Construction of MCDMs

We constructed the MCDMs using scRNA-seq data from colorectal cancer, mouse AIA (sick or healthy lymph nodes and joints), and human RA synovium. The MCDMs showed genome-wide mRNA expression of each cell type as well as potential types and directions of intercellular interactions. For MCDM construction, we started by identifying cell-type-specific genes, i.e., DEGs in one cell type compared with all others, using the methods described above. Using those gene lists, MCDMs were constructed. First, the Ingenuity Pathway Analysis (IPA) software was queried for prediction of the upstream regulators of cell-type-specific DEGs for each cell type separately. Here, we focused on upstream regulators that were secreted or membrane-bound. Next, we searched for predicted upstream regulators among the DEGs of other cell types. If such an upstream regulator was found, an interaction was assumed between the cell types.

To systematically validate the MCDM cellular interactions derived from Ingenuity, we used the novel CellPhoneDB [40] framework. CellPhoneDB is a publicly available curated repository of ligands, receptors, and their interactions, which integrates a statistical tool for the inference of cell-cell communication networks from human single-cell transcriptomic data. Specifically, cell-type interactions between ligands and receptors from mouse RA and healthy joint MCDMs, and mouse RA lymph node MCDM were analyzed with CellPhoneDB, using the default parameters (the ligands and receptors included should be expressed in at least 10% of the cells for each cluster, and the cluster labels of every cell were randomly permuted 1000 times). As CellPhoneDB is developed for human scRNA-seq data, mouse genes were mapped to human orthologs using the BioMart database [41]. In total, 6203 (82.2%) and 4808 (87.4%) mouse genes from RA and healthy joint, respectively, could be mapped to humans. An interaction between two cell types was considered significant if the CellPhoneDB analysis predicted any interaction between the cell types with a significance score of p < 0.05.