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Profiling Tumor Infiltrating Immune Cells with CIBERSORT

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Cancer Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1711))

Abstract

Tumor infiltrating leukocytes (TILs) are an integral component of the tumor microenvironment and have been found to correlate with prognosis and response to therapy. Methods to enumerate immune subsets such as immunohistochemistry or flow cytometry suffer from limitations in phenotypic markers and can be challenging to practically implement and standardize. An alternative approach is to acquire aggregative high dimensional data from cellular mixtures and to subsequently infer the cellular components computationally. We recently described CIBERSORT, a versatile computational method for quantifying cell fractions from bulk tissue gene expression profiles (GEPs). Combining support vector regression with prior knowledge of expression profiles from purified leukocyte subsets, CIBERSORT can accurately estimate the immune composition of a tumor biopsy. In this chapter, we provide a primer on the CIBERSORT method and illustrate its use for characterizing TILs in tumor samples profiled by microarray or RNA-Seq.

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Acknowledgments

We would like to thank David Steiner, M.D., Ph.D. for his assistance in generating the RNA-Seq derived signature matrix. This work is supported by grants from the Doris Duke Charitable Foundation (A.A.A.), the Damon Runyon Cancer Research Foundation (A.A.A.), the B&J Cardan Oncology Research Fund (A.A.A.), the Ludwig Institute for Cancer Research (A.A.A.), NIH grant 1K99CA187192-01A1 (A.M.N.), NIH grant PHS NRSA 5T32 CA09302-35 (A.M.N.), US Department of Defense grant W81XWH-12-1-0498 (A.M.N.), a grant from the Siebel Stem Cell Institute and the Thomas and Stacey Siebel Foundation (A.M.N.), an NIH/Stanford MSTP training grant (B.C.), and a PD Soros Fellowship (B.C.).

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Authors and Affiliations

  1. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA

    Binbin Chen

  2. Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, 875 Blake Wilbur Drive, Stanford, CA, 94305, USA

    Michael S. Khodadoust, Chih Long Liu, Aaron M. Newman & Ash A. Alizadeh

  3. Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA

    Michael S. Khodadoust & Ash A. Alizadeh

  4. Stanford Cancer Institute, Stanford University, Stanford, CA, USA

    Michael S. Khodadoust & Ash A. Alizadeh

  5. Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA

    Aaron M. Newman & Ash A. Alizadeh

Authors
  1. Binbin Chen
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  2. Michael S. Khodadoust
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  3. Chih Long Liu
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  4. Aaron M. Newman
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  5. Ash A. Alizadeh
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Corresponding authors

Correspondence to Aaron M. Newman or Ash A. Alizadeh .

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Editors and Affiliations

  1. NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

    Louise von Stechow

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Chen, B., Khodadoust, M.S., Liu, C.L., Newman, A.M., Alizadeh, A.A. (2018). Profiling Tumor Infiltrating Immune Cells with CIBERSORT. In: von Stechow, L. (eds) Cancer Systems Biology. Methods in Molecular Biology, vol 1711. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7493-1_12

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  • DOI: https://doi.org/10.1007/978-1-4939-7493-1_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7492-4

  • Online ISBN: 978-1-4939-7493-1

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