Single-cell RNA-seq of in vitro fusion-derived colorectal cancer-macrophage hybrid cells and parental controls

This study profiles tumor-macrophage hybrid cells in colorectal cancer using single-cell transcriptomic and epigenomic approaches. Fusion-derived hybrid cells were generated by co-culture of MC38-H2B-RFP colorectal cancer cells with beta-actin-GFP bone marrow-derived macrophages, and patient-derived hybrid cells were isolated from primary colorectal tumors and peripheral blood by fluorescence-activated cell sorting based on co-expression of epithelial (EpCAM and/or ECAD) and immune (CD45) markers. The study compares hybrid cells with parental tumor and immune controls and includes artificial macrophage-tumor doublets generated on the ICELL8 platform to distinguish bona fide hybrids from technical doublets. This submission contains two biological replicates of in vitro fusion-derived mouse hybrid cells and their parental controls profiled by 10x Genomics single-cell RNA-seq. MC38-H2B-RFP colorectal cancer cells were co-cultured with beta-actin-GFP bone marrow-derived macrophages. After 4 days, nascent GFP+/RFP+ hybrid cells (hybrid-M) were FACS-isolated. A second hybrid population (hybrid-T) consisted of expanded, purity-sorted GFP+/RFP+ hybrids after serial passaging. Parental MC38 tumor cells and parental macrophages were processed in parallel. Two independent hybrid fusion / sorting / 10x sequencing experiments were performed. Nuclei were isolated and libraries were prepared with the 10x Genomics Single Cell 3' Gene Expression kit and sequenced on an Illumina NextSeq 2000.