Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs

Significant alterations in signaling pathways and transcriptional regulatory programs together represent major hallmarks of many cancers. These, among all, include the reactivation of stemness, which is registered by the expression of pathways that are active in the embryonic stem cells (ESCs). Here, we assembled gene sets that reflect the stemness and proliferation signatures and used them to analyze a large panel of RNA-seq data from The Cancer Genome Atlas (TCGA) Consortium in order to specifically assess the expression of stemness-related and proliferation-related genes across a collection of different tumor types. We introduced a metric that captures the collective similarity of the expression profile of a tumor to that of ESCs, which showed that stemness and proliferation signatures vary greatly between different tumor types. We also observed a high degree of intertumoral heterogeneity in the expression of stemness- and proliferation-related genes, which was associated with increased hazard ratios in a fraction of tumors and mirrored by high intratumoral heterogeneity across cancer cells in single cell RNA-seq datasets. Taken together, these results indicate that the expression of stemness signatures is highly heterogeneous and cannot be used as a universal determinant of cancer. This calls into question the universal validity of diagnostic tests that are based on stem cell markers. Author summaryCancer is a deadly human disease which is characterized by uncontrolled proliferation of abnormal cells. Stemness, or the expression of stem cell markers, has been identified as a key feature for cancer progression and in many cases correlates with patient survival. In this work, we reanalyzed a large cohort of cancers from TCGA (The Cancer Genome Atlas) collection and single-cell cancer data, and found that the degree of stemness reactivation varies greatly between different tumor types, between different tumors of the same type, and also different cells within a tumor. The observed stemness heterogeneity implies that the expression of stemness markers cannot be used as a universal determinant of cancer and calls into question the validity of stemness-based tests that are frequently used for cancer diagnostics.