Single-cell analysis reveals a close relationship between differentiating dopamine and subthalamic nucleus neuronal lineages
Open accessAbstract
Stem cell engineering and grafting of mesencephalic dopamine (mesDA) neurons is a promising strategy for brain repair in Parkinson's disease (PD). Refinement of differentiation protocols to optimize this approach will require deeper understanding of mesDA neuron development. Here, we studied this process using transcriptome-wide single-cell RNA sequencing of mouse neural progenitors expressing the mesDA neuron determinant Lmx1a. This approach resolved the differentiation of mesDA and neighboring neuronal lineages and revealed a remarkably close relationship between developing mesDA and subthalamic nucleus (STN) neurons, while also highlighting a distinct transcription factor set that can distinguish between them. While previous hESC mesDA differentiation protocols have relied on markers that are shared between the two lineages, we found that application of these highlighted markers can help to refine current stem cell engineering protocols, increasing the proportion of appropriately patterned mesDA progenitors. Our results, therefore, have important implications for cell replacement therapy in PD.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The boundaries of the dopamine primordium are defined by transcription factor expression: the caudal extent by the Otx2/Gbx2 boundary, the rostral extent by the En1/Dbx1 boundary, and the dorsal extent by the Lmx1a/Nkx6.1 boundary.
“The caudal extent is defined by the Otx2/Gbx2 boundary coincident with the morphological mid-hindbrain boundary [74]. The rostral extent is defined by the En1/Dbx1 gene expression boundary which is located in the diencephalic region [75–78]. The dorsal extent is defined by the Lmx1a/Nkx6.1 gene expression boundary [71,79–81].”
From Classification of midbrain dopamine neurons using single-cell gene expression profiling approaches (2020) · cites this paper as [76]
Cites
WGCNA: an R package for weighted correlation network analysis
Langfelder, P., & Horvath, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-559 · Cited by 27,252 · see citing works
Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2859 · Cited by 7,314 · see citing works
Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.
Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110 · see citing works
Maps of random walks on complex networks reveal community structure
Rosvall, M., & Bergstrom, C. T. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706851105 · Cited by 4,583 · see citing works
Full-length RNA-seq from single cells using Smart-seq2
Picelli, S., Faridani, O. R., Björklund, Å. K., Winberg, G., Sagasser, S., & Sandberg, R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.006 · Cited by 4,137 · see citing works
Self-citationPrimate models of movement disorders of basal ganglia origin
DeLong, M. R. (1990) · Trends in Neurosciences · doi:10.1016/0166-2236(90)90110-v · Cited by 3,824 · see citing works
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
Klein, A. M., Mazutis, L., Akartuna, I., Tallapragada, N., Veres, A., Li, V., Peshkin, L., Weitz, D. A., & Kirschner, M. W. (2015) · Cell · doi:10.1016/j.cell.2015.04.044 · Cited by 3,356 · see citing works
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
Zeisel, A., Muñoz-Manchado, A. B., Codeluppi, S., Lönnerberg, P., La Manno, G., Juréus, A., Marques, S., Munguba, H., He, L., Betsholtz, C., et al. (2015) · Science · doi:10.1126/science.aaa1934 · Cited by 3,124 · see citing works
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
Picelli, S., Björklund, Å. K., Faridani, O. R., Sagasser, S., Winberg, G., & Sandberg, R. (2013) · Nature Methods · doi:10.1038/nmeth.2639 · Cited by 2,358 · see citing works
