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.

人类多能干细胞是用于移植的宝贵资源，但是由于难以轻易分离出用于转录和/或蛋白质组分析的移植物，因此我们对异种移植物进行分析的能力在很大程度上限于低通量免疫组织化学分析。在这里，我们提出了一种简单的方法，利用物种之间的RNA序列差异来区分异种移植物与宿主基因表达（使用qPCR或RNA测序[RNA-seq]）。为了证明这一方法，我们评估了啮齿动物大脑中未分化的人类干细胞和神经祖细胞的移植物。异种移植物特异性qPCR提供了对增殖细胞的灵敏检测，并鉴定了整个移植物类型的胚层标记和适当的神经成熟基因。异种移植物特异的RNA-seq能够分析完整的转录组，并能对移植物成分进行无偏性表征。对于移植物的临床前表征和治疗细胞制剂的批量测试，以确保翻译前的安全性和功能可预测性，此类异种移植物特异性谱分析至关重要。