| Summary: | Summary: Human pluripotent stem cells are a valuable resource for transplantation, yet our ability to profile xenografts is largely limited to low-throughput immunohistochemical analysis by difficulties in readily isolating grafts for transcriptomic and/or proteomic profiling. Here, we present a simple methodology utilizing differences in the RNA sequence between species to discriminate xenograft from host gene expression (using qPCR or RNA sequencing [RNA-seq]). To demonstrate the approach, we assessed grafts of undifferentiated human stem cells and neural progenitors in the rodent brain. Xenograft-specific qPCR provided sensitive detection of proliferative cells, and identified germ layer markers and appropriate neural maturation genes across the graft types. Xenograft-specific RNA-seq enabled profiling of the complete transcriptome and an unbiased characterization of graft composition. Such xenograft-specific profiling will be crucial for pre-clinical characterization of grafts and batch-testing of therapeutic cell preparations to ensure safety and functional predictability prior to translation. : In this article, Bye and colleagues establish a simple and robust method to transcriptionally profile xenogeneic transplants. Exploiting species differences in the RNA sequence between human stem cell grafts and the rodent host, xenograft-specific qPCR or xenograft-specific RNA-seq provided a sensitive approach for characterization and exploration of transplanted cell populations that will be critical for ensuring safety and functionality. Keywords: transcriptomics, RNA-seq, xenograft, stem cells, transplantation, xenome, midbrain dopamine, species-specific, qPCR
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