Abstract
Neural stem and progenitor cells produce one of the most remarkable organs in nature, the human brain. Among neural stem cell progeny, post-mitotic neurons are likewise remarkably diverse. Single-cell transcriptomic approaches are now cataloging a long-sought-after molecular taxonomy of neuronal diversity in the brain. Contemporary single-cell omic classifications of neuronal diversity build from electrophysiological approaches that for decades have measured and cataloged diverse biophysical properties of single neurons. With the widespread application of human pluripotent stem cell-based models of neurogenesis to investigate disease pathology and to develop new drugs, a high-resolution understanding of neuronal diversity in vivo is essential to benchmark the state of in vitro models of human neurological disease.
Similar content being viewed by others
References
Avaliani N, Sorensen AT, Ledri M, Bengzon J, Koch P, Brustle O, … Kokaia M (2014) Optogenetics reveal delayed afferent synaptogenesis on grafted human-induced pluripotent stem cell-derived neural progenitors. Stem Cells 32(12):3088–3098. doi:https://doi.org/10.1002/stem.1823
Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F., … Faulkner GJ (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature, 479(7374):534–537. doi:https://doi.org/10.1038/nature10531
Bandura DR, Baranov VI, Ornatsky OI, Antonov A, Kinach R, Lou X, … Tanner SD (2009) Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem 81(16):6813–6822. doi:https://doi.org/10.1021/ac901049w
Bardy C, van den Hurk M, Eames T, Marchand C, Hernandez RV, Kellogg M, … Gage FH (2015) Neuronal medium that supports basic synaptic functions and activity of human neurons in vitro. Proc Natl Acad Sci USA 112(20):E2725–2734. doi:https://doi.org/10.1073/pnas.1504393112
Bardy C, van den Hurk M, Kakaradov B, Erwin JA, Jaeger BN, Hernandez RV, … Gage FH (2016) Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology. Mol Psychiatry 21(11):1573–1588. doi:https://doi.org/10.1038/mp.2016.158
Belinsky GS, Rich MT, Sirois CL, Short SM, Pedrosa E, Lachman HM, Antic SD (2014) Patch-clamp recordings and calcium imaging followed by single-cell PCR reveal the developmental profile of 13 genes in iPSC-derived human neurons. Stem Cell Res 12(1):101–118. https://doi.org/10.1016/j.scr.2013.09.014
Bendall SC, Davis KL, Amir el-AD., Tadmor MD, Simonds EF, Chen TJ., … Pe'er D (2014) Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell 157(3):714–725. doi:https://doi.org/10.1016/j.cell.2014.04.005
Bock C, Farlik M, Sheffield NC (2016) Multi-Omics of single cells: strategies and applications. Trends Biotechnol 34(8):605–608. https://doi.org/10.1016/j.tibtech.2016.04.004
Brennand K, Savas JN., Kim, Y., Tran, N., Simone, A., Hashimoto-Torii, K., … Gage, F. H. (2015a) Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. Mol Psychiatry 20(3):361–368. doi:https://doi.org/10.1038/mp.2014.22
Brennand, K. J., Marchetto, M. C., Benvenisty, N., Brustle, O., Ebert, A., Izpisua Belmonte, J. C., … Jaenisch, R. (2015b) Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders. Stem Cell Reports 5(6):933–945. doi:https://doi.org/10.1016/j.stemcr.2015.10.011
Brennand, K. J., Simone, A., Jou, J., Gelboin-Burkhart, C., Tran, N., Sangar, S., … Gage, F. H. (2011) Modelling schizophrenia using human induced pluripotent stem cells. Nature 473(7346):221–225. doi:https://doi.org/10.1038/nature09915
Budnik BLE, Slavov N (2017) Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation. bioRxiv. https://doi.org/10.1101/102681
Cadwell, C. R., Palasantza, A., Jiang, X., Berens, P., Deng, Q., Yilmaz, M., … Tolias, A. S. (2016) Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq. Nat Biotechnol 34(2):199–203. doi:https://doi.org/10.1038/nbt.3445
