STAG2 mutations in the normal colon induce upregulation of oncogenic pathways in neighbouring wildtype cells

Introduction
There has been interest in the role of somatic driver mutations n phenotypically normal organs. One such driver mutation is STAG2, a component of the cohesin complex involved in mitosis. We sought to characterise the role of STAG2 mutants in the normal colon in relation to oncogenesis.
Methods
We performed this study using patient-derived human colonic organoids, in which the STAG2 mutation was introduced using CRISPR-Cas9 gene editing. We performed single-cell RNA sequencing (scRNAseq) to determine transcriptomic changes in co-cultured wildtype and STAG2 mutant organoids.
Results
Co-cultured cells on scRNAseq clustered into four clusters. Cluster 0 and 2 were predominantly comprised of cells from the STAG2 wildtype population. We observed that the "HALLMARK_TNFA_SIGNALING_VIA_NFKB" which had been upregulated in wildtype cells was also upregulated in both clusters with FDR < 25% and nominal p-value < 5%. In Cluster 0, other gene sets which were upregulated included "HALLMARK_ANGIOGENESIS" and "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION". In Cluster 2, other gene sets which were upregulated included "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION", "HALLMARK_KRAS_SIGNALING_UP", and "HALLMARK_P53_PATHWAY". Notably, Cluster 3, which predominantly comprised of cells which were STAG2 mutant, none of the Hallmark gene sets were observed to have been upregulated or downregulated at FDR < 25%.
Conclusion
These observations confirm that oncogenic pathways are upregulated in co-cultured wildtype cells while oncogenic pathways in STAG2 mutant cells themselves remain relatively quiescent, suggesting a novel cell-cell interactive modality of oncogenesis hitherto undescribed.