Mapping cell-cell fusion at single-cell resolution

Cell-cell fusion is a tightly controlled process in the human body known to be involved in fertilization, placental development, muscle growth, bone remodeling, and viral response. Fusion between cancer cells results first in a whole-genome doubled state, which may be followed by the generation of aneuploidies; these genomic alterations are known drivers of tumor evolution. The role of cell-cell fusion in cancer progression and treatment response has been understudied due to limited experimental systems for tracking and analyzing individual fusion events. To meet this need, we developed a molecular toolkit to map the origins and outcomes of individual cell fusion events within a tumor cell population. This platform, ClonMapper Duo ('CMDuo'), identifies cells that have undergone cell-cell fusion through a combination of reporter expression and engineered fluorescence-associated index sequences paired to random barcode sets. scRNA-seq of the indexed barcodes enables the mapping of each set of parental cells and fusion progeny throughout the cell population. In triple negative breast cancer cells CMDuo uncovered subclonal transcriptomic hybridization and unveiled distinct cell-states which arise in direct consequence of homotypic cell-cell fusion. CMDuo is a platform that enables mapping of cell-cell fusion events in high-throughput single cell data and enables the study of cell fusion in disease progression and therapeutic response. Overall design: scRNA-seq and targeted barcode sequencing for a longitudinal study on cell-cell fusion in HCC1806 and MDA-MB-231 cells. For each cell line, there is 1 'initial' population replicate, 4 replicates before flourescence-activated cell sorting to enrich for fusion or control cells ('pre-sort'), 4 replicates for the final enriched fusion populations ('fusion-enriched'), and 4 replicates for final parallel sorted controls ('ctrl').