title: Mutation Drivers of Immunological Responses to Cancer.
abstract: In cancer immunology, somatic missense mutations have been mostly studied with regard to their role in the generation of neoantigens. However, growing evidence suggests that mutations in certain genes, such as CASP8 or TP53, influence the immune response against a tumor by other mechanisms. Identifying these genes and mechanisms is important because, just as the identification of cancer driver genes led to the development of personalized cancer therapies, a comprehensive catalog of such cancer immunity drivers will aid in the development of therapies aimed at restoring antitumor immunity. Here, we present an algorithm, domainXplorer, that can be used to identify potential cancer immunity drivers. To demonstrate its potential, we used it to analyze a dataset of 5,164 tumor samples from The Cancer Genome Atlas (TCGA) and to identify protein domains in which mutation status correlates with the presence of immune cells in cancer tissue (immune infiltrate). We identified 122 such protein regions, including several that belong to proteins with known roles in immune response, such as C2, CD163L1, or FCγR2A. In several cases, we show that mutations within the same protein can be associated with more or less immune cell infiltration, depending on the specific domain mutated. These results expand the catalog of potential cancer immunity drivers and highlight the importance of taking into account the structural context of somatic mutations when analyzing their potential association with immune phenotypes. Cancer Immunol Res; 4(9); 789-98. ©2016 AACR.
authors.affiliation: Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.
authors.forename: Eduard
authors.initials: E
authors.lastname: Porta-Pardo
authors.affiliation: Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. adam@godziklab.org.
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
mesh_terms: D000951:Antigens, Neoplasm / Q000276:immunology; D015415:Biomarkers; D015820:Cadherins / Q000737:chemistry / Q000378:metabolism; D003165:Complement System Proteins / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D006801:Humans; D056747:Immunomodulation / Q000235:genetics*; D008958:Models, Molecular; D009154:Mutation; D009369:Neoplasms / Q000235:genetics* / Q000276:immunology* / Q000378:metabolism; D010641:Phenotype; D011485:Protein Binding; D040901:Proteomics; D013329:Structure-Activity Relationship; D051176:beta Catenin / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism
chemical_list: D000951:Antigens, Neoplasm; D015415:Biomarkers; C495270:CTNNB1 protein, human; D015820:Cadherins; D051176:beta Catenin; C086960:osteoblast cadherin; D003165:Complement System Proteins