To analyze cell-cell communication differences in individuals with AUD, we used MultiNicheNet48. All samples used for differential expression testing (see “RNA pseudobulk samples creation”) were used for this analysis. User-set parameters were as follows:The minimum number of cells per cell type per sample was set to 10, the recommended default;Sex, ethnic origin, and age were used as covariates;For a DEG to be further considered when calculating ligand activity, we choose a minimum log2 fold change of 0.50, a maximum FDR of 0.2, and a minimum fraction of expression of 0.05;For the NicheNet ligand-target inference, the top 250 predicted target genes were considered;The weights of the prioritization of expression, differential expression, and NicheNet activity information were set to the recommended defaults (see https://github.com/saeyslab/multinichenetr);Sender cell types were defined as astrocytes, microglia, and oligodendrocytes;Receiver cell types were defined as astrocytes, microglia, and oligodendrocytes.
