Serotonergic neuron regulation informed by in vivo single‐cell transcriptomics
Open accessAbstract
Despite the recognized importance of the dorsal raphe (DR) serotonergic (5‐HT) nuclei in the pathophysiology of depression and anxiety, the molecular components/putative drug targets expressed by these neurons are poorly characterized. Utilizing the promoter of an ETS domain transcription factor that is a stable marker of 5‐HT neurons (Pet‐1) to drive 5‐HT neuronal expression of YFP, we identified 5‐HT neurons in live acute slices. We isolated RNA from single 5‐HT neurons in the ventromedial and lateral wings of the DR and performed single‐cell RNA‐Seq analysis identifying >500 G‐protein coupled receptors (GPCRs) including receptors for classical transmitters, lipid signals, and peptides as well as dozens of orphan‐GPCRs. Using these data to inform our selection of receptors to assess, we found that oxytocin and lysophosphatidic acid 1 receptors are translated and active in costimulating, with the α 1 ‐adrenergic receptor, the firing of DR 5‐HT neurons, while the effects of histamine are inhibitory and exerted at H3 histamine receptors. The inhibitory histamine response provides evidence for tonic in vivo histamine inhibition of 5‐HT neurons. This study illustrates that unbiased single‐cell transcriptomics coupled with functional analyses provides novel insights into how neurons and neuronal systems are regulated.—Spaethling, J. M., Piel, D., Dueck, H., Buckley, P. T., Morris, J. F., Fisher, S. A., Lee, J., Sul, J.‐Y., Kim, J., Bartfai, T., Beck, S. G., Eberwine, J. H. Serotonergic neuron regulation informed by in vivo single‐cell transcriptomics. FASEB J. 28, 771–780 (2014). www.fasebj.org
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Systematic analysis and integration of multiple cellular characteristics at single-cell resolution within each raphe nucleus is still lacking.
“Pioneering work has introduced the molecular diversity of serotonin neurons across the midbrain and hindbrain (Okaty et al., 2015; Spaethling et al., 2014; Wylie et al., 2010), yet systematic analysis and integration of multiple cellular characteristics at single-cell resolution within each raphe nucleus is still lacking.”
From Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nuclei (2019) · cites this paper as Spaethling et al., 2014
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206 · see citing works
Differential expression analysis for sequence count data
Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581 · see citing works
Analysis of gene expression in single live neurons.
Eberwine, J. H., Yeh, H., Miyashiro, K., Cao, Y., Nair, S., Finnell, R. H., Zettel, M. F., & Coleman, P. D. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.7.3010 · Cited by 953 · see citing works
Self-citationYoshida, M., Takayanagi, Y., Inoue, K., Kimura, T., Young, L. J., Onaka, T., & Nishimori, K. (2009) · The Journal of Neuroscience · doi:10.1523/jneurosci.5593-08.2009 · Cited by 608 · see citing works
A detailed mapping of the histamine H3 receptor and its gene transcripts in rat brain
Pillot, C., Héron, A., Cochois, V., Tardivel‐Lacombe, J., Ligneau, X., Schwartz, J. C., & Arrang, J. M. (2002) · Neuroscience · doi:10.1016/s0306-4522(02)00135-5 · Cited by 340 · see citing works
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
Grant, G. R., Farkas, M. H., Pizarro, A., Lahens, N. F., Schug, J., Brunk, B. P., Stoeckert, C. J., Hogenesch, J. B., & Pierce, E. A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr427 · Cited by 336 · see citing works
Ring, R. H., Malberg, J. E., Potestio, L., Ping, J., Boikess, S., Luo, B., Schechter, L. E., Rizzo, S., Rahman, Z., & Rosenzweig-Lipson, S. (2006) · Psychopharmacology · doi:10.1007/s00213-005-0293-z · Cited by 319 · see citing works
Axel, R. (1995) · Scientific American · doi:10.1038/scientificamerican1095-154 · Cited by 314 · see citing works
