title: Gene expression markers of Tumor Infiltrating Leukocytes.
abstract: Assays of the abundance of immune cell populations in the tumor microenvironment promise to inform immune oncology research and the choice of immunotherapy for individual patients. We propose to measure the intratumoral abundance of various immune cell populations with gene expression. In contrast to IHC and flow cytometry, gene expression assays yield high information content from a clinically practical workflow. Previous studies of gene expression in purified immune cells have reported hundreds of genes showing enrichment in a single cell type, but the utility of these genes in tumor samples is unknown. We use co-expression patterns in large tumor gene expression datasets to evaluate previously reported candidate cell type marker genes lists, eliminate numerous false positives and identify a subset of high confidence marker genes.
  
  
  
  Using a novel statistical tool, we use co-expression patterns in 9986 samples from The Cancer Genome Atlas (TCGA) to evaluate previously reported cell type marker genes. We compare immune cell scores derived from these genes to measurements from flow cytometry and immunohistochemistry. We characterize the reproducibility of our cell scores in replicate runs of RNA extracted from FFPE tumor tissue.
  
  
  
  We identify a list of 60 marker genes whose expression levels measure 14 immune cell populations. Cell type scores calculated from these genes are concordant with flow cytometry and IHC readings, show high reproducibility in replicate RNA samples from FFPE tissue and enable detailed analyses of the anti-tumor immune response in TCGA. In an immunotherapy dataset, they separate responders and non-responders early on therapy and provide an intricate picture of the effects of checkpoint inhibition. Most genes previously reported to be enriched in a single cell type have co-expression patterns inconsistent with cell type specificity.
  
  
  
  Due to their concise gene set, computational simplicity and utility in tumor samples, these cell type gene signatures may be useful in future discovery research and clinical trials to understand how tumors and therapeutic intervention shape the immune response.
authors.affiliation: NanoString Technologies, Inc., 530 Fairview Ave N, Seattle, WA 98109 USA.
authors.forename: Patrick
authors.identifier: 0000-0002-2844-5883
authors.initials: P
authors.lastname: Danaher
authors.affiliation: NanoString Technologies, Inc., 530 Fairview Ave N, Seattle, WA 98109 USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Warren
authors.affiliation: NanoString Technologies, Inc., 530 Fairview Ave N, Seattle, WA 98109 USA.
authors.forename: Lucas
authors.initials: L
authors.lastname: Dennis
authors.affiliation: Tumor Vaccine Group, University of Washington, 850 Republican Street, Box 358050, Seattle, WA 98109 USA.
authors.forename: Leonard
authors.initials: L
authors.lastname: D'Amico
authors.affiliation: NanoString Technologies, Inc., 530 Fairview Ave N, Seattle, WA 98109 USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: White
authors.affiliation: Department of Medicine, Division of Oncology, University of Washington, 825 Eastlake Ave E., Seattle, WA 98109-1023 USA.
authors.forename: Mary L
authors.initials: ML
authors.lastname: Disis
authors.affiliation: Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Mayo Building, 420 Delaware St SE, Minneapolis, MN 55455 USA.
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Geller
authors.affiliation: Department of Gynecologic Oncology and Center for Immunotherapy, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263 USA.
authors.forename: Kunle
authors.initials: K
authors.lastname: Odunsi
authors.affiliation: NanoString Technologies, Inc., 530 Fairview Ave N, Seattle, WA 98109 USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Beechem
authors.affiliation: Tumor Vaccine Group, University of Washington, 850 Republican Street, Box 358050, Seattle, WA 98109 USA.
authors.forename: Steven P
authors.initials: SP
authors.lastname: Fling
mesh_terms: D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D016246:Lymphocytes, Tumor-Infiltrating / Q000378:metabolism*; D009369:Neoplasms / Q000235:genetics*
keywords: Cell types; Gene expression; Immunotherapies; TILs; Tumor infiltrating lymphocytes