Impact of Tumor Purity on Immune Gene Expression and Clustering Analyses across Multiple Cancer Types

Abstract

Surgical archives of tumor specimens are often impure. The presence of RNA transcripts from nontumor cells, such as immune and stromal cells, can impede analyses of cancer expression profiles. To systematically analyze the impact of tumor purity, the gene expression profiles and tumor purities were obtained for 7,794 tumor specimens across 21 tumor types (available in The Cancer Genome Atlas consortium). First, we observed that genes with roles in immunity and oxidative phosphorylation were significantly inversely correlated and correlated with the tumor purity, respectively. The expression of genes implicated in immunotherapy and specific immune cell genes, along with the abundance of immune cell infiltrates, was substantially inversely correlated with tumor purity. This relationship may explain the correlation between immune gene expression and mutation burden, highlighting the need to account for tumor purity in the evaluation of expression markers obtained from bulk tumor transcriptome data. Second, examination of cluster membership of gene pairs, with or without controlling for tumor purity, revealed that tumor purity may have a substantial impact on gene clustering across tumor types. Third, feature genes for molecular taxonomy were analyzed for correlation with tumor purity, and for some tumor types, feature genes representing the mesenchymal and classical subtypes were inversely correlated and correlated with tumor purity, respectively. Our findings indicate that tumor purity is an important confounder in evaluating the correlation between gene expression and clinicopathologic features such as mutation burden, as well as gene clustering and molecular taxonomy. .

Tumour purity as a prognostic factor in colon cancer

“…To explore the underlying mechanism of purity’s prognostic value, we performed differential expression analysis on TCGA RNA-Seq data between low and high purity groups divided by median purity. Notably, the expression level of immunotherapy-associated markers (PD-1, PD-L1, CTLA-4, LAG-3, and TIM-3) was inversely correlated with tumour purity in all three datasets (Figure 4, Figure S8, and Figure S9), which was similar to a previous pan-cancer analysis (26). Genes with FDR < 0.05 in differential expression analysis were further accessed using GSEA.…”

Chemokine receptor 4 expression is correlated with the occurrence and prognosis of gastric cancer

“…Tumor purity is another aspect that has been thoroughly investigated in recent years. Many studies showed that tumor purity could become an important parameter in tumor research [18,41]. By calculating the tumor purity in our cohorts, we observed that in the CXCR4‐H group, the tumor stromal score and the immune score were higher than in the CXCR4‐L group, while the tumor purity was lower than that in the CXCR4‐L group.…”

“…In recent years, researchers have focused their attention on different cancer parameters, including immune infiltration, tumor mutation burden (TMB), somatic copy number alterations (SCNA), tumor purity, cytolytic activity (CYT), and drug sensitivity [15–20]. These parameters have all been reported to be prognostic factors and potential therapeutic markers for various cancers.…”

Correlation-based and feature-driven mutation signature analyses to identify genetic features associated with DNA mutagenic processes in cancer genomes

“…For the latter, the correlating features can be taken into account in TMB-centric correlative analysis. An example of this being the assessment of clinical benefits for immunotherapy in cases with high TMB, as we have recently demonstrated that tumor purity was a confounding factor for cancer genome analyses [19]. Some mechanistic insights can be inferred from the correlation results, e.g., the overall positive correlation between TMB and the level of aneuploidy may indicate that chromosome-(ploidy and aneuploidy levels) and mutation-level instability (TMB) are related to each other in cancer genomes.…”

“…First, we observed that the log-transformed TMB was inversely correlated with tumor purity (r = -0.118; Figs 1A and 1B). We previously showed that tumor purity represents a surrogate marker for the level of tumor-infiltrating immune cells, including cytotoxic T cells [19], and the observed purity-TMB relationship may reflect an association between the level of tumor-infiltrating immune cells and TMB. We also observed that TMB was positively correlated with the level of aneuploidy, i.e., TMB was correlated with tumor ploidy (r = 0.161; Figs 1C and 1D) and also with the number of dosageimbalanced copy number segments (r = 0.291; Figs.…”