Analysis of mutually exclusive expression in cancer cells identifies a previously unknown intergenic regulatory paradigm

Abstract

Mutual exclusion of gene expression has received limited attention. Gene (expression) plasticity analysis provides an efficient way to identify highly plastic genes (HPGs) based on changes in expression rank. In this study, we quantitatively measured the expression plasticity of 19 961 protein-coding genes in 24 human cancer cell lines and identified HPGs in these cells. By comparing methods, we showed that virtual sorting and cosine similarity, rather than Pearson and Spearman rank correlations, are suitable for mutual exclusion. Mutually exclusive gene pairs were identified in each cell type. Experimental validation showed that thiol methyltransferase 1B (TMT1B; also known as METTL7B) and CD274 molecule (CD274; also known as PD-L1) were mutually exclusively expressed at either the mRNA or protein level. METTL7B negatively regulated PD-L1 expression in several cell types, and the JAK/STAT3 pathway was involved. Knockdown of METTL7B in Huh7 cells inhibited interleukin 2 (IL-2) secretion by Jurkat cells in co-culture experiments, and the inhibition was blocked by anti-PD-L1 antibodies. Therefore, this study provides an efficient method of expressional mutual exclusion and implies a newly identified intergenic regulatory paradigm.