Unified single-cell analysis of testis gene regulation and pathology in 5 mouse strains

  1. Min Jung
  2. Daniel Wells
  3. Jannette Rusch
  4. Suhaira Ahmad
  5. Jonathan Marchini
  6. Simon R Myers  Is a corresponding author
  7. Donald F Conrad  Is a corresponding author
  1. Washington University School of Medicine, United States
  2. University of Oxford, United Kingdom
  3. Oregon Health and Science University, United States

Abstract

To fully exploit the potential of single-cell functional genomics in the study of development and disease, robust methods are needed to simplify the analysis of data across samples, time-points and individuals. Here we introduce a model-based factor analysis method, SDA, to analyse a novel 57,600-cell dataset from the testes of wild-type mice and mice with gonadal defects due to disruption of the genes Mlh3, Hormad1, Cul4a or Cnp. By jointly analysing mutant and wild-type cells we decomposed our data into 46 components that identify novel meiotic gene-regulatory programmes, mutant-specific pathological processes, and technical effects, and provide a framework for imputation. We identify, de novo, DNA sequence motifs associated with individual components that define temporally varying modes of gene expression control. Analysis of SDA components also led us to identify a rare population of macrophages within the seminiferous tubules of Mlh3-/- and Hormad1-/- mice, an area typically associated with immune privilege.

Data availability

Raw data and processed files for Drop-seq and 10X Genomics experiments are available in GEO under accession number: GSE113293

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Min Jung

    Department of Genetics, Washington University School of Medicine, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Daniel Wells

    Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2007-8978
  3. Jannette Rusch

    Department of Genetics, Washington University School of Medicine, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Suhaira Ahmad

    Department of Genetics, Washington University School of Medicine, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jonathan Marchini

    Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Simon R Myers

    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    For correspondence
    myers@stats.ox.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
  7. Donald F Conrad

    Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Portland, United States
    For correspondence
    conradon@ohsu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3828-8970

Funding

Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD078641)

  • Donald F Conrad

National Institute of Mental Health (R01MH101810)

  • Donald F Conrad

Wellcome (098387/Z/12/Z)

  • Simon R Myers

Wellcome (109109/Z/15/Z)

  • Daniel Wells

European Research Council (617306)

  • Jonathan Marchini

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 animal experiments were performed in compliance with the regulations of the Animal Studies Committee at Washington University in St. Louis under approved protocol #20160089.

Reviewing Editor

  1. Deborah Bourc'his, Institut Curie, France

Publication history

  1. Received: November 28, 2018
  2. Accepted: June 17, 2019
  3. Accepted Manuscript published: June 25, 2019 (version 1)
  4. Version of Record published: July 9, 2019 (version 2)

Copyright

© 2019, Jung 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

  • 7,145
    Page views
  • 751
    Downloads
  • 47
    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. Min Jung
  2. Daniel Wells
  3. Jannette Rusch
  4. Suhaira Ahmad
  5. Jonathan Marchini
  6. Simon R Myers
  7. Donald F Conrad
(2019)
Unified single-cell analysis of testis gene regulation and pathology in 5 mouse strains
eLife 8:e43966.
https://doi.org/10.7554/eLife.43966

Further reading

    1. Computational and Systems Biology
    2. Medicine
    David J Jörg et al.
    Research Article

    For the treatment of postmenopausal osteoporosis, several drug classes with different mechanisms of action are available. Since only a limited set of dosing regimens and drug combinations can be tested in clinical trials, it is currently unclear whether common medication strategies achieve optimal bone mineral density gains or are outperformed by alternative dosing schemes and combination therapies that have not been explored so far. Here, we develop a mathematical framework of drug interventions for postmenopausal osteoporosis that unifies fundamental mechanisms of bone remodeling and the mechanisms of action of four drug classes: bisphosphonates, parathyroid hormone analogs, sclerostin inhibitors, and receptor activator of NF-κB ligand inhibitors. Using data from several clinical trials, we calibrate and validate the model, demonstrating its predictive capacity for complex medication scenarios, including sequential and parallel drug combinations. Via simulations, we reveal that there is a large potential to improve gains in bone mineral density by exploiting synergistic interactions between different drug classes, without increasing the total amount of drug administered.

    1. Computational and Systems Biology
    Zhuang Liu et al.
    Research Article

    MicroRNAs (miR), as important epigenetic control factors, reportedly regulate wound repair. However, our insufficient knowledge of clinically relevant miRs hinders their potential therapeutic use. For this, we performed paired small RNA and long RNA sequencing and integrative omics analysis in human tissue samples, including matched skin and acute wounds collected at each healing stage and chronic non-healing venous ulcers (VU). On the basis of the findings, we developed a compendium (https://www.xulandenlab.com/humanwounds-mirna-mrna), which will be an open, comprehensive resource to broadly aid wound healing research. With this first clinical, wound-centric resource of miRs and mRNAs, we identified 17 pathologically relevant miRs that exhibited abnormal VU expression and displayed their targets enriched explicitly in the VU gene signature. Intermeshing regulatory networks controlled by these miRs revealed their high cooperativity in contributing to chronic wound pathology characterized by persistent inflammation and proliferative phase initiation failure. Furthermore, we demonstrated that miR-34a, miR-424, and miR-516, upregulated in VU, cooperatively suppressed keratinocyte migration and growth while promoting inflammatory response. By combining miR expression patterns with their specific target gene expression context, we identified miRs highly relevant to VU pathology. Our study opens the possibility of developing innovative wound treatment that targets pathologically relevant cooperating miRs to attain higher therapeutic efficacy and specificity.