Differential Expression Analyses on Human Aortic Tissue Reveal Novel Genes and Pathways Associated With Abdominal Aortic Aneurysm Onset and Progression

Abstract

Background: Abdominal aortic aneurysms (AAAs) are focal dilatations of the abdominal aorta that expand progressively, increasing their risk of rupture. Rupture of an AAA is associated with high mortality rates, but the mechanisms underlying the initiation, expansion, and rupture of AAAs are not yet fully understood. We aimed to characterize the pathophysiology of AAAs and identify new genes associated with AAA initiation and progression.

Methods and results: This study used RNA sequencing data on 140 samples, becoming the largest RNA sequencing data set for differential expression studies of AAAs. We performed differential expression analyses and analyses of differential splicing between dilated and nondilated aortic tissue samples, and between AAAs of different diameters. We identified 3002 differentially expressed genes between AAAs and controls that were independent of ischemic time, 1425 of which were new. Additionally, 8 genes (EXTL3, ZFR, DUSP8, DISP1, USP33, VPS37C, ZNF784, RFX1) were differentially expressed between AAAs of varying diameters and between AAAs and control samples. Finally, 7 genes (SPP1, FHL1, GNAS, MORF4L2, HMGN1, ARL1, RNASE4) with differential splicing patterns were also differentially expressed genes between AAAs and controls, suggesting that splicing differences in these genes may contribute to the observed expression changes and disease development.

Conclusions: This study identifies new genes and splicing patterns associated with AAAs and validates previous relevant pathways on AAAs. These findings contribute to the understanding of the complex mechanisms underlying AAAs and may provide potential targets to limit AAA progression and mortality risk.

Keywords: abdominal aortic aneurysm; allele‐specific expression; alternative splicing; differential expression; transcriptomics.

Figure 1. Study design flowchart.

AAA indicates abdominal aortic aneurysm; RNA‐seq, RNA sequencing; and TABS, Triple A Barcelona Study.

Figure 2. Differential gene expression and immune cells analyses in AAA.

Hierarchical clustering analysis results with all the DEGs between AAA and control samples (A) and after removing DEGs by ischemic time (B). The cluster name “Regulation of mononuclear cell proliferation” in 2A is an abbreviation for “Regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.” C, Comparison of the proportion of inflammatory cells between AAA and control samples, using CIBERSORTx. P values correspond to a t test comparing the proportions' means of each cell type between AAAs and controls. AAA indicates abdominal aortic aneurysm; CD, cluster of differentiation; DEGs, differentially expressed genes; MHC, major histocompatibility complex; and NK, natural killer.

Figure 3. Alternative splicing and differential gene expression analyses results.

A, Significant alternative splicing types identified between AAA and control samples. B, Venn diagram showing the overlap between DEGs in AAA and control samples, and genes with differential alternative splicing patterns in AAA and control samples. C, Venn diagram showing the overlap between DEGs in AAA and control samples, and DEGs by AAA diameter. DIAMTER, DEGs by AAA diameter; SPLICING, genes with differential alternative splicing patterns in AAA and control samples; and STATUS, DEGs between AAA and control samples. AAA indicates abdominal aortic aneurysm; DEGs, differentially expressed genes; and MHC, major histocompatibility complex.

Figure 4. Allelic specific expression results.

A, Results of principal component analysis clustering based on allele‐specific patterns between AAA and control samples. B, Hierarchical clustering analysis results with genes with different allele‐specific patterns between AAA and control samples. AAA indicates abdominal aortic aneurysm; Dim1, dimension 1; Dim2, dimension 2; and MHC, major histocompatibility complex.