SETDB1 overexpression sets an intertumoral transcriptomic divergence in non-small cell lung carcinoma

Abstract

An increasing volume of evidence suggests that SETDB1 plays a role in the tumorigenesis of various cancers, classifying SETDB1 as an oncoprotein. However, owing to its numerous protein partners and their global-scale effects, the molecular mechanism underlying SETDB1-involved oncogenesis remains ambiguous. In this study, using public transcriptome data of lung adenocarcinoma (ADC) and squamous-cell carcinoma (SCC), we compared tumors with high-level SETDB1 (SH) and those with low-level SETDB1 (comparable with normal samples; SL). The results of principal component analysis revealed a transcriptomic distinction and divergence between the SH and SL samples in both ADCs and SCCs. The results of gene set enrichment analysis indicated that genes involved in the "epithelial-mesenchymal transition," "innate immune response," and "autoimmunity" collections were significantly depleted in SH tumors, whereas those involved in "RNA interference" collections were enriched. Chromatin-modifying genes were highly expressed in SH tumors, and the variance in their expression was incomparably high in SCC-SH, which suggested greater heterogeneity within SCC tumors. DNA methyltransferase genes were also overrepresented in SH samples, and most differentially methylated CpGs (SH/SL) were undermethylated in a highly biased manner in ADCs. We identified interesting molecular signatures associated with the possible roles of SETDB1 in lung cancer. We expect these SETDB1-associated molecular signatures to facilitate the development of biologically relevant targeted therapies for particular types of lung cancer.