Self-citationData-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
Levine, J. H., Simonds, E. F., Bendall, S. C., Davis, K. L., Amir, E.-A. D., Tadmor, M. D., Litvin, O., Fienberg, H. G., Jager, A., Zunder, E. R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.047 · Cited by 2,303 · see citing works
Accelerating t-SNE using tree-based algorithms
van der Maaten, L. (2014) · Journal of machine learning research · doi:10.5555/2627435.2697068 · Cited by 2,207 · see citing works
Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo
Zufferey, R., Nagy, D., Mandel, R. J., Naldini, L., & Trono, D. (1997) · Nature Biotechnology · doi:10.1038/nbt0997-871 · Cited by 1,977 · see citing works
Kriks, S., Shim, J., Piao, J., Ganat, Y. M., Wakeman, D. R., Xie, Z., Carrillo‐Reid, L., Auyeung, G., Antonacci, C. L., Buch, A., et al. (2011) · Nature · doi:10.1038/nature10648 · Cited by 1,912 · see citing works
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types
Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Elefant, N., Paul, F., Zaretsky, I., Mildner, A., Cohen, N., Jung, S., Tanay, A., et al. (2014) · Science · doi:10.1126/science.1247651 · Cited by 1,795 · see citing works
A survey of human brain transcriptome diversity at the single cell level
Darmanis, S., Sloan, S. A., Zhang, Y., Enge, M., Caneda, C., Shuer, L. M., Hayden Gephart, M. G., Barres, B. A., & Quake, S. R. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1507125112 · Cited by 1,401 · see citing works
Bayesian approach to single-cell differential expression analysis
Kharchenko, P. V., Silberstein, L., & Scadden, D. T. (2014) · Nature Methods · doi:10.1038/nmeth.2967 · Cited by 1,348 · see citing works
Hayashi, S., & McMahon, A. P. (2002) · Developmental Biology · doi:10.1006/dbio.2002.0597 · Cited by 1,347 · see citing works
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
Treutlein, B., Brownfield, D. G., Wu, A. R., Neff, N. F., Mantalas, G. L., Espinoza, F. H., Desai, T. J., Krasnow, M. A., & Quake, S. R. (2014) · Nature · doi:10.1038/nature13173 · Cited by 1,342 · see citing works
Deep brain stimulation of the subthalamic nucleus for the treatment of Parkinson's disease
Benabid, A. L., Chabardes, S., Mitrofanis, J., & Pollak, P. (2009) · The Lancet Neurology · doi:10.1016/s1474-4422(08)70291-6 · Cited by 1,285 · see citing works
Dopamine Neuron Agenesis in Nurr1-Deficient Mice
Zetterström, R. H., Solomin, L., Jansson, L., Hoffer, B. J., Olson, L., & Perlmann, T. (1997) · Science · doi:10.1126/science.276.5310.248 · Cited by 1,096 · see citing works
Self-citationSingle-cell RNA-seq reveals dynamic paracrine control of cellular variation
Shalek, A. K., Satija, R., Shuga, J., Trombetta, J. J., Gennert, D., Lu, D., Chen, P., Gertner, R. S., Gaublomme, J. T., Yosef, N., et al. (2014) · Nature · doi:10.1038/nature13437 · Cited by 1,000 · see citing works
Pollen, A. A., Nowakowski, T. J., Shuga, J., Wang, X., Leyrat, A. A., Lui, J. H., Li, N., Szpankowski, L., Fowler, B., Chen, P., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2967 · Cited by 920 · see citing works
Kirkeby, A., Grealish, S., Wolf, D. A., Nelander, J., Wood, J., Lundblad, M., Lindvall, O., & Parmar, M. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.04.009 · Cited by 662 · see citing works
Self-citationIdentification of intrinsic determinants of midbrain dopamine neurons
Andersson, E., Tryggvason, U., Deng, Q., Friling, S., Alekseenko, Z., Robert, B., Perlmann, T., & Ericson, J. (2006) · Cell · doi:10.1016/j.cell.2005.10.037 · Cited by 587 · see citing works
Self-citationNicholas, C. R., Chen, J., Tang, Y., Southwell, D. G., Chalmers, N., Vogt, D. L., Arnold, C. M., Chen, Y.-J. J., Stanley, E. G., Elefanty, A. G., et al. (2013) · Cell stem cell · doi:10.1016/j.stem.2013.04.005 · Cited by 513 · see citing works