Cai X, Evrony GD, Lehmann HS, Elhosary PC, Mehta BK, Poduri A, Walsh CA (2014) Single-cell, genome-wide sequencing identifies clonal somatic copy-number variation in the human brain. Cell Rep 8(5):1280–1289. https://doi.org/10.1016/j.celrep.2014.07.043
Cajal S (1890) Textura de las circunvoluticiones cerebrales de los mamiferos inferiores. Gaceta Medica Catalana:22–31
Cajal, S. (1891) Sur la structure de l'ecorce cerebrale de quelques mammiferes. La Cellule, 125–176
Connors BW, Gutnick MJ (1990) Intrinsic firing patterns of diverse neocortical neurons. Trends Neurosci 13(3):99–104
Contreras D (2004) Electrophysiological classes of neocortical neurons. Neural Netw 17(5–6):633–646. https://doi.org/10.1016/j.neunet.2004.04.003
Coufal, N. G., Garcia-Perez, J. L., Peng, G. E., Yeo, G. W., Mu, Y., Lovci, M. T., … Gage, F. H. (2009) L1 retrotransposition in human neural progenitor cells. Nature 460(7259):1127–1131. doi:https://doi.org/10.1038/nature08248
Dulken BW, Leeman DS, Boutet SC, Hebestreit K, Brunet A (2017) Single-cell Transcriptomic analysis defines heterogeneity and transcriptional dynamics in the adult neural stem cell lineage. Cell Rep 18(3):777–790. https://doi.org/10.1016/j.celrep.2016.12.060
Eberwine J, Kim J (2015) Cellular deconstruction: finding meaning in individual cell variation. Trends Cell Biol 25(10):569–578. https://doi.org/10.1016/j.tcb.2015.07.004
Erwin, J. A., Paquola, A. C., Singer, T., Gallina, I., Novotny, M., Quayle, C., … Gage, F. H. (2016) L1-associated genomic regions are deleted in somatic cells of the healthy human brain. Nat Neurosci 19(12):1583–1591. doi:https://doi.org/10.1038/nn.4388
Espuny-Camacho, I., Michelsen, K. A., Gall, D., Linaro, D., Hasche, A., Bonnefont, J., … Vanderhaeghen, P. (2013) Pyramidal neurons derived from human pluripotent stem cells integrate efficiently into mouse brain circuits in vivo. Neuron 77(3):440–456. doi:https://doi.org/10.1016/j.neuron.2012.12.011
Evrony, G. D., Cai, X., Lee, E., Hills, L. B., Elhosary, P. C., Lehmann, H. S., … Walsh, C. A. (2012) Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151(3):483–496. doi:https://doi.org/10.1016/j.cell.2012.09.035
Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schonegger A, Klughammer J, Bock C (2015) Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep 10(8):1386–1397. https://doi.org/10.1016/j.celrep.2015.02.001
Foldy C, Darmanis S, Aoto J, Malenka RC, Quake SR, Sudhof TC (2016) Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons. Proc Natl Acad Sci U S A 113(35):E5222–E5231. https://doi.org/10.1073/pnas.1610155113
Fuzik, J., Zeisel, A., Mate, Z., Calvigioni, D., Yanagawa, Y., Szabo, G., … Harkany, T. (2016) Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes. Nat Biotechnol 34(2):175–183. doi:https://doi.org/10.1038/nbt.3443
Gobel W, Kampa BM, Helmchen F (2007) Imaging cellular network dynamics in three dimensions using fast 3D laser scanning. Nat Methods 4(1):73–79. https://doi.org/10.1038/nmeth989
Golgi C (1886) Sulla Fina Anatomia degli Organi Centrali del Sistema Nervosa. U. Hoepli, Milano
Gravina S, Dong X, Yu B, Vijg J (2016) Single-cell genome-wide bisulfite sequencing uncovers extensive heterogeneity in the mouse liver methylome. Genome Biol 17(1):150. https://doi.org/10.1186/s13059-016-1011-3
Grindberg, R. V., Yee-Greenbaum, J. L., McConnell, M. J., Novotny, M., O'Shaughnessy, A. L., Lambert, G. M., … Lasken, R. S. (2013) RNA-sequencing from single nuclei. Proc Natl Acad Sci U S A 110(49):19802–19807. doi:https://doi.org/10.1073/pnas.1319700110
Handel, A. E., Chintawar, S., Lalic, T., Whiteley, E., Vowles, J., Giustacchini, A., … Cader, M. Z. (2016) Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics. Hum Mol Genet 25(5):989–1000. doi:https://doi.org/10.1093/hmg/ddv637
Hazen, J. L., Faust, G. G., Rodriguez, A. R., Ferguson, W. C., Shumilina, S., Clark, R. A., … Baldwin, K. K. (2016) The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning. Neuron 89(6):1223–1236. doi:https://doi.org/10.1016/j.neuron.2016.02.004
