Journal Article

Cross-tissue gene expression interactions from bulk, single cell and spatial transcriptomics with crossWGCNA

Iannuzzi, Raffaele M., Savino, Aurora, Provero, Paolo, Lobascio, Andrea, Poli, Valeria, Iorio, Francesco, Avalle, Lidia

2025

Overview

Background Understanding the molecular interactions between cells, tissues or organs is key to understanding the functioning of a biological system as a whole. Results Here, we propose crossWGCNA : a co-expression-based method that identifies highly interacting genes unbiasedly and that we employ to study stroma-epithelium communication in breast cancer. CrossWGCNA can be applied to bulk, single cell and spatial transcriptomics data. We validate it both in silico and experimentally, and we provide a fully documented R package allowing users to employ it. Conclusions The wide applicability and agnostic nature of our tool make it complementary to existing methods overcoming the limitations arising from strong baseline assumptions. Graphical Abstract

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Biomedical and Life Sciences / Breast cancer / Breast Neoplasms - genetics / Breast Neoplasms - pathology / Cell–cell communication / Co-expression networks / Communication / Computational Biology - methods / Epithelium / Female / Gene expression / Gene Expression Profiling - methods / Humans / Laser capture microdissection / Life Sciences / Ligands / Methods / Microarrays / Microbial Genetics and Genomics / Molecular interactions / Plant Genetics and Genomics / Proteomics / Single-Cell Analysis - methods / Software / Spatial transcriptomics / Stroma / Transcriptome / Transcriptomics / Tumor microenvironment