scPheNOME · single-cell Phenomics for Navigating Oncogene-induced Morphological and Expression heterogeneity

Sustained proliferation is a hallmark of cancer cells, frequently driven by alterations in proto-oncogenes (e.g., HRAS or MYC). While oncogene activation increases the cellular proliferation rate, it also triggers cellular stress responses. This dynamic creates a delicate equilibrium between continued cell growth and cell cycle arrest, making oncogene activation a powerful model for studying divergent cell fate decisions at the single-cell level. Despite extensive studies, the phenotypic traits that drive this equilibrium toward proliferation or arrest remain poorly understood. In this project, I propose to study the phenotypic heterogeneity of oncogene activation using ‘IRIS’ (Bues et al., in preparation), a novel single-cell phenomics approach developed by my host lab. IRIS enables the simultaneous acquisition of high-resolution images and transcriptomic profiles from individual cells at a high throughput (>1,000 cells/h). Using this technology, I aim to test our hypothesis that the dosage of c-Myc oncoprotein and the heterogeneity of HRASV12 subcellular localization modulate cell fate decisions through differential activation of biosynthetic and stress-response pathways. Specifically, I will (1) identify phenotypic determinants modulating oncogene-induced heterogeneity, (2) develop a screening platform to map morphological-to-transcriptomic changes associated with oncogene activation, and (3) functionally characterize the phenotypic traits associated with oncogene-indicated heterogeneity. By linking image-based traits to functional cell states through transcriptome analysis, I aim to uncover molecular determinants of cell fate in response to oncogenic stress. This work will provide fundamental insight into heterogeneity of early stages of cancer, and also reveal phenotypes with long-term translational potential for cancer diagnostics.