Johnson MB, Wang PP, Atabay KD, Murphy EA, Doan RN, Hecht JL, Walsh CA (2015) Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex. Nat Neurosci 18(5):637–646. https://doi.org/10.1038/nn.3980
Kemp, P. J., Rushton, D. J., Yarova, P. L., Schnell, C., Geater, C., Hancock, J. M., … Telezhkin, V. (2016) Improving and accelerating the differentiation and functional maturation of human stem cell-derived neurons: role of extracellular calcium and GABA. J Physiol 594(22):6583–6594. doi:https://doi.org/10.1113/JP270655
Knouse KA, Wu J, Amon A (2016) Assessment of megabase-scale somatic copy number variation using single-cell sequencing. Genome Res 26(3):376–384. https://doi.org/10.1101/gr.198937.115
Kuijlaars, J., Oyelami, T., Diels, A., Rohrbacher, J., Versweyveld, S., Meneghello, G., … Verheyen, A. (2016) Sustained synchronized neuronal network activity in a human astrocyte co-culture system. Sci Rep 6:36529. doi:https://doi.org/10.1038/srep36529
Kuwabara, T., Hsieh, J., Muotri, A., Yeo, G., Warashina, M., Lie, D. C., … Gage, F. H. (2009) Wnt-mediated activation of NeuroD1 and retro-elements during adult neurogenesis. Nat Neurosci 12(9):1097–1105. doi:https://doi.org/10.1038/nn.2360
Lacar, B., Linker, S. B., Jaeger, B. N., Krishnaswami, S., Barron, J., Kelder, M., … Gage, F. H. (2016) Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Nat Commun 7:11022. doi:https://doi.org/10.1038/ncomms11022
Lake, B. B., Ai, R., Kaeser, G. E., Salathia, N. S., Yung, Y. C., Liu, R., … Zhang, K. (2016) Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science 352(6293):1586–1590. doi:https://doi.org/10.1126/science.aaf1204
Lam RS, Topfer FM, Wood PG, Busskamp V, Bamberg E (2017) Functional maturation of human stem cell-derived neurons in long-term cultures. PLoS One 12(1):e0169506. https://doi.org/10.1371/journal.pone.0169506
Lancaster, M. A., Renner, M., Martin, C. A., Wenzel, D., Bicknell, L. S., Hurles, M. E., … Knoblich, J. A. (2013) Cerebral organoids model human brain development and microcephaly. Nature 501(7467):373–379. doi:https://doi.org/10.1038/nature12517
Linnarsson S (2013) Single-cell biology meeting marks rebirth of an old science. Genome Biol 14(4):305. https://doi.org/10.1186/gb-2013-14-4-305
Liu, S. J., Nowakowski, T. J., Pollen, A. A., Lui, J. H., Horlbeck, M. A., Attenello, F. J., … Lim, D. A. (2016) Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol 17:67. doi:https://doi.org/10.1186/s13059-016-0932-1
Liu, Y., Lopez-Santiago, L. F., Yuan, Y., Jones, J. M., Zhang, H., O'Malley, H. A., … Parent, J. M. (2013) Dravet syndrome patient-derived neurons suggest a novel epilepsy mechanism. Ann Neurol 74(1):128–139. doi:https://doi.org/10.1002/ana.23897
Livesey MR, Magnani D, Hardingham GE, Chandran S, Wyllie DJ (2016) Functional properties of in vitro excitatory cortical neurons derived from human pluripotent stem cells. J Physiol 594(22):6573–6582. https://doi.org/10.1113/JP270660
Lodato, M. A., Woodworth, M. B., Lee, S., Evrony, G. D., Mehta, B. K., Karger, A., … Walsh, C. A. (2015) Somatic mutation in single human neurons tracks developmental and transcriptional history. Science 350(6256):94–98. doi:https://doi.org/10.1126/science.aab1785
Lodato S, Arlotta P (2015) Generating neuronal diversity in the mammalian cerebral cortex. Annu Rev Cell Dev Biol 31:699–720. https://doi.org/10.1146/annurev-cellbio-100814-125353
Lui JH, Hansen DV, Kriegstein AR (2011) Development and evolution of the human neocortex. Cell 146(1):18–36. https://doi.org/10.1016/j.cell.2011.06.030
Lynch M (2010) Rate, molecular spectrum, and consequences of human mutation. Proc Natl Acad Sci U S A 107(3):961–968. https://doi.org/10.1073/pnas.0912629107
