MatriCom: a scRNA-Seq data mining tool to infer ECM-ECM and cell-ECM communication systems
Lamba, Rijuta; Paguntalan, Asia M; Petrov, Petar B; Naba, Alexandra; Izzi, Valerio (2025-06-12)
Company of Biologists
12.06.2025
Rijuta Lamba, Asia M. Paguntalan, Petar B. Petrov, Alexandra Naba, Valerio Izzi; MatriCom: a scRNA-Seq data mining tool to infer ECM-ECM and cell-ECM communication systems. J Cell Sci 2025; jcs.263927. doi: https://doi.org/10.1242/jcs.263927
https://creativecommons.org/licenses/by/4.0/
© 2025. Published by The Company of Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by /4.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
https://creativecommons.org/licenses/by/4.0/
© 2025. Published by The Company of Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by /4.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
https://creativecommons.org/licenses/by/4.0/
Julkaisun pysyvä osoite on
https://urn.fi/URN:NBN:fi:oulu-202506164493
https://urn.fi/URN:NBN:fi:oulu-202506164493
Tiivistelmä
Abstract
The 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 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 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.
The 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 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 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.
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