Hendricks, T. J., Francis, N. J., Fyodorov, D. V., & Deneris, E. S. (1999) · Journal of Neuroscience · doi:10.1523/jneurosci.19-23-10348.1999 · Cited by 300 · see citing works
Identification of Rat H3 Receptor Isoforms with Different Brain Expression and Signaling Properties
Drutel, G., Peitsaro, N., Karlstedt, K. A., Wieland, K., Smit, M. J., Timmerman, H., Panula, P., & Leurs, R. (2001) · Molecular Pharmacology · doi:10.1124/mol.59.1.1 · Cited by 288 · see citing works
Serotonergic Systems, Anxiety, and Affective Disorder
Lowry, C. A., Hale, M. W., Evans, A. K., Heerkens, J., Staub, D. R., Gasser, P. J., & Shekhar, A. (2008) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1410.004 · Cited by 265 · see citing works
The timing of antidepressant effects: a comparison of diverse pharmacological and somatic treatments
Machado-Vieira, R., Baumann, J., Wheeler-Castillo, C., Latov, D., Henter, I. D., Salvadore, G., & Zarate, C. A. (2010) · Pharmaceuticals · doi:10.3390/ph3010019 · Cited by 263 · see citing works
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
Blake, J. A., Bult, C. J., Kadin, J. A., Richardson, J. E., Eppig, J. T., & the Mouse Genome Database Group (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1008 · Cited by 263 · see citing works
Calizo, L. H., Akanwa, A., Ma, X., Pan, Y.-Z., Lemos, J. C., Craige, C., Heemstra, L. A., & Beck, S. G. (2011) · Neuropharmacology · doi:10.1016/j.neuropharm.2011.04.008 · Cited by 252 · see citing works
Self-citationA genetic approach to access serotonin neurons for in vivo and in vitro studies
Scott, M. M., Wylie, C. J., Lerch, J. K., Murphy, R., Lobur, K. J., Herlitze, S., Jiang, W., Conlon, R. A., Strowbridge, B. W., & Deneris, E. S. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504510102 · Cited by 233 · see citing works
Im, D., Heise, C. E., Harding, M. A., et al. (2000) · Molecular Pharmacology · doi:10.1124/mol.57.4.753 · Cited by 201 · see citing works
How does pindolol improve antidepressant action?
Artigas, F., Celada, P., Laruelle, M. A., & Adell, A. (2001) · Trends in Pharmacological Sciences · doi:10.1016/s0165-6147(00)01682-5 · Cited by 174 · see citing works
Bosch, O. J. (2010) · Hormones and Behavior · doi:10.1016/j.yhbeh.2010.11.012 · Cited by 153 · see citing works
Sakai, K., & Crochet, S. (2001) · Neuroscience · doi:10.1016/s0306-4522(01)00103-8 · Cited by 148 · see citing works
Buckley, P. T., Lee, M. T., Sul, J., Miyashiro, K., Bell, T. J., Fisher, S. A., Kim, J., & Eberwine, J. H. (2011) · Neuron · doi:10.1016/j.neuron.2011.02.028 · Cited by 141 · see citing works
Self-citationKim, M., Lee, H. S., Lee, B. Y., & Waterhouse, B. D. (2004) · Brain Research · doi:10.1016/j.brainres.2004.08.022 · Cited by 126 · see citing works
Histamine H3Receptors Inhibit Serotonin Release in Substantia Nigra Pars Reticulata
Threlfell, S., Cragg, S. J., Kalló, I., Turi, G. F., Coen, C. W., & Greenfield, S. A. (2004) · Journal of Neuroscience · doi:10.1523/jneurosci.2690-04.2004 · Cited by 118 · see citing works
Selective ligands as tools to study histamine receptors
der Goot, H. V. (2000) · European Journal of Medicinal Chemistry · doi:10.1016/s0223-5234(00)00101-x · Cited by 108 · see citing works
Anxiety and cognition in histamine H3 receptor−/− mice
Rizk‐Jackson, A., Curley, J., Robertson, J., & Raber, J. (2004) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2004.03251.x · Cited by 102 · see citing works
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data
Sharman, J. L., Mpamhanga, C. P., Spedding, M., Germain, P., Staels, B., Dacquet, C., Laudet, V., Harmar, A. J., & NC-IUPHAR (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1062 · Cited by 102 · see citing works
Johnson, P. L., Lightman, S. L., & Lowry, C. A. (2004) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1296.006 · Cited by 98 · see citing works
Crawford, L. K., Craige, C. P., & Beck, S. G. (2010) · Journal of Neurophysiology · doi:10.1152/jn.01132.2009 · Cited by 96 · see citing works
