GraphComm: A Graph-based Deep Learning Method to Predict Cell-Cell Communication in single-cell RNAseq data

Abstract

AbstractCell-cell interactions coordinate various functions across cell-types in health and disease. Novel single-cell techniques allow us to investigate cellular crosstalk at single-cell resolution. Cell-cell communication (CCC) is mediated by underlying gene-gene networks, however most current methods are unable to account for complex inter-connections within the cell as well as incorporate the effect of pathway and protein complexes on interactions. This results in the inability to infer overarching signalling patterns within a dataset as well as limit the ability to successfully explore other data types such as spatial cell dimension. Therefore, to represent transcriptomic data as intricate networks connecting cells to ligands and receptors for relevant cell-cell communication inference as well as incorporating descriptive information independent of gene expression, we present GraphComm - a new graph-based deep learning method for predicting cell-cell communication in single-cell RNAseq datasets. GraphComm improves CCC inference by capturing detailed information such as cell location and intracellular signalling patterns from a database of more than 30,000 protein interaction pairs. With this framework, GraphComm is able to predict biologically relevant results in datasets previously validated for CCC,datasets that have undergone chemical or genetic perturbations and datasets with spatial cell information.