Transcriptional profiling of the ductus arteriosus: Comparison of rodent microarrays and human RNA sequencing

Abstract

DA closure is crucial for the transition from fetal to neonatal life. This closure is supported by changes to the DA's signaling and structural properties that distinguish it from neighboring vessels. Examining transcriptional differences between these vessels is key to identifying genes or pathways responsible for DA closure. Several microarray studies have explored the DA transcriptome in animal models but varied experimental designs have led to conflicting results. Thorough transcriptomic analysis of the human DA has yet to be performed. A clear picture of the DA transcriptome is key to guiding future research endeavors, both to allow more targeted treatments in the clinical setting, and to understand the basic biology of DA function. In this review, we use a cross-species cross-platform analysis to consider all available published rodent microarray data and novel human RNAseq data in order to provide high priority candidate genes for consideration in future DA studies.

Keywords: Aorta; Ductus arteriosus; Microarray; PDA; RNA-seq; Transcriptional profiling.

Figure 1. Venn diagram of compared rodent microarray studies

Darkly shaded areas represent 444 DEGs (p-value ≤ 0.05, fold change ≥ 1.2) identified by at least 3 of 4 studies. Of these, 168 genes had conflicting direction of expression and were excluded from further analysis. Of the remaining 276 genes, 87 were consistently increased, while 189 were consistently decreased in DA versus aorta (genes are listed in Tables S1 and S2, respectively).

Figure 2. Dendogram of Human RNA-seq samples

Heat map analysis of RNA-seq data showing separation of samples by vessel identity. Gene identities are specified in Tables S4, S5.

Figure 3. Volcano plot of RNA-seq differentially expressed genes

With p-value 0.05 and fold change >2, 2082 genes showed differential expression in the human DA compared to aorta: 1027 up-regulated, and 1055 down-regulated. Of these, 186 genes had an FDR (Benjamini-Hochberg) of 0.10 or less: 118 up-regulated, and 68 down-regulated (genes are listed in Tables S4 and S5, respectively).

Figure 4. Venn diagram of DA vs. Ao genes common between Microarray and RNA-seq analyses

11 genes were identified as differentially expressed between DA and aorta in both the human RNA-seq and the rodent microarray comparison. 186 genes from RNA-seq are listed in Tables S4, S5; 276 genes from microarray comparisons are listed in Tables S1, S2.

Figure 5. ‘Tornadogram’ showing top 30 UniProt (UP) Keywords common between Microarray and RNA-seq analyses

Genes differentially expressed in DA vs. Ao were categorized by UP Keywords (DAVID), plotted by p-value, and compared across platforms. Number of genes represented in each category shown at the end of bars.