Hippocampal adenosine-to-inosine RNA editing in sepsis: dynamic changes and influencing factors

Abstract

Sepsis-associated encephalopathy is a diffuse brain dysfunction secondary to infection. It has been established that factors such as age and sex can significantly contribute to the development of sepsis-associated encephalopathy. Our recent study implicated a possible link between adenosine-to-inosine RNA editing and sepsis-associated encephalopathy, yet the dynamics of adenosine-to-inosine RNA editing during sepsis-associated encephalopathy and how it could be influenced by factors such as age, sex and antidepressants remain uninvestigated. Our current study analysed and validated transcriptome-wide changes in adenosine-to-inosine RNA editing in the hippocampus of different septic mouse models. Seventy-four sites in 64 genes showed significant differential RNA editing over time in septic mice induced by caecal ligation and perforation. The differential RNA editing might contribute to the RNA expression regulation of the edited genes, with 42.2% differentially expressed. These differentially edited genes, especially those with missense editing, such as glutamate receptor, ionotropic, kainate 2 (Grik2, p.M620V), filamin A (Flna, p.S2331G) and capicua transcriptional repressor (Cic, p.E2270G), were mainly involved in abnormal social behaviour and neurodevelopmental and psychiatric disorders. Significant effects of age and sex were also observed on sepsis-associated RNA editing. Further comparison highlighted 40 common differential RNA editing sites that caecal ligation and perforation-induced and lipopolysaccharide-induced septic mouse models shared. Interestingly, these findings demonstrate temporal dynamics of adenosine-to-inosine RNA editing in the mouse hippocampus during sepsis, add to the understanding of age and sex differences in the disease and underscore the role of the epigenetic process in sepsis-associated encephalopathy.

Keywords: RNA editing; age; hippocampus; sepsis-associated encephalopathy; sex.

Graphical Abstract

Figure 1

Epitranscriptomic analysis of hippocampal A-to-I RNA editing in septic and control mice in the current study. (A) Manhattan and density plot showing the distribution of the A-to-I RNA editing sites in the hippocampus of D1 and D4 sepsis groups and the control group (N = 16, respectively). Statistics of A-to-I RNA editing variants’ functional consequences (B) and overlapping repeats (C). Repeat types in the murine genome contain the SINE families of B1, B2, B3 and ID elements. Chr, chromosome.

Figure 2

Temporal dynamics of sepsis-associated A-to-I RNA editing in the mouse hippocampus. (A) The sample-wide average level of RNA editing among the control, D1 and D4 sepsis groups (N = 16, respectively). *P < 0.05. Overall and post hoc P-values are calculated using the ANOVA and Tukey tests. (B, C) The Pearson correlation analysis of RNA editing level with both the numbers of edited genes (B) and editing sites (C) in the hippocampal samples. (D) The functional categories of DRE sites. (E) PPI network of genes differentially edited in the hippocampus during sepsis. The network is constructed based on the STRING database. (F) Mammalian phenotypes enriched by the differentially edited genes. The enrichment analysis is conducted according to the Monarch database.

Figure 3

Missense sites showed DRE in the mouse hippocampus during CLP-induced sepsis. (A–E) Grik2 (p.M620V), Flna (p.S2331G), Mfn1 (p.I328V), Phka2 (p.S907G) and capicua transcriptional repressor (Cic, p.E2270G) A-to-I RNA editing level, respectively (N = 16, respectively). *P < 0.05; **P < 0.01. P-values are calculated using the GLM model and LRT.

Figure 4

Functional relevance of DRE A-to-I RNA editing in the mouse hippocampus. (A–D) The enrichment analysis results of biological processes (A), molecular functions (B), cellular components (C) and KEGG pathway (D) enriched by differentially edited genes are shown. (E) Wordcloud plot of RBPs with binding sites overlapped with SAE-associated DRE. GLM, generalized linear model; LRT, likelihood ratio test.

Figure 5

The age effect on sepsis-associated A-to-I RNA editing in the mouse hippocampus. (A) The age effect on the average level of A-to-I RNA editing among groups. The age-dependent RNA editing of Meg3:chr12:109546744 (B), Map3k7:chr4:32022582 (C) and Odf2:chr2:29925446 (D) are shown. The overall P-value is calculated using the GLM model and LRT with age (young or old, each containing three subgroups of control, D1 and D4, N = 8 for each subgroup) as a covariate. *P < 0.05; **P < 0.01. The post hoc analysis is conducted using the Tukey test. GLM, generalized linear model; LRT, likelihood ratio test.

Figure 6

Comparison of DRE among different data sets of septic mouse models induced by CLP and LPS. (A) Venn plot showing DRE sites shared by different mouse model data sets. (B, C) Manhattan and density plots showing the distribution of the DRE sites in the hippocampus of two LPS-induced mice models (B for data set PRJNA827615 and C for data set PRJNA894332). The vertical straight line indicates a P-value of 10⁻⁷, and points above the line are with P < 10⁻⁷.

Figure 7

Six sites with sepsis-associated RNA editing alterations are rescued by fullerenol pre-treatment in the hippocampus. There are three missense editing including (A) Flna p.S2331G, (B) Grik2 p.M620V and (C) Ptprn p.I783M and three 3′UTR editing including (D) Hspa4l c.*4873A>G, (E) Kif3c c.*1731A>G and (F) Spock2 c.*1797A>G were rescued by fullerenol pre-treatment. Adult mice contained three groups, including CON, LPS and FUL (N = 3, each). *P < 0.05. P-values are calculated using the GLM model and LRT. CON, controls; LPS, mice receiving a peritoneal injection of LPS; FUL, mice pre-treated with fullerenol and receiving a peritoneal injection of LPS.