The Cancer Genome Atlas (TCGA) is primarily oriented towards revealing the status of cancer cells but TCGA RNASeq data have the potential of representing gene expression for a variety of cells that are included during RNA preparation, i.e., cells that cannot be removed from the microenvironment during cancer sample isolation.
Researchers at the University of South Florida sought to determine whether RNASeq data can be used to pioneer greater precision for immunoscoring. They obtained the RNASeq results for HLA class II genes, the class II transactivator (CIITA) and T-cell receptor (TCR) alpha segments. The data indicated strong degrees of correlation of HLA class II expression with TCR expression. Furthermore, biomarkers of professional antigen-presenting cells also correlated with TCR expression, with the kidney renal papillary cell carcinoma (KIRP) dataset indicative of the highest level, immune function microenvironment. These analyses indicate that an immune function signature, with probable internal HLA class II-TCR verifications, can be obtained from individual TCGA samples; this in turn indicates that such signatures might provide a basis for correlations with prognosis or for convenient indications of therapy options, such as tumor-infiltrating lymphocyte availability for ex-vivo amplification. Although tumor immunoscoring has been proposed, the above analysis represents the first immunoscoring approach that correlates antigen presentation capacity with TCR mRNA expression.
a HLA-DRA and HLA-DRB RNA expression levels for 30 KRIP samples (see also: SOM Butler Table 1 DRA DRB). Note, in particular, that each vertical bar of the HLA-DRA histogram represents a single TCGA sample and corresponds to the vertical bar representing the same sample immediately below in the HLA-DRB histogram. The y-axis numbers represent TCGA designations for level of RNA, as indicated in: SOM Butler Table 1 DRA DRB. b Linear regression plot for data in a