Identifying markers predicting successful graft outcome for clinical translation of hESC-based cell therapy for Parkinson’s disease. Homo sapiens

Stem cell treatments for neurodegenerative diseases are expected to reach clinical trials soon. Most of the approaches currently under development involve transplantation of immature progenitors that subsequently undergo phenotypic and functional maturation in vivo, and predicting the long term graft outcome already at the progenitor stage remains a challenge. Here, we took an unbiased approach to identify predictive markers expressed in dopamine neuron progenitors that correlate with graft outcome in an animal model of Parkinson's disease through gene expression analysis of >30 batches of grafted hESC-derived progenitors. We found that many of the commonly-used markers did not accurately predict in vivo subtype-specific maturation. Instead, we identified a specific set of markers associated with the caudal midbrain that correlate with high dopaminergic yield after transplantation in vivo. Using these markers, we developed a GMP differentiation protocol for highly efficient and reproducible production of transplantable dopamine progenitors from hESCs. Overall design: H9 hESCs were differentiated in different batches towards ventral midbrain (VM) progenitors, and were grafted to the rat brain. Based on graft outcome, the batches were divided into two groups: DA-high and DA-low. The batch names listed here correspond to the batch names listed in Kirkeby et al (2016), Table S1. Sequencing libraries were prepared from isolated RNA from each of the batches of differentiated hESCs using the Smart-Seq2 protocol (Picelli et al. Nature Methods 2013)