Doi, D., Samata, B., Katsukawa, M., Kikuchi, T., Morizane, A., Ono, Y., Sekiguchi, K., Nakagawa, M., Parmar, M., & Takahashi, J. B. (2014) · Stem Cell Reports · doi:10.1016/j.stemcr.2014.01.013 · Cited by 434 · see citing works
Self-citationDefining midbrain dopaminergic neuron diversity by single-cell gene expression profiling
Poulin, J.-F., Zou, J., Drouin-Ouellet, J., Kim, K.-Y. A., Cicchetti, F., & Awatramani, R. B. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.10.008 · Cited by 352 · see citing works
A High-Resolution Spatiotemporal Atlas of Gene Expression of the Developing Mouse Brain
Thompson, C. L., Ng, L., Menon, V., Martı́nez, S., Lee, C., Glattfelder, K. J., Sunkin, S. M., Henry, A. M., Lau, C., Dang, C., et al. (2014) · Neuron · doi:10.1016/j.neuron.2014.05.033 · Cited by 324 · see citing works
Smidt, M. P., Smits, S. M., Bouwmeester, H., Hamers, F. P. T., van der Linden, A. J. A., Hellemons, A. J. C. G. M., Graw, J., & Burbach, J. P. H. (2004) · Development · doi:10.1242/dev.01022 · Cited by 317 · see citing works
Cell-based therapies for Parkinson disease—past insights and future potential
Barker, R. A., Drouin‐Ouellet, J., & Parmar, M. (2015) · Nature Reviews Neurology · doi:10.1038/nrneurol.2015.123 · Cited by 310 · see citing works
Self-citationHow to make a midbrain dopaminergic neuron
Arenas, E., Denham, M., & Villaescusa, C. (2015) · Development · doi:10.1242/dev.097394 · Cited by 306 · see citing works
Kirkeby, A., Nolbrant, S., Tiklová, K., Heuer, A., Kee, N., Cardoso, T., Ottosson, D. R., Lelos, M. J., Rifes, P., Dunnett, S. B., et al. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.09.004 · Cited by 259 · see citing works
Self-citationNeurogenin 2 is required for the development of ventral midbrain dopaminergic neurons
Kele, J., Simplicio, N., Ferri, L., Mira, H., Guillemot, F., Arenas, E., & Ang, S. (2006) · Development · doi:10.1242/dev.02223 · Cited by 247 · see citing works
Specification of Midbrain Dopamine Neurons from Primate Pluripotent Stem Cells
Xi, J., Liu, Y., Liu, H., Chen, H., Emborg, M. E., & Zhang, S. (2012) · Stem Cells · doi:10.1002/stem.1152 · Cited by 205 · see citing works
Andersson, E., Jensen, J. B., Parmar, M., Guillemot, F., & Björklund, A. (2006) · Development · doi:10.1242/dev.02224 · Cited by 166 · see citing works
Self-citationYan, C. H., Levesque, M., Claxton, S., Johnson, R. L., & Ang, S.-L. (2011) · The Journal of Neuroscience · doi:10.1523/jneurosci.1077-11.2011 · Cited by 144 · see citing works
Identification of embryonic stem cell–derived midbrain dopaminergic neurons for engraftment
Ganat, Y. M., Calder, E. L., Kriks, S., Nelander, J., Tu, E. Y., Jia, F., Battista, D., Harrison, N. L., Parmar, M., Tomishima, M. J., et al. (2012) · Journal of Clinical Investigation · doi:10.1172/jci58767 · Cited by 139 · see citing works
Self-citationMoving Stem Cells to the Clinic: Potential and Limitations for Brain Repair
Steinbeck, J. A., & Studer, L. (2015) · Neuron · doi:10.1016/j.neuron.2015.03.002 · Cited by 134 · see citing works
Specific and integrated roles of Lmx1a, Lmx1b and Phox2a in ventral midbrain development
Deng, Q., Andersson, E., Hedlund, E., Alekseenko, Z., Coppola, E., Panman, L., Millonig, J. H., Brunet, J., Ericson, J., & Perlmann, T. (2011) · Development · doi:10.1242/dev.065482 · Cited by 126 · see citing works
Self-citationJaeger, I. S., Arber, C., Risner-Janiczek, J. R., Küchler, J., Pritzsche, D., Chen, I., Naveenan, T., Ungless, M. A., & Li, M. C. (2011) · Development · doi:10.1242/dev.066746 · Cited by 112 · see citing works
PITX2 is required for normal development of neurons in the mouse subthalamic nucleus and midbrain
Martin, D. M., Skidmore, J. M., Philips, S. T., et al. (2003) · Developmental Biology · doi:10.1016/j.ydbio.2003.10.035 · Cited by 110 · see citing works
