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      Profiling tumor infiltrating immune cells with CIBERSORT

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          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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          Author and article information

          Journal
          9214969
          2488
          Methods Mol Biol
          Methods Mol. Biol.
          Methods in molecular biology (Clifton, N.J.)
          1064-3745
          1940-6029
          29 March 2018
          2018
          01 January 2019
          : 1711
          : 243-259
          Affiliations
          [1 ]Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
          [2 ]Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
          [3 ]Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
          [4 ]Stanford Cancer Institute, Stanford University, Stanford, CA, USA
          [5 ]Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
          Author notes
          [# ]Co-corresponding authors: amnewman@ 123456stanford.edu (A.M.N.), arasha@ 123456stanford.edu (A.A.A.)
          Article
          PMC5895181 PMC5895181 5895181 nihpa954292
          10.1007/978-1-4939-7493-1_12
          5895181
          29344893
          a76e1020-de83-482e-9031-dbc08692b3b1
          History
          Categories
          Article

          TCGA,Cancer immunology,Deconvolution,Support vector regression (SVR),Tumor infiltrating leukocytes,RNA-Seq,Microarray,Gene expression,Tumor heterogeneity,Tumor microenvironment,TILs

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