Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis

Abstract

Background: Ulcerative colitis (UC) is a disorder with unknown etiology, and animal models play an essential role in studying its molecular pathophysiology. Here, we aim to identify common conserved pathological UC-related gene expression signatures between humans and mice that can be used as treatment targets and/or biomarker candidates. Methods: To identify differentially regulated protein-coding genes and non-coding RNAs, we sequenced total RNA from the colon and blood of the most widely used dextran sodium sulfate Ulcerative colitis mouse. By combining this with public human Ulcerative colitis data, we investigated conserved gene expression signatures and pathways/biological processes through which these genes may contribute to disease development/progression. Results: Cross-species integration of human and mouse Ulcerative colitis data resulted in the identification of 1442 genes that were significantly differentially regulated in the same direction in the colon and 157 in blood. Of these, 51 genes showed consistent differential regulation in the colon and blood. Less known genes with importance in disease pathogenesis, including SPI1, FPR2, TYROBP, CKAP4, MCEMP1, ADGRG3, SLC11A1, and SELPLG, were identified through network centrality ranking and validated in independent human and mouse cohorts. Conclusion: The identified Ulcerative colitis conserved transcriptional signatures aid in the disease phenotyping and future treatment decisions, drug discovery, and clinical trial design.

Keywords: biomarkers; coding RNAs; conserved expression signature; non-coding RNAs; ulcerative colitis.

FIGURE 1

DSS-UC mouse transcriptional signature. Heatmaps of SDE PCGs, lncRNAs, and miRNAs, based on z-scores of normalized log counts for (A) colon and (C) blood. Volcano plots log2FC ratio on the x-axis versus -log10 padj on the y axis for colon (B) and blood (D). (UC, n = 3 and CO, n = 3).

FIGURE 2

Commonly dysregulated SDE genes in UC mouse colon and blood. (A) Venn diagram of the SDE genes overlap between colon and blood; Other RNAs include pseudogenes, TEC, snoRNA, miscRNA, etc. Contra-regulated genes are commonly SDE genes in both tissues, which are regulated in opposite directions (B) MA Plot showing the relationships between log₂FC in colon and blood for each of the common SDE genes; y-axis indicates whether the gene has a higher FC in colon or blood, x-axis reflects the cumulative FCs magnitude in colon and blood. Genes labeled as an outlier in each tissue were removed from the plot. (C) Top 15 enriched KEGG pathways and (D) Top 15 enriched GO biological processes for the common SDE genes between mouse blood and colon. Gene ratio corresponds to the ratio between the number of common SDE and all expressed genes in the pathway. The dot size indicates the number of SDE genes (gene counts), while the color represents the enrichment significance as given by the FDR adjusted p-values.

FIGURE 3

Comparison between SDE genes of human and mouse UC. (A) Gene overlap diagram between human combined sets and mouse colon and blood SDE genes with padj ≤ 0.05. The total number of genes in the sets and orthologous genes (in parenthesis) is shown. (B) Top 15 enriched KEGG pathways for the common SDE genes between human, mouse colon, and blood. Gene ratio corresponds to the ratio between the number of common SDE genes in mouse-human and all human genes in the pathway. The dot size indicates the SDE gene number (gene counts), while the color represents the enrichment significance given by the FDR adjusted p-values. (C) Differential gene expression visualization on the STRING network of genes shared between mouse (inner node circle) and human (outer node circle) in the blood (left node half) and colon (right node half). log2FC values are shown with a blue-white-red gradient, and dark grey color indicates missing values. The size of the nodes corresponds to their network importance as measured by a combination of degree, closeness, and betweenness centrality. (D) To validate the expression level of a few selected genes common in the colon and blood of human and mouse UC, qRT-PCR was performed. S100A8 and S100A9 were used as positive inflammatory controls.