and Gene Expression

Abstract

Clear cell renal cell carcinoma (ccRCC) is the most prevalent type of kidney cancer characterized by its diverse tumor composition featuring various subclonal populations that hinder effective treatment responses. Tumoroids present an avenue for modelling this diversity and replicating the intricate tumor heterogeneity. Spatial transcriptomics preserves the spatial context of gene expression enabling us to study distinct tumor areas and the influence on overall diversity. Our spatial transcriptomics analysis uncovered tumor clusters with distinct genetic profiles that showcase various functional areas in depth and offer valuable understandings into the diversity of ccRCC types. Some of these tumor clusters exhibited activity in genes responsible for protein catabolism and reduced abundance of genes related to mitochondrial respiration processes. We also show isoform expression within tumoroids, in particular glutaminase (GLS) especially with the prevalence of the highly metabolically active GAC isoform that is expressed in regions where mitochondrial gene abundance is lower; whereas the KGA isoform displayed a more focal expression pattern. Combining long-read spatial transcriptomics with organoid models presents a novel strategy for unravelling gene and transcript level complexity.