Self-citationAman, T. K., Shen, R., & Haj‐Dahmane, S. (2006) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1124/jpet.106.111690 · Cited by 96 · see citing works
Larsen, P. J., Hay‐Schmidt, A., Vrang, N., & Mikkelsen, J. D. (1996) · Neuroscience · doi:10.1016/0306-4522(95)00415-7 · Cited by 94 · see citing works
Oxytocin-induced excitation of neurones in the rat central and medial amygdaloid nuclei
Terenzi, M. G., & Ingram, C. D. (2005) · Neuroscience · doi:10.1016/j.neuroscience.2005.04.004 · Cited by 91 · see citing works
Rawson, N. E., Eberwine, J., Dotson, R., Jackson, J., Ulrich, P. M., & Restrepo, D. (2000) · Journal of Neurochemistry · doi:10.1046/j.1471-4159.2000.0750185.x · Cited by 91 · see citing works
Self-citationSerotonergic dorsal raphe neurons cease firing by disfacilitation during paradoxical sleep
Sakai, K., & Crochet, S. (2000) · Neuroreport · doi:10.1097/00001756-200009280-00037 · Cited by 84 · see citing works
Santín, L. J., Bilbao, A., Pedraza, C., Matas-Rico, E., López-Barroso, D., Castilla‐Ortega, E., Sánchez‐López, J., Riquelme, R., Varela‐Nieto, I., de la Villa, P., et al. (2009) · Genes Brain & Behavior · doi:10.1111/j.1601-183x.2009.00524.x · Cited by 84 · see citing works
Eberwine, J. H., & Bartfai, T. (2010) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2010.09.010 · Cited by 82 · see citing works
Self-citationSugiura, T., Tokumura, A., Gregory, L., et al. (1994) · Archives of Biochemistry and Biophysics · doi:10.1006/abbi.1994.1249 · Cited by 81 · see citing works
Schizophrenia severity and clozapine treatment outcome association with oxytocinergic genes
de Souza, R. P., Luca, V. D., Meltzer, H. Y., Lieberman, J. A., & Kennedy, J. L. (2010) · The International Journal of Neuropsychopharmacology · doi:10.1017/s1461145710000167 · Cited by 74 · see citing works
Lysophospholipid receptors in vertebrate development, physiology, and pathology
Skoura, A., & Hla, T. (2008) · Journal of Lipid Research · doi:10.1194/jlr.r800047-jlr200 · Cited by 74 · see citing works
Effects of histamine H 3 receptor ligands in experimental models of anxiety and depression
Pérez‐García, C., Morales, L., Cano, V., et al. (1999) · Psychopharmacology · doi:10.1007/s002130050882 · Cited by 69 · see citing works
Neurochemical Changes in LPA1 Receptor Deficient Mice – A Putative Model of Schizophrenia
Roberts, C., Winter, P. H., Shilliam, C. S., Hughes, Z. A., Langmead, C. J., Maycox, P. R., & Dawson, L. A. (2005) · Neurochemical Research · doi:10.1007/s11064-005-2611-6 · Cited by 67 · see citing works
Jansen, F. P., Wu, T., Voss, H., et al. (1994) · British Journal of Pharmacology · doi:10.1111/j.1476-5381.1994.tb16995.x · Cited by 63 · see citing works
Social Stress Alters Inhibitory Synaptic Input to Distinct Subpopulations of Raphe Serotonin Neurons
Crawford, L. K., Rahman, S. F., & Beck, S. G. (2013) · ACS Chemical Neuroscience · doi:10.1021/cn300238j · Cited by 42 · see citing works
Self-citationWocławek-Potocka, I., Kondraciuk, K., & Skarzynski, D. J. (2009) · Experimental Biology and Medicine · doi:10.3181/0901-rm-36 · Cited by 38 · see citing works
Internuclear coupling of hypothalamic magnocellular nuclei by glutamate synaptic circuits
Boudaba, C., & Tasker, J. G. (2006) · American Journal of Physiology-Regulatory, Integrative and Comparative Physiology · doi:10.1152/ajpregu.00795.2005 · Cited by 31 · see citing works
Lakoski, J. M., Gallager, D. W., & Aghajanian, G. K. (1984) · European Journal of Pharmacology · doi:10.1016/0014-2999(84)90202-4 · Cited by 28 · see citing works
Drug targets: single-cell transcriptomics hastens unbiased discovery
Bartfai, T., Buckley, P. T., & Eberwine, J. H. (2011) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2011.09.006 · Cited by 27 · see citing works
Self-citationAnalysis of mRNA Populations from Single Live and Fixed Cells of the Central Nervous System
