1. Cancer Biology
  2. Computational and Systems Biology
Download icon

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

  1. Julien Racle
  2. Kaat de Jonge
  3. Petra Baumgaertner
  4. Daniel E Speiser
  5. David Gfeller Is a corresponding author
  1. University of Lausanne, Switzerland
  2. Lausanne University Hospital, Switzerland
Tools and Resources
Cited
0
Views
398
Comments
0
Cite as: eLife 2017;6:e26476 doi: 10.7554/eLife.26476

Abstract

Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene expression data. Our method integrates novel gene expression profiles from each major non-malignant cell type found in tumors, renormalization based on cell-type specific mRNA content, and the ability to consider uncharacterized and possibly highly variable cell types. Feasibility is demonstrated by validation with flow cytometry, immunohistochemistry and single-cell RNA-Seq analyses of human melanoma and colorectal tumor specimens. Altogether, our work not only improves accuracy but also broadens the scope of absolute cell fraction predictions from tumor gene expression data, and provides a unique novel experimental benchmark for immunogenomics analyses in cancer research.

Article and author information

Author details

  1. Julien Racle

    Ludwig Centre for Cancer Research, Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon 0000-0002-0100-0323
  2. Kaat de Jonge

    Department of Fundamental Oncology, Lausanne University Hospital, Epalinges, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  3. Petra Baumgaertner

    Department of Fundamental Oncology, Lausanne University Hospital, Epalinges, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  4. Daniel E Speiser

    Department of Fundamental Oncology, Lausanne University Hospital, Epalinges, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  5. David Gfeller

    Ludwig Centre for Cancer Research, Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland
    For correspondence
    david.gfeller@unil.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon 0000-0002-3952-0930

Funding

Center for Advanced Modelling Science

  • Julien Racle
  • David Gfeller

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Project grant 31003A_173156)

  • Julien Racle
  • David Gfeller

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

Ethics

Human subjects: Patients involved in this study agreed to donate metastatic tissues upon informed consent, based on dedicated clinical investigation protocols established according to the relevant regulatory standards. The protocols were approved by the local IRB, i.e. the Commission cantonale d'éthique de la recherche sur l'être humain du Canton de Vaud.

Reviewing Editor

  1. Alfonso Valencia, Reviewing Editor, Barcelona Supercomputing Center - BSC, Spain

Publication history

  1. Received: March 2, 2017
  2. Accepted: November 10, 2017
  3. Accepted Manuscript published: November 13, 2017 (version 1)

Copyright

© 2017, Racle 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

  • 398
    Page views
  • 96
    Downloads
  • 0
    Citations

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

Comments

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)

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

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