Transcriptomic Context of RUNX3 Expression in Monocytes: A Cross-Sectional Analysis

Abstract

The runt-related transcription factor 3 (RUNX3) regulates the differentiation of monocytes and their response to inflammation. However, the transcriptomic context of RUNX3 expression in blood monocytes remains poorly understood. We aim to learn about RUNX3 from its relationships within transcriptomes of bulk CD14+ cells in adults. This study used immunomagnetically sorted CD14+ cell gene expression microarray data from the Multi-Ethnic Study of Atherosclerosis (MESA, n = 1202, GSE56047) and the Correlated Expression and Disease Association Research (CEDAR, n = 281, E-MTAB-6667) cohorts. The data were preprocessed, subjected to RUNX3-focused correlation analyses and random forest modeling, followed by the gene ontology analysis. Immunity-focused differential ratio analysis with intermediary inference (DRAIMI) was used to integrate the data with protein–protein interaction network. Correlation analysis of RUNX3 expression revealed the strongest positive association for EVL (rmean = 0.75, pFDR-MESA = 5.37 × 10−140, pFDR-CEDAR = 5.52 × 10−80), ARHGAP17 (rmean = 0.74, pFDR-MESA = 1.13 × 10−169, pFDR-CEDAR = 9.20 × 10−59), DNMT1 (rmean = 0.74, pFDR-MESA = 1.10 × 10−169, pFDR-CEDAR = 1.67 × 10−58), and CLEC16A (rmean = 0.72, pFDR-MESA = 3.51 × 10−154, pFDR-CEDAR = 2.27 × 10−55), while the top negative correlates were C2ORF76 (rmean = −0.57, pFDR-MESA = 8.70 × 10−94, pFDR-CEDAR = 1.31 × 10−25) and TBC1D7 (rmean = −0.55, pFDR-MESA = 1.36 × 10−69, pFDR-CEDAR = 7.81 × 10−30). The RUNX3-associated transcriptome signature was involved in mRNA metabolism, signal transduction, and the organization of cytoskeleton, chromosomes, and chromatin, which may all accompany mitosis. Transcriptomic context of RUNX3 expression in monocytes hints at its relationship with cell growth, shape maintenance, and aspects of the immune response, including tyrosine kinases.