Macaulay IC, Ponting CP, Voet T (2017) Single-cell Multiomics: multiple measurements from single cells. Trends Genet 33(2):155–168. https://doi.org/10.1016/j.tig.2016.12.003
Macaulay IC, Voet T (2014) Single cell genomics: advances and future perspectives. PLoS Genet 10(1):e1004126. https://doi.org/10.1371/journal.pgen.1004126
Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., … McCarroll, S. A. (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 161(5):1202–1214. doi:https://doi.org/10.1016/j.cell.2015.05.002
Mainen ZF, Sejnowski TJ (1996) Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382(6589):363–366. https://doi.org/10.1038/382363a0
Manganas, L. N., Zhang, X., Li, Y., Hazel, R. D., Smith, S. D., Wagshul, M. E., … Maletic-Savatic, M. (2007) Magnetic resonance spectroscopy identifies neural progenitor cells in the live human brain. Science 318(5852):980–985. doi:https://doi.org/10.1126/science.1147851
Mariani, J., Simonini, M. V., Palejev, D., Tomasini, L., Coppola, G., Szekely, A. M., … Vaccarino, F. M. (2012) Modeling human cortical development in vitro using induced pluripotent stem cells. Proc Natl Acad Sci U S A 109(31):12770–12775. doi:https://doi.org/10.1073/pnas.1202944109
Masland RH (2004) Neuronal cell types. Curr Biol 14(13):R497–R500. https://doi.org/10.1016/j.cub.2004.06.035
Mason A, Larkman A (1990) Correlations between morphology and electrophysiology of pyramidal neurons in slices of rat visual cortex. II. Electrophysiology. J Neurosci 10(5):1415–1428
McConnell, M. J., Lindberg, M. R., Brennand, K. J., Piper, J. C., Voet, T., Cowing-Zitron, C., … Gage, F. H. (2013) Mosaic copy number variation in human neurons. Science 342(6158):632–637. doi:https://doi.org/10.1126/science.1243472
McConnell, M. J., Moran, J. V., Abyzov, A., Akbarian, S., Bae, T., Cortes-Ciriano, I., … Brain Somatic Mosaicism, N. (2017). Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science 356(6336). doi:https://doi.org/10.1126/science.aal1641
Migliore M, Shepherd GM (2005) Opinion: an integrated approach to classifying neuronal phenotypes. Nat Rev Neurosci 6(10):810–818. https://doi.org/10.1038/nrn1769
Mizrahi A (2007) Dendritic development and plasticity of adult-born neurons in the mouse olfactory bulb. Nat Neurosci 10(4):444–452. https://doi.org/10.1038/nn1875
Moore AR, Filipovic R, Mo Z, Rasband MN, Zecevic N, Antic SD (2009) Electrical excitability of early neurons in the human cerebral cortex during the second trimester of gestation. Cereb Cortex 19(8):1795–1805. https://doi.org/10.1093/cercor/bhn206
Mountcastle VB, Talbot WH, Sakata H, Hyvarinen J (1969) Cortical neuronal mechanisms in flutter-vibration studied in unanesthetized monkeys. Neuronal periodicity and frequency discrimination. J Neurophysiol 32(3):452–484
Muller, F. J., Schuldt, B. M., Williams, R., Mason, D., Altun, G., Papapetrou, E. P., … Loring, J. F. (2011) A bioinformatic assay for pluripotency in human cells. Nat Methods 8(4):315–317. doi:https://doi.org/10.1038/nmeth.1580
Namba, T., & Huttner, W. B. (2017) Neural progenitor cells and their role in the development and evolutionary expansion of the neocortex. Wiley Interdiscip Rev Dev Biol 6(1). doi:https://doi.org/10.1002/wdev.256
Neher E, Sakmann B (1976) Single-channel currents recorded from membrane of denervated frog muscle fibres. Nature 260(5554):799–802
Pasca, A. M., Sloan, S. A., Clarke, L. E., Tian, Y., Makinson, C. D., Huber, N., … Pasca, S. P. (2015) Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat Methods 12(7):671–678. doi:https://doi.org/10.1038/nmeth.3415
Pruszak J, Sonntag KC, Aung MH, Sanchez-Pernaute R, Isacson O (2007) Markers and methods for cell sorting of human embryonic stem cell-derived neural cell populations. Stem Cells 25(9):2257–2268. https://doi.org/10.1634/stemcells.2006-0744
Randall AD (2016) Are stem cell-derived neural cells physiologically credible? J Physiol 594(22):6569–6572. https://doi.org/10.1113/JP273348
