Cell type-specific interaction analysis using doublets in scRNA-seq

SUMMARY: Doublets are usually considered an unwanted artifact of single-cell RNA-sequencing (scRNA-seq) and are only identified in datasets for the sake of removal. However, if cells have a juxtacrine interaction with one another in situ and maintain this association through an scRNA-seq processing pipeline that only partially dissociates the tissue, these doublets can provide meaningful biological information regarding the intercellular signals and processes occurring in the analyzed tissue. This is especially true for cases such as the immune compartment of the tumor microenvironment, where the frequency and the type of immune cell juxtacrine interactions can be a prognostic indicator. We developed Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA) as a pipeline for identifying and analyzing biologically meaningful doublets in scRNA-seq data. CIcADA identifies putative doublets using multi-label cell type scores and characterizes interaction dynamics through a comparison against synthetic doublets of the same cell type composition. In performing CIcADA on several scRNA-seq tumor datasets, we found that the identified doublets were consistently upregulating expression of immune response genes. AVAILABILITY AND IMPLEMENTATION: An R package implementing the CIcADA method is in development and will be released on CRAN, but for now it is available at https://github.com/schiebout/CAMML.