Transcriptional profiles associated with coronary artery disease in type 2 diabetes mellitus

Abstract

Background: Coronary artery disease (CAD) is a common complication of Type 2 diabetes mellitus (T2DM). Understanding the pathogenesis of this complication is essential in both diagnosis and management. Thus, this study aimed to characterize the presence of CAD in T2DM using molecular markers and pathway analyses.

Methods: The study is a sex- and age-frequency matched case-control design comparing 23 unrelated adult Filipinos with T2DM-CAD to 23 controls (DM with CAD). Healthy controls served as a reference. Total RNA from peripheral blood mononuclear cells (PBMCs) underwent whole transcriptomic profiling using the Illumina HumanHT-12 v4.0 expression beadchip. Differential gene expression with gene ontogeny analyses was performed, with supporting correlational analyses using weighted correlation network analysis (WGCNA).

Results: The study observed that 458 genes were differentially expressed between T2DM with and without CAD (FDR<0.05). The 5 top genes the transcription factor 3 (TCF3), allograft inflammatory factor 1 (AIF1), nuclear factor, interleukin 3 regulated (NFIL3), paired immunoglobulin-like type 2 receptor alpha (PILRA), and cytoskeleton-associated protein 4 (CKAP4) with AUCs >89%. Pathway analyses show differences in innate immunity activity, which centers on the myelocytic (neutrophilic/monocytic) theme. SNP-module analyses point to a possible causal dysfunction in innate immunity that triggers the CAD injury in T2DM.

Conclusion: The study findings indicate the involvement of innate immunity in the development of T2DM-CAD, and potential immunity markers can reflect the occurrence of this injury. Further studies can verify the mechanistic hypothesis and use of the markers.

Keywords: coronary artery disease; differential gene expression; pathway analysis; transcriptomics; type 2 diabetes mellitus.

Figure 1

TCF3, AIF1, NFIL3, PILRA and CKAP4 are potential biomarkers for T2DM CAD. In T2DM with CAD, expression levels of TCF3 (A, F) were higher while that of AIF1 (B, G), NFIL3 (C, H), PILRA (D, I) and CKAP4 (E, J) were lower compared with T2DM without CAD and with healthy controls. TCF3 displayed the highest diagnostic potential with the largest ROC-AUC in differentiating diabetic individuals with and without CAD. Significant differences in gene expression were determined through Kruskal Wallis test with posthoc Dunn’s multiple comparisons test: ***p<0.001.

Figure 2

Differential expression of genes involved in immune processes in T2DM CAD. Comparison and gene enrichment of differentially expressed genes (FDR<0.05) common in DMCAD, DMNoCAD, and NoDMNoCAD conditions display potential association of immune system processes with diabetic CAD.

Figure 3

Gene modules correlated with T2DM CAD. T2DM CAD significantly correlates with reduced expression of the black and green modules and increased expression of the turquoise, blue, and purple modules. The black module is enriched for genes responsible for NK cell-mediated cytotoxicity, while the turquoise and blue module is enriched for immune system process-related genes. The purple module is enriched for oxygen transport-genes, while the green module is not enriched for any biological theme. The arrows point to the top modules of interest. Upper values in each box indicate Pearson correlation values (i.e., mean gene significance) while the lower values indicate the corresponding p-value; red shading indicates direct correlation; blue shading indicates inverse correlation).