Molecular and anatomical organization of the dorsal raphe nucleus

  1. Kee Wui Huang
  2. Nicole E Ochandarena
  3. Adrienne C Philson
  4. Minsuk Hyun
  5. Jaclyn E Birnbaum
  6. Marcelo Cicconet
  7. Bernardo L Sabatini  Is a corresponding author
  1. Howard Hughes Medical Institute, Harvard Medical School, United States
  2. Harvard Medical School, United States

Abstract

The dorsal raphe nucleus (DRN) is an important source of neuromodulators and has been implicated in a wide variety of behavioral and neurological disorders. The DRN is subdivided into distinct anatomical subregions comprised of multiple cell types, and its complex cellular organization has impeded efforts to investigate the distinct circuit and behavioral functions of its subdomains. Here we used single-cell RNA sequencing, in situ hybridization, anatomical tracing, and spatial correlation analysis to map the transcriptional and spatial profiles of cells from the mouse DRN. Our analysis of 39,411 single-cell transcriptomes revealed at least 18 distinct neuron subtypes and 5 serotonergic neuron subtypes with distinct molecular and anatomical properties, including a serotonergic neuron subtype that preferentially innervates the basal ganglia. Our study lays out the molecular organization of distinct serotonergic and non-serotonergic subsystems, and will facilitate the design of strategies for further dissection the DRN and its diverse functions.

Data availability

The sequencing datasets generated in this study are available on the NCBI Gene Expression Omnibus (accession number: GSE134163). R data files containing the processed and annotated scRNA-seq data in the form of Seurat objects are also available on the Harvard Dataverse (https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/QB5CC8).

The following data sets were generated

Article and author information

Author details

  1. Kee Wui Huang

    Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Nicole E Ochandarena

    Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Adrienne C Philson

    Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Minsuk Hyun

    Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jaclyn E Birnbaum

    Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Marcelo Cicconet

    Image and Data Analysis Core, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Bernardo L Sabatini

    Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
    For correspondence
    bsabatini@hms.harvard.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0095-9177

Funding

National Institute of Neurological Disorders and Stroke (NS103226)

  • Bernardo L Sabatini

Howard Hughes Medical Institute

  • Bernardo L Sabatini

National Institute of Mental Health (MH100568)

  • Bernardo L Sabatini

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All procedures were performed in accordance with protocols approved by the Harvard Standing Committee on Animal Care following guidelines described in the U.S. National Institutes of Health Guide for the Care and Use of Laboratory Animals (HMS IACUC protocol #IS00000571). All surgery was performed under isoflurane anesthesia.

Reviewing Editor

  1. Julie A Kauer, Stanford University, United States

Publication history

  1. Received: February 28, 2019
  2. Accepted: August 13, 2019
  3. Accepted Manuscript published: August 14, 2019 (version 1)
  4. Version of Record published: September 4, 2019 (version 2)

Copyright

© 2019, Huang et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 9,972
    Page views
  • 1,460
    Downloads
  • 75
    Citations

Article citation count generated by polling the highest count across the following sources: Scopus, Crossref, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Kee Wui Huang
  2. Nicole E Ochandarena
  3. Adrienne C Philson
  4. Minsuk Hyun
  5. Jaclyn E Birnbaum
  6. Marcelo Cicconet
  7. Bernardo L Sabatini
(2019)
Molecular and anatomical organization of the dorsal raphe nucleus
eLife 8:e46464.
https://doi.org/10.7554/eLife.46464

Further reading

    1. Neuroscience
    Kevin Vinberg, Jörgen Rosén ... Fredrik Ahs
    Research Article Updated

    Understanding the neural basis for individual differences in the skin conductance response (SCR) during discriminative fear conditioning may inform on our understanding of autonomic regulation in fear-related psychopathology. Previous region-of-interest (ROI) analyses have implicated the amygdala in regulating conditioned SCR, but whole brain analyses are lacking. This study examined correlations between individual differences in SCR during discriminative fear conditioning to social stimuli and neural activity throughout the brain, by using data from a large functional magnetic resonance imaging study of twins (N = 285 individuals). Results show that conditioned SCR correlates with activity in the dorsal anterior cingulate cortex/anterior midcingulate cortex, anterior insula, bilateral temporoparietal junction, right frontal operculum, bilateral dorsal premotor cortex, right superior parietal lobe, and midbrain. A ROI analysis additionally showed a positive correlation between amygdala activity and conditioned SCR in line with previous reports. We suggest that the observed whole brain correlates of SCR belong to a large-scale midcingulo-insular network related to salience detection and autonomic-interoceptive processing. Altered activity within this network may underlie individual differences in conditioned SCR and autonomic aspects of psychopathology.

    1. Neuroscience
    Rong Zhao, Stacy D Grunke ... Joanna L Jankowsky
    Research Article

    Neurodegenerative diseases are characterized by selective vulnerability of distinct cell populations; however, the cause for this specificity remains elusive. Here we show that entorhinal cortex layer 2 (EC2) neurons are unusually vulnerable to prolonged neuronal inactivity compared with neighboring regions of the temporal lobe, and that reelin+ stellate cells connecting EC with the hippocampus are preferentially susceptible within the EC2 population. We demonstrate that neuronal death after silencing can be elicited through multiple independent means of activity inhibition, and that preventing synaptic release, either alone or in combination with electrical shunting, is sufficient to elicit silencing-induced degeneration. Finally, we discovered that degeneration following synaptic silencing is governed by competition between active and inactive cells, which is a circuit refinement process traditionally thought to end early in postnatal life. Our data suggests that the developmental window for wholesale circuit plasticity may extend into adulthood for specific brain regions. We speculate that this sustained potential for remodeling by entorhinal neurons may support lifelong memory but renders them vulnerable to prolonged activity changes in disease.