Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex

  1. Cathryn R Cadwell  Is a corresponding author
  2. Federico Scala
  3. Paul G Fahey
  4. Dmitry Kobak
  5. Shalaka Mulherkar
  6. Fabian H Sinz
  7. Stelios Papadopoulos
  8. Zheng H Tan
  9. Per Johnsson
  10. Leonard Hartmanis
  11. Shuang Li
  12. Ronald J Cotton
  13. Kimberley F Tolias
  14. Rickard Sandberg
  15. Philipp Berens
  16. Xiaolong Jiang  Is a corresponding author
  17. Andreas Savas Tolias  Is a corresponding author
  1. University of California, San Francisco, United States
  2. Baylor College of Medicine, United States
  3. University of Tübingen, Germany
  4. Karolinska Institutet, Sweden

Abstract

Clones of excitatory neurons derived from a common progenitor have been proposed to serve as elementary information processing modules in the neocortex. To characterize the cell types and circuit diagram of clonally related neurons, we performed multi-cell patch clamp recordings and Patch-seq on neurons derived from Nestin-positive progenitors labeled by tamoxifen induction at embryonic day 10.5. The resulting clones are derived from two radial glia on average, span cortical layers 2-6, and are composed of a random sampling of transcriptomic cell types. We find an interaction between shared lineage and connectivity: related neurons are more likely to be connected vertically across cortical layers, but not laterally within the same layer. These findings challenge the view that related neurons show uniformly increased connectivity and suggest that integration of vertical intra-clonal input with lateral inter-clonal input may represent a developmentally programmed connectivity motif supporting the emergence of functional circuits.

Data availability

Sequencing data have been deposited in GEO under accession code GSE140946. All data generated or analyzed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 1, 2, 3 and 4. The source data provided for Figure 4 also apply to Figure 5 and Table 1.

The following data sets were generated

Article and author information

Author details

  1. Cathryn R Cadwell

    Anatomic Pathology, University of California, San Francisco, San Francisco, United States
    For correspondence
    Cathryn.Cadwell@ucsf.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1963-8285
  2. Federico Scala

    Neuroscience, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Paul G Fahey

    Neuroscience, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Dmitry Kobak

    Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Shalaka Mulherkar

    Department of Neuroscience, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8736-527X
  6. Fabian H Sinz

    Neuroscience, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Stelios Papadopoulos

    Neuroscience, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Zheng H Tan

    Neuroscience, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Per Johnsson

    Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  10. Leonard Hartmanis

    Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  11. Shuang Li

    Neuroscience, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Ronald J Cotton

    Neuroscience, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Kimberley F Tolias

    Department of Neuroscience, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2092-920X
  14. Rickard Sandberg

    Ludwig Institute for Cancer Research, Karolinska Institutet, Stockholm, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  15. Philipp Berens

    Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0199-4727
  16. Xiaolong Jiang

    Department of Neuroscience, Baylor College of Medicine, Houston, United States
    For correspondence
    xiaolonj@bcm.edu
    Competing interests
    The authors declare that no competing interests exist.
  17. Andreas Savas Tolias

    Neuroscience, Baylor College of Medicine, Houston, United States
    For correspondence
    astolias@bcm.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4305-6376

Funding

Baylor College of Medicine (Optical Imaging and Vital Microscopy Core)

  • Andreas Savas Tolias

Baylor College of Medicine (Faculty start-up fund)

  • Xiaolong Jiang

National Institutes of Health (F30MH095440,T32GM007330)

  • Cathryn R Cadwell

National Institutes of Health (F30MH112312)

  • Paul G Fahey

Baylor Research Advocates for Student Scientists (BRASS Scholar Award)

  • Cathryn R Cadwell
  • Paul G Fahey

National Institutes of Health (R01MH103108,R01DA028525,DP1EY023176,P30EY002520,T32EY07001,DP1OD008301)

  • Andreas Savas Tolias

National Science Foundation (707359)

  • Andreas Savas Tolias

Svenska Forskningsrådet Formas

  • Rickard Sandberg

Vallee Foundation

  • Rickard Sandberg

Deutsche Forschungsgemeinschaft (EXC 2064,BE5601/4-1)

