Human neural progenitors derived from pluripotent stem cells develop into electrophysiologically active neurons at heterogeneous rates, which can confound disease-relevant discoveries in neurology and psychiatry. By combining patch clamping, morphological and transcriptome analysis on single-human neurons in vitro, we defined a continuum of poor to highly functional electrophysiological states of differentiated neurons. The strong correlations between action potentials, synaptic activity, dendritic complexity and gene expression highlight the importance of methods for isolating functionally comparable neurons for in vitro investigations of brain disorders. Although whole-cell electrophysiology is the gold standard for functional evaluation, it often lacks the scalability required for disease modeling studies. Here, we demonstrate a multimodal machine-learning strategy to identify new molecular features that predict the physiological states of single neurons, independently of the time spent in vitro. As further proof of concept, we selected one of the potential neurophysiological biomarkers identified in this study—GDAP1L1—to isolate highly functional live human neurons in vitro.
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We are grateful to Elisabeth Santo and Sarah Marshall for help with the morphological reconstruction. We thank Gage lab members Bobbie Miller and Lynne Moore for preparation of viral vectors and Eunice Meija for immunohistochemistry. Thanks to Gage lab (Prattap Venepalli, Apua Paquola, Sara Linker, Son Pham) and Yeo lab (Olga Botvinnik) members for fruitful bioinformatics discussions on single-cell transcriptomics. We thank Mary Lynn Gage for edits on the manuscript. This study was supported by grants from Ipsen Pharma, Annette C. Merle-Smith, The Leona M. and Harry B. Helmsley Charitable Trust Grant #2012-PG-MED002, Bob and Mary Jane Engman, the JPB Foundation, G Harold and Leila Y. Mathers Foundation, and NIH Grants MH095741 (to F.H.G.); also by a Fay/Frank Seed Grant from the Brain Research Foundation and NIH Grants NS075449, HG004659, HG007005 (to G.W.Y.). G.W.Y. is an Alfred P Sloan Research Fellow. This work was also supported by NSF Graduate Research Fellowship (to B.K.), the George E. Hewitt Foundation for Medical Research (to J.E.) the EMBO Long-term fellowship, the Bettencourt Schueller Foundation and the Philippe Foundation (B.N.J.) and the FP7 Marie Curie International Outgoing Fellowship for Career Development (to C.B.).
CB designed and analyzed all experiments and wrote the manuscript with input from GWY and FHG. MVDH and JE prepared the single-cell cDNA libraries and performed the cDNA QC. CB and BK analyzed the single-cell transcriptome data. BNJ, JB, AP and CB performed the FACS experiments. CB, MG, RVH and CM performed the patch-clamping experiments. TE, AP and CB performed the tissue culture. MK and AKB reconstructed the neuronal morphology. RJ designed the viral vector constructs.
The authors declare no conflict of interest.
Supplementary Information accompanies the paper on the Molecular Psychiatry website
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Bardy, C., van den Hurk, M., Kakaradov, B. et al. Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology. Mol Psychiatry 21, 1573–1588 (2016). https://doi.org/10.1038/mp.2016.158
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