Guo, C., Qiu, H., Huang, Y., Chen, H., Yang, R.-Q., Chen, S.-D., Johnson, R. L., Chen, Z., & Ding, Y. (2006) · Development · doi:10.1242/dev.02745 · Cited by 110 · see citing works
Marı́n, F., Herrero, M. T., Vyas, S., & Puelles, L. (2005) · Developmental Dynamics · doi:10.1002/dvdy.20467 · Cited by 90 · see citing works
Asbreuk, C. (2002) · Molecular and Cellular Neuroscience · doi:10.1006/mcne.2002.1182 · Cited by 59 · see citing works
Zhao, T., Szabó, N., Ma, J., Luo, L., Zhou, X., & Álvarez-Bolado, G. (2008) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2008.06503.x · Cited by 58 · see citing works
Smidt, M. P., Cox, J. J., van Schaick, H. S. A., et al. (2000) · Journal of Neurochemistry · doi:10.1046/j.1471-4159.2000.0751818.x · Cited by 44 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Molecular architecture of the developing mouse brain
La Manno, G., Siletti, K., Furlan, A., Gyllborg, D., Vinsland, E., Mossi Albiach, A., Mattsson Langseth, C., Khven, I., Lederer, A. R., Dratva, L. M., et al. (2021) · Nature · doi:10.1038/s41586-021-03775-x · Cited by 563 · see citing works
Tiklová, K., Björklund, Å. K., Lahti, L., Fiorenzano, A., Nolbrant, S., Gillberg, L., Volakakis, N., Yokota, C., Hilscher, M. M., Hauling, T., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08453-1 · Cited by 276 · see citing works
Self-citationNeural Subtype Specification from Human Pluripotent Stem Cells
Tao, Y., & Zhang, S.-C. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.10.015 · Cited by 287 · see citing works
Classification of midbrain dopamine neurons using single-cell gene expression profiling approaches
Poulin, J.-F., Gaertner, Z., Moreno-Ramos, O. A., & Awatramani, R. (2020) · Trends in Neurosciences · doi:10.1016/j.tins.2020.01.004 · Cited by 238 · see citing works
SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
Han, K. Y., Kim, K.-T., Joung, J.-G., Son, D.-S., Kim, Y. J., Jo, A., Jeon, H.-J., Moon, H.-S., Yoo, C. E., Chung, W., et al. (2018) · Genome Research · doi:10.1101/gr.223263.117 · Cited by 143 · see citing works
- Authors
- Kee, N., Volakakis, N., Kirkeby, A., Dahl, L., Storvall, H., Nolbrant, S., Lahti, L., Björklund, Å. K., Gillberg, L., Joodmardi, E., Sandberg, R., Parmar, M., & Perlmann, T.
- Affiliations
- Ludwig Cancer Research (BE)
- Ludwig Cancer Research (SE)
- Lund University (SE)
- Uppsala University (SE)
- Corresponding author
- Kee, Nigel
- Perlmann, Thomas
- ORCID
- Venue
- Cell stem cell
- Publisher
- Elsevier BV
- Published
- 2017-01
- Volume
- 20
- Issue
- 1
- Pages
- 29-40
- ISSN
- 1875-9777 (ISSN-L)
- 1934-5909
- OpenAlex
- W2544973020
- Cited by
- 149
- References
- 46
- Citations by year
- 2026: 6 · 2025: 13 · 2024: 11 · 2023: 13 · 2022: 16 · 2021: 22 · 2020: 29 · 2019: 10 · 2018: 13 · 2017: 13 · 2016: 2
- FWCI
- 6.59
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell stem cell (publishedVersion)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- Funders
- Seventh Framework Programme (FP/2007-2013, 222999, 222943)
- Knut och Alice Wallenbergs Stiftelse (2013.0075)
- Vetenskapsrådet (K2014-61X-20391-08-4)
- European Research Council (309712, 602278)
- Stiftelsen för Strategisk Forskning
- Sigrid Juséliuksen Säätiö
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- mesencephalic dopamine neurons, Parkinson's disease, neural progenitor differentiation, Lmx1a, transcription factors, stem cell engineering, cell replacement therapy, single-cell transcriptomics
- MeSH terms
- Cell Differentiation, Humans, Immunohistochemistry, Transcription Factors, Signal Transduction, Biomarkers, Sequence Analysis, RNA, Cell Lineage, Body Patterning, Subthalamic Nucleus, Gene Expression Profiling, Gene Regulatory Networks, Embryonic Stem Cells, Neurogenesis, Single-Cell Analysis, Dopaminergic Neurons, LIM-Homeodomain Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