Rushton DJ, Mattis VB, Svendsen CN, Allen ND, Kemp PJ (2013) Stimulation of GABA-induced Ca2+ influx enhances maturation of human induced pluripotent stem cell-derived neurons. PLoS ONE 8(11):e81031. https://doi.org/10.1371/journal.pone.0081031
Schroeder T (2011) Long-term single-cell imaging of mammalian stem cells. Nat Methods 8(4 Suppl):S30–S35. https://doi.org/10.1038/nmeth.1577
Song M, Mohamad O, Chen D, Yu SP (2013) Coordinated development of voltage-gated Na+ and K+ currents regulates functional maturation of forebrain neurons derived from human induced pluripotent stem cells. Stem Cells Dev 22(10):1551–1563. https://doi.org/10.1089/scd.2012.0556
Steriade M (2004) Neocortical cell classes are flexible entities. Nat Rev Neurosci 5(2):121–134. https://doi.org/10.1038/nrn1325
Tang X, Zhou L, Wagner AM, Marchetto MC, Muotri AR, Gage FH, Chen G (2013) Astroglial cells regulate the developmental timeline of human neurons differentiated from induced pluripotent stem cells. Stem Cell Res 11(2):743–757. https://doi.org/10.1016/j.scr.2013.05.002
Tasic, B., Menon, V., Nguyen, T. N., Kim, T. K., Jarsky, T., Yao, Z., … Zeng, H. (2016) Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nat Neurosci 19(2):335–346. doi:https://doi.org/10.1038/nn.4216
Tsankov, A. M., Akopian, V., Pop, R., Chetty, S., Gifford, C. A., Daheron, L., … Meissner, A. (2015) A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells. Nat Biotechnol 33(11):1182–1192. doi:https://doi.org/10.1038/nbt.3387
Tyler WA, Medalla M, Guillamon-Vivancos T, Luebke JI, Haydar TF (2015) Neural precursor lineages specify distinct neocortical pyramidal neuron types. J Neurosci 35(15):6142–6152. https://doi.org/10.1523/JNEUROSCI.0335-15.2015
Upton, K. R., Gerhardt, D. J., Jesuadian, J. S., Richardson, S. R., Sanchez-Luque, F. J., Bodea, G. O., … Faulkner, G. J. (2015) Ubiquitous L1 mosaicism in hippocampal neurons. Cell 161(2):228–239. doi:https://doi.org/10.1016/j.cell.2015.03.026
Yokota Y, Gashghaei HT, Han C, Watson H, Campbell KJ, Anton ES (2007) Radial glial dependent and independent dynamics of interneuronal migration in the developing cerebral cortex. PLoS ONE 2(8):e794. https://doi.org/10.1371/journal.pone.0000794
Yu YC, Bultje RS, Wang X, Shi SH (2009) Specific synapses develop preferentially among sister excitatory neurons in the neocortex. Nature 458(7237):501–504. https://doi.org/10.1038/nature07722
Zeisel, A., Munoz-Manchado, A. B., Codeluppi, S., Lonnerberg, P., La Manno, G., Jureus, A., … Linnarsson, S. (2015) Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347(6226):1138–1142. doi:https://doi.org/10.1126/science.aaa1934
Zhu G, Du L, Jin L, Offenhausser A (2016) Effects of morphology constraint on electrophysiological properties of cortical neurons. Sci Rep 6:23086. https://doi.org/10.1038/srep23086
Zunder ER, Lujan E, Goltsev Y, Wernig M, Nolan GP (2015) A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry. Cell Stem Cell 16(3):323–337. https://doi.org/10.1016/j.stem.2015.01.015
Acknowledgements
We thank M. Beenhakker for helpful insights into the history of the patch-clamp technique and assessment of neuronal diversity by electrophysiological methods. We also acknowledge that the single-cell field is rapidly evolving and apologize, in advance, to many colleagues whose advances in single-cell measurement of neuronal diversity will undoubtably be reported after this review was prepared. This work was supported by NIMH U01 MH106882 to M.J.M., NIGMS T32 GM008328-24 to L.J.H., and T32 GM008136-30 to N.M.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Harbom, L.J., Michel, N. & McConnell, M.J. Single-cell analysis of diversity in human stem cell-derived neurons. Cell Tissue Res 371, 171–179 (2018). https://doi.org/10.1007/s00441-017-2728-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00441-017-2728-3