There is broad consensus that the malignant epithelial cells of human pancreatic ductal adenocarcinoma (PDA) comprise multiple, molecularly distinct states. Yet precise characterization of how these are regulated-including their mechanistic determinants, dependencies, plasticity and functional properties-remains elusive. Single-cell master regulator (MR) analysis of multiple PDA cohorts identified malignant cells in three co-existing, molecularly distinct developmental lineage states, with distinct histopathological morphologies and spatial architecture. These include a poorly differentiated lineage driven by epithelial-mesenchymal-transition-related MRs and two well-differentiated states driven by gastrointestinal epithelial development and pancreatic development MRs, respectively. Furthermore, each state comprises two epigenetically distinct substates with low versus high MAPK signaling activity. Barcode-based lineage tracing confirmed both spontaneous and treatment-dependent cross-state plasticity. Furthermore, loss-of-function studies confirmed state-specific MR essentiality, while their ectopic expression effectively reprogrammed cell state, in vitro and in vivo, thus providing a mechanism-based foundation for PDA heterogeneity and a roadmap for pharmacological targeting.
P. Laise, Mikko M. Turunen, Álvaro Curiel-García et al.· Nature Genetics· 0 citations
The state of a cell depends not only on protein abundance, but also on the biochemical and cellular activities of proteins, which are largely invisible to abundance profiling alone. Here, we introduce a multi-omics framework that infers context-specific protein activities from transcriptomic, phosphoproteomic, and protein correlation-based protein-protein interaction data, integrating modality-specific algorithms via network diffusion. Applying it to a panel of phenotypically diverse HeLa cell lines, whose genetic drift provides a natural perturbation system, we make three findings. First, physical separation of monomeric and assembled protein fractions by protein correlation profiling provides direct evidence that complex assembly buffers variation in gene copy number and transcription, a mechanism previously only inferred from bulk measurements. Second, using Let7 perturbation data, CRISPR gene dependency scores, and subcellular localization, we orthogonally validate that inferred protein activities capture functional regulation linked to cellular phenotypes inaccessible from abundance data alone. Third, differential analysis of context-specific activity profiles identifies molecular mechanisms underlying phenotypic divergence, including a WIPF1/WIPF2--Arp2/3 axis governing invadopodium formation and infection susceptibility, and an immunoproteasome switch linked to immune adaptation.
George A. Rosenberger, Peng Xue, Isabell Bludau et al.· Molecular Systems Biology· 0 citations