iScience · 2024 · 10 citations · 48 references
MedicineCancer BiologyOncologyCell SignalingMolecular OncologyTumor MicroenvironmentCancer Cell SignalingCancer ProgressionSignal Transduction In CancerTumor Microenvironment InteractionsTumor-associated MacrophagesTumor-stroma InteractionsCancer-associated Fibroblast InteractionsCancer-associated Fibroblast SignalingCrosstalkStromal CrosstalkTumor CrosstalkTumor Microenvironment RegulationTumor-associated Fibroblast CrosstalkTumor-immune Crosstalk
Interactions between cells in the tumor microenvironment (TME) shape cancer progression and patient prognosis. To gain insights into how the TME influences cancer outcomes, we derive gene expression signatures indicative of signaling between stromal fibroblasts and cancer cells, and demonstrate their prognostic significance in multiple and independent squamous cell carcinoma cohorts. By leveraging information within the signatures, we discover that the HB-EGF/EGFR/MAPK axis represents a hub of tumor-stroma crosstalk, promoting the expression of CSF2 and LIF and favoring the recruitment of macrophages. Together, these analyses demonstrate the utility of our approach for interrogating the extent and consequences of TME crosstalk.
48
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin, Carrie Davis, Felix Schlesinger et al. · Bioinformatics · 2012 · 56.2K citations · Full text