A survey on cellular RNA editing activity in response to Candida albicans infections

Abstract

Background: Adenosine-to-Inosine (A-to-I) RNA editing is catalyzed by the adenosine deaminase acting on RNA (ADAR) family of enzymes, which induces alterations in mRNA sequence. It has been shown that A-to-I RNA editing events are of significance in the cell's innate immunity and cellular response to viral infections. However, whether RNA editing plays a role in cellular response to microorganism/fungi infection has not been determined. Candida albicans, one of the most prevalent human pathogenic fungi, usually act as a commensal on skin and superficial mucosal, but has been found to cause candidiasis in immunosuppression patients. Previously, we have revealed the up-regulation of A-to-I RNA editing activity in response to different types of influenza virus infections. The current work is designed to study the effect of microorganism/fungi infection on the activity of A-to-I RNA editing in infected hosts.

Results: We first detected and characterized the A-to-I RNA editing events in oral epithelial cells (OKF6) and primary human umbilical vein endothelial cells (HUVEC), under normal growth condition or with C. albicans infection. Eighty nine thousand six hundred forty eight and 60,872 A-to-I editing sites were detected in normal OKF6 and HUVEC cells, respectively. They were validated against the RNA editing databases, DARNED, RADAR, and REDIportal with 50, 80, and 80% success rates, respectively. While over 95% editing sites were detected in Alu regions, among the rest of the editing sites in non repetitive regions, the majority was located in introns and UTRs. The distributions of A-to-I editing activity and editing depth were analyzed during the course of C. albicans infection. While the normalized editing levels of common editing sites exhibited a significant increase, especially in Alu regions, no significant change in the expression of ADAR1 or ADAR2 was observed. Second, we performed further analysis on data from in vivo mouse study with C. albicans infection. One thousand one hundred thirty three and 955 A-to-I editing sites were identified in mouse tongue and kidney tissues, respectively. The number of A-to-I editing events was much smaller than in human epithelial or endothelial cells, due to the lack of Alu elements in mouse genome. Furthermore, during the course of C. albicans infection we observed stable level of A-to-I editing activity in 131 and 190 common editing sites in the mouse tongue and kidney tissues, and found no significant change in ADAR1 or ADAR2 expression (with the exception of ADAR2 displaying a significant increase at 12 h after infection in mouse kidney tissue before returning to normal).

Conclusions: This work represents the first comprehensive analysis of A-to-I RNA editome in human epithelial and endothelial cells. C. albicans infection of human epithelial and endothelial cells led to the up-regulation of A-to-I editing activities, through a mechanism different from that of viral infections in human hosts. However, the in vivo mouse model with C. albicans infection did not show significant changes in A-to-I editing activities in tongue and kidney tissues. The different results in the mouse model were likely due to the presence of more complex in vivo environments, e.g. circulation and mixed cell types.

Keywords: A-to-I RNA-editing; ADAR; Candida albicans; Fungi-host interaction; Infection.

Fig. 1

Characterization of A-to-I RNA-editing events in human epithelial and endothelial cells. a Overview of 12 types of mismatches identified in epithelial and endothelial cells. b Distribution of epithelial and endothelial RNA editing sites in Alu, non repetitive (Nonre), repetitive non Alu (Renonalu) region (left panel) and genomic distribution of RNA editing sites in none repetitive region (right panel). 3’UTR, three prime untranslated region. 5’UTR, five prime untranslated region. CDS, coding DNA sequence. c The pattern of the 15 flanking bases around editing sites in epithelial and endothelial cell. d Comparison between the RNA editing sites of epithelial and endothelial cells

Fig. 2

Pattern of RNA editing during the course of infection in epithelial and endothelial cells. a Distribution of editing level in different infection conditions. b Distribution of editing level in stable expression genes. c Distribution of editing level in significant differential expression genes. d Pattern of ADAR genes expression and the normalized editing level of common editing site

Fig. 3

Charactrization of RNA-editing sites of mouse tissues. a Overlap of RNA-editing sites between mouse tongue and kidney. b Distribution of RNA-editing sites in mouse genomic regions. c Pattern of the 15 flanking bases of RNA-editing sites in mouse tongue and kidney tissues

Fig. 4

Pattern of RNA editing sites in mouse tissues. a Distribution of editing level in mouse tongue and kidney tissues. b Pattern of editing level in stable expression genes. c Pattern of editing level in differentially expression genes. d Pattern of ADAR genes expression and normalized editing level of common editing sites