Single cell transcriptome atlas of the Drosophila larval brain

  1. Clarisse Brunet Avalos
  2. Rémy Bruggmann
  3. Simon G Sprecher  Is a corresponding author
  1. University of Fribourg, Switzerland
  2. University of Bern, Switzerland

Abstract

Cell diversity of the brain and how it is affected by starvation, remains largely unknown. Here we introduce a single cell transcriptome atlas of the entire Drosophila first instar larval brain. We first assigned cell-type identity based on known marker genes, distinguishing five major groups: neural progenitors, differentiated neurons, glia, undifferentiated neurons and non-neural cells. All major classes were further subdivided into multiple subtypes, revealing biological features of various cell-types. We further assessed transcriptional changes in response to starvation at the single-cell level. While after starvation the composition of the brain remains unaffected, transcriptional profile of several cell clusters changed. Intriguingly, different cell-types show very distinct responses to starvation, suggesting the presence of cell-specific programs for nutrition availability. Establishing a single-cell transcriptome atlas of the larval brain provides a powerful tool to explore cell diversity and assess genetic profiles from developmental, functional and behavioral perspectives.

Data availability

The single-cell sequencing data has been deposited in GEO under the accession code GSE134722.

The following data sets were generated

Article and author information

Author details

  1. Clarisse Brunet Avalos

    Department of Biology, University of Fribourg, Fribourg, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  2. Rémy Bruggmann

    Department of Biology, Institute of Cell Biology, University of Bern, Bern, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4733-7922
  3. Simon G Sprecher

    Department of Biology, University of Fribourg, Fribourg, Switzerland
    For correspondence
    simon.sprecher@unifr.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9060-3750

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (31003A_149499)

  • Simon G Sprecher

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SystemsX- SynaptiX RTD)

  • Rémy Bruggmann
  • Simon G Sprecher

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

Reviewing Editor

  1. K VijayRaghavan, National Centre for Biological Sciences, Tata Institute of Fundamental Research, India

Version history

  1. Received: July 19, 2019
  2. Accepted: November 19, 2019
  3. Accepted Manuscript published: November 20, 2019 (version 1)
  4. Version of Record published: December 5, 2019 (version 2)

Copyright

© 2019, Brunet Avalos 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

  • 12,190
    views
  • 1,511
    downloads
  • 113
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Clarisse Brunet Avalos
  2. Rémy Bruggmann
  3. Simon G Sprecher
(2019)
Single cell transcriptome atlas of the Drosophila larval brain
eLife 8:e50354.
https://doi.org/10.7554/eLife.50354

Share this article

https://doi.org/10.7554/eLife.50354

Further reading

    1. Immunology and Inflammation
    2. Neuroscience
    Nicolas Aubert, Madeleine Purcarea ... Gilles Marodon
    Research Article

    CD4+CD25+Foxp3+ regulatory T cells (Treg) have been implicated in pain modulation in various inflammatory conditions. However, whether Treg cells hamper pain at steady state and by which mechanism is still unclear. From a meta-analysis of the transcriptomes of murine Treg and conventional T cells (Tconv), we observe that the proenkephalin gene (Penk), encoding the precursor of analgesic opioid peptides, ranks among the top 25 genes most enriched in Treg cells. We then present various evidence suggesting that Penk is regulated in part by members of the Tumor Necrosis Factor Receptor (TNFR) family and the transcription factor Basic leucine zipper transcription faatf-like (BATF). Using mice in which the promoter activity of Penk can be tracked with a fluorescent reporter, we also show that Penk expression is mostly detected in Treg and activated Tconv in non-inflammatory conditions in the colon and skin. Functionally, Treg cells proficient or deficient for Penk suppress equally well the proliferation of effector T cells in vitro and autoimmune colitis in vivo. In contrast, inducible ablation of Penk in Treg leads to heat hyperalgesia in both male and female mice. Overall, our results indicate that Treg might play a key role at modulating basal somatic sensitivity in mice through the production of analgesic opioid peptides.

    1. Neuroscience
    James Malkin, Cian O'Donnell ... Laurence Aitchison
    Research Article

    Biological synaptic transmission is unreliable, and this unreliability likely degrades neural circuit performance. While there are biophysical mechanisms that can increase reliability, for instance by increasing vesicle release probability, these mechanisms cost energy. We examined four such mechanisms along with the associated scaling of the energetic costs. We then embedded these energetic costs for reliability in artificial neural networks (ANNs) with trainable stochastic synapses, and trained these networks on standard image classification tasks. The resulting networks revealed a tradeoff between circuit performance and the energetic cost of synaptic reliability. Additionally, the optimised networks exhibited two testable predictions consistent with pre-existing experimental data. Specifically, synapses with lower variability tended to have (1) higher input firing rates and (2) lower learning rates. Surprisingly, these predictions also arise when synapse statistics are inferred through Bayesian inference. Indeed, we were able to find a formal, theoretical link between the performance-reliability cost tradeoff and Bayesian inference. This connection suggests two incompatible possibilities: evolution may have chanced upon a scheme for implementing Bayesian inference by optimising energy efficiency, or alternatively, energy-efficient synapses may display signatures of Bayesian inference without actually using Bayes to reason about uncertainty.