Identification of phenotype-specific networks from paired gene expression–cell shape imaging data

Abstract

The morphology of breast cancer cells is often used as an indicator of tumor severity and prognosis. Additionally, morphology can be used to identify more fine-grained, molecular developments within a cancer cell, such as transcriptomic changes and signalling pathway activity. Delineating the interface between morphology and signalling is important to understand the mechanical cues that a cell processes in order to undergo epithelial-to-mesenchymal transition and consequently metastasize. However, the exact regulatory systems that define these changes remain poorly characterized. In this study, we employ a network-systems approach to integrate imaging data and RNA-seq expression data. Our workflow allows the discovery of unbiased and context-specific gene expression signatures and cell signalling sub-networks relevant to the regulation of cell shape, rather than focusing on the identification of previously known, but not always representative, pathways. By constructing a cell-shape signalling network from shape-correlated gene expression modules and their upstream regulators, we found central roles for developmental pathways such as WNT and Notch as well as evidence for the fine control of NF-kB signalling by numerous kinase and transcriptional regulators. Further analysis of our network implicates a gene expression module enriched in the RAP1 signalling pathway as a mediator between the sensing of mechanical stimuli and regulation of NF-kB activity, with specific relevance to cell shape in breast cancer.

Inter-gastruloid heterogeneity revealed by single cell transcriptomics time course: implications for organoid based perturbation studies

“…To investigate the origins of the intergastruloid heterogeneity, we used Weighted Gene Co-Expression Network Analysis (WGCNA) to find biological properties significantly associated with our phenotype of interesty (Barker et al, 2022;Langfelder and Horvath, 2008). For this we first ran single cell WGCNA (Feregrino and Tschopp, 2021) on only the day 3 MULTI-seq cells.…”

Morphoregulatory ADD3 underlies glioblastoma growth and formation of tumor-tumor connections

“…Taken together, GBM cell morphology mediates intercellular communication and thus has important consequences on tumor cell proliferation, survival, invasiveness and resistance to therapy. Hence, in GBM, like in other cancers (Alizadeh et al, 2020; Barker et al, 2022; Wu et al, 2020), cell morphology has a strong potential to be used as a diagnostic and prognostic marker, through microscopy-based analysis of the tumor.…”

Low HER2 expression in normal breast epithelium enables dedifferentiation and malignant transformation via chromatin opening

“…The morphological changes in breast cancer models are often used to indicate the high transformational characteristics of those cells ( Barker et al, 2022 ). We found that proteins associated with aggressive basal-like phenotype were found to be increased in our phosphoproteomic screen, which included ADGRA2 (S1079) and DENND4C (S1250).…”