  • Philipp Berens

Bundesministerium für Bildung und Forschung (FKZ 01GQ1601)

  • Philipp Berens

McKnight Foundation (McKnight Scholar Award)

  • Andreas Savas Tolias

Arnold and Mabel Beckman Foundation (Young Investigator Award)

  • Andreas Savas Tolias

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

Reviewing Editor

  1. Anne E West, Duke University School of Medicine, United States

Ethics

Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to an approved institutional animal care and use committee (IACUC) protocol of Baylor College of Medicine (protocol # AN-4703). Every effort was made to minimize suffering.

Version history

  1. Received: October 22, 2019
  2. Accepted: March 2, 2020
  3. Accepted Manuscript published: March 5, 2020 (version 1)
  4. Accepted Manuscript updated: March 6, 2020 (version 2)
  5. Version of Record published: April 16, 2020 (version 3)

Copyright

© 2020, Cadwell 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

  • 3,957
    Page views
  • 616
    Downloads
  • 26
    Citations

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

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. Cathryn R Cadwell
  2. Federico Scala
  3. Paul G Fahey
  4. Dmitry Kobak
  5. Shalaka Mulherkar
  6. Fabian H Sinz
  7. Stelios Papadopoulos
  8. Zheng H Tan
  9. Per Johnsson
  10. Leonard Hartmanis
  11. Shuang Li
  12. Ronald J Cotton
  13. Kimberley F Tolias
  14. Rickard Sandberg
  15. Philipp Berens
  16. Xiaolong Jiang
  17. Andreas Savas Tolias
(2020)
Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex
eLife 9:e52951.
https://doi.org/10.7554/eLife.52951

Share this article

https://doi.org/10.7554/eLife.52951

Further reading

    1. Developmental Biology
    2. Immunology and Inflammation
    Amir Hossein Kayvanjoo, Iva Splichalova ... Elvira Mass
    Research Article Updated

    During embryogenesis, the fetal liver becomes the main hematopoietic organ, where stem and progenitor cells as well as immature and mature immune cells form an intricate cellular network. Hematopoietic stem cells (HSCs) reside in a specialized niche, which is essential for their proliferation and differentiation. However, the cellular and molecular determinants contributing to this fetal HSC niche remain largely unknown. Macrophages are the first differentiated hematopoietic cells found in the developing liver, where they are important for fetal erythropoiesis by promoting erythrocyte maturation and phagocytosing expelled nuclei. Yet, whether macrophages play a role in fetal hematopoiesis beyond serving as a niche for maturing erythroblasts remains elusive. Here, we investigate the heterogeneity of macrophage populations in the murine fetal liver to define their specific roles during hematopoiesis. Using a single-cell omics approach combined with spatial proteomics and genetic fate-mapping models, we found that fetal liver macrophages cluster into distinct yolk sac-derived subpopulations and that long-term HSCs are interacting preferentially with one of the macrophage subpopulations. Fetal livers lacking macrophages show a delay in erythropoiesis and have an increased number of granulocytes, which can be attributed to transcriptional reprogramming and altered differentiation potential of long-term HSCs. Together, our data provide a detailed map of fetal liver macrophage subpopulations and implicate macrophages as part of the fetal HSC niche.

    1. Developmental Biology
    2. Neuroscience
    Smrithi Prem, Bharati Dev ... Emanuel DiCicco-Bloom
    Research Article Updated

    Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets. To identify signaling differences that may contribute to these developmental defects, an unbiased phospho-(p)-proteome screen was performed. Surprisingly despite the genetic heterogeneity, hundreds of shared p-peptides were identified between autism subtypes including the mTOR pathway. mTOR signaling alterations were confirmed in all NPCs across both ASD subtypes, and mTOR modulation rescued ASD phenotypes and reproduced autism NPC-associated phenotypes in control NPCs. Thus, our studies demonstrate that genetically distinct ASD subtypes have common defects in neurite outgrowth and migration which are driven by the shared pathogenic mechanism of mTOR signaling dysregulation.