Eberwine, J. H., & Crino, P. B. (1997) · Current Protocols in Neuroscience · doi:10.1002/0471142301.ns0503s00 · Cited by 20 · see citing works
Self-citationTemplin, J. S., Bang, S. J., Soiza‐Reilly, M., Berde, C. B., & Commons, K. G. (2012) · Brain Research · doi:10.1016/j.brainres.2012.03.066 · Cited by 16 · see citing works
Carolina, H. M., & Giovanni, C. M. (2010) · Clinical Practice and Epidemiology in Mental Health · doi:10.2174/1745017901006010001 · Cited by 14 · see citing works
Allen, M. C. (1998) · European Journal of Pharmacology · doi:10.1016/s0014-2999(98)00719-5 · Cited by 6 · see citing works
Histaminergic effects on the frequency of repetitive spike firing in rat insular cortex
Takei, H., Song, L., Ebihara, K., et al. (2012) · Neuroscience Letters · doi:10.1016/j.neulet.2012.04.056 · Cited by 6 · see citing works
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Okaty, B. W., Commons, K. G., & Dymecki, S. M. (2019) · Nature Reviews Neuroscience · doi:10.1038/s41583-019-0151-3 · Cited by 319 · see citing works
Ren, J., Isakova, A., Friedmann, D., Zeng, J., Grutzner, S. M., Pun, A., Zhao, G. Q., Kolluru, S. S., Wang, R., Lin, R., et al. (2019) · eLife · doi:10.7554/elife.49424 · Cited by 304 · see citing works
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Poulin, J.-F., Tasic, B., Hjerling-Leffler, J., Trimarchi, J. M., & Awatramani, R. (2016) · Nature Neuroscience · doi:10.1038/nn.4366 · Cited by 293 · see citing works
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Okaty, B. W., Freret, M. E., Rood, B. D., Brust, R. D., Hennessy, M. L., deBairos, D., Kim, J. C., Cook, M. N., & Dymecki, S. M. (2015) · Neuron · doi:10.1016/j.neuron.2015.10.007 · Cited by 217 · see citing works
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Niederkofler, V., Asher, T. E., Okaty, B. W., Rood, B. D., Narayan, A., Hwa, L. S., Beck, S. G., Miczek, K. A., & Dymecki, S. M. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.10.063 · Cited by 113 · see citing works
Fernandez, S. P., Cauli, B., Cabezas, C., Muzerelle, A., Poncer, J.-C., & Gaspar, P. (2016) · Brain Structure and Function · doi:10.1007/s00429-015-1142-4 · Cited by 100 · see citing works
Calcagnoli, F., Stubbendorff, C., Meyer, N., de Boer, S. F., Althaus, M., & Koolhaas, J. M. (2015) · Neuropharmacology · doi:10.1016/j.neuropharm.2014.11.012 · Cited by 77 · see citing works
- Authors
- Spaethling, J. M., Piel, D., Dueck, H., Buckley, P. T., Morris, J. F., Fisher, S. A., Lee, J., Sul, J., Kim, J., Bartfai, T., Beck, S. G., & Eberwine, J. H.
- Affiliations
- University of Pennsylvania (US)
- Children's Hospital of Philadelphia (US)
- Department of Chemical Physiology The Scripps Research Institute La Jolla California USA
- Corresponding author
- Eberwine, James H.
- ORCID
- Venue
- The FASEB Journal
- Publisher
- Wiley
- Published
- 2013-11-05
- Volume
- 28
- Issue
- 2
- Pages
- 771-780
- ISSN
- 0892-6638 (ISSN-L)
- 1530-6860
- PMC
- PMC3898651
- OpenAlex
- W2144217996
- Cited by
- 57
- References
- 51
- Citations by year
- 2026: 3 · 2024: 1 · 2023: 1 · 2022: 4 · 2021: 3 · 2020: 7 · 2019: 6 · 2018: 1 · 2017: 7 · 2016: 11 · 2015: 11 · 2014: 2
- FWCI
- 3.92
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- The FASEB Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (MH075047, DP1OD004117)
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neurotransmitter Receptor Influence on Behavior
- Health Sciences › Medicine › Pharmacology › Treatment of Major Depression
- Keywords
- serotonergic neurons, dorsal raphe nucleus, single-cell transcriptomics, G protein-coupled receptors, orphan G protein-coupled receptor, oxytocin receptor, alpha1-adrenoceptors, histamine H3 receptor, depression, anxiety
- MeSH terms
- Animals, Electrophysiology, Male, Serotonin, Receptors, G-Protein-Coupled, Mice, Serotonergic Neurons, In Vitro Techniques
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