MatriCom, a single-cell RNA-sequencing data mining tool to infer cell-extracellular matrix interactions.

Abstract

The extracellular matrix (ECM) is a complex meshwork of proteins forming the framework of all multicellular organisms. Protein interactions are critical to building and remodeling the ECM meshwork, while interactions between ECM proteins and their receptors are essential to initiate signal transduction. Here, we present MatriCom, a web application (https://matrinet.shinyapps.io/matricom) and a companion R package, devised to infer communications between ECM components and between different cell populations and the ECM from single-cell RNA-sequencing (scRNA-Seq) datasets. MatriCom relies on a unique database, MatriComDB, of over 25,000 curated interactions involving matrisome components to impute interactions from expression data. MatriCom offers the option to query user-generated or open-access datasets sourced from large sequencing efforts. MatriCom also accounts for specific rules governing ECM protein interactions. We illustrate how MatriCom can generate novel biological insights by building the first human kidney matrisome communication network. Last, applied to a panel of 46 scRNA-Seq datasets of healthy adult tissues, we demonstrate how MatriCom can shed light on the mechanisms of conservation and diversification of ECM assemblies and cell-ECM interactions.