Brain region-specific alterations of RNA editing in PDE8A mRNA in suicide decedents

Abstract

Phosphodiesterases (PDE) are key modulators of signal transduction and are involved in inflammatory cell activation, memory and cognition. There is a two-fold decrease in the expression of phosphodiesterase 8A (PDE8A) in the temporal cortex of major depressive disorder (MDD) patients. Here, we studied PDE8A mRNA-editing profile in two architectonically distinct neocortical regions in a clinically well-characterized cohort of age- and sex-matched non-psychiatric drug-free controls and depressed suicide decedents. By using capillary electrophoresis single-stranded conformational polymorphism (CE-SSCP), a previously validated technique to identify A-to-I RNA modifications, we report the full editing profile of PDE8A in the brain, including identification of two novel editing sites. Editing of PDE8A mRNA displayed clear regional difference when comparing dorsolateral prefrontal cortex (BA9) and anterior cingulate cortex (BA24). Furthermore, we report significant intra-regional differences between non-psychiatric control individuals and depressed suicide decedents, which could discriminate the two populations. Taken together, our results (i) highlight the importance of immune/inflammatory markers in major depressive disorder and suicide and (ii) establish a direct relationship between A-to-I RNA modifications of peripheral markers and A-to-I RNA editing-related modifications in brain. This work provides the first immune response-related brain marker for suicide and could pave the way for the identification of a blood-based biomarker that predicts suicidal behavior.

Conflict of interest statement

J.J.M. receives royalties from the Research Foundation of Mental Hygiene for commercial use of the C-SSRS. The remaining authors declare that they have no conflict of interest.

Figures

Fig. 1. Editing sites in the intron 9 of PDE8A pre-mRNA from human brain.

Putative PDE8A intron 9 mRNA secondary structure as predicted by Vienna RNA Websuite. The mRNA positions where significant editing events have been detected are highlighted with arrows. Editing Sites A to G have been previously described in T cells. Newly identified sites in the brain are highlighted in red. Most of the editing sites are in close proximity to each other. All bases are annotated on chromosome 15 according to the last GRCh38 genebuild

Fig. 2. Relative isoform proportion of PDE8A mRNA in (a) Brodmann area 24 (BA24) and (b) Brodmann area 9 (BA9) measured by CE-SSCP on samples of the control group.

Histograms represent relative isoform proportion (%) of the 30 detected PDE8A isoform (mean ± s.e.m.; n = 8). Only isoforms representing more than 0.5% of relative proportion were included in the analysis

Fig. 3. Relative proportion of PDE8A mRNA isoforms in two discrete brain regions of control (A) and suicide (B) subjects.

a Comparison of the relative isoform proportion of PDE8A in BA24 and BA9 within the control group. The PDE8A isoforms are depicted in order of significance and abundance in BA24. b Comparison of the relative isoform proportion of PDE8Ain BA24 and BA9 in the suicide group. In this representation, a negative percentage from the median indicates that the relative proportion of the isoform is higher in BA9 compared with BA24. Filled bars in (a) and (b) indicate the most significant differences of the isoform proportion between the two brain structures in both control and suicide groups. Criteria for the selection are (1) a p-value (FDR) ≤ 0.05 using the one-sample Wilcoxon signed rank test (where null hypothesis H0: median variation = 0) and (2) a median variation ≥ ± 20%. The symbol * indicates a p-value (FDR) ≤ 0.05, ** indicate a p-value (FDR) ≤ 0.01 and *** indicate a p-value (FDR) ≤ 0.001

Fig. 4. Brain regional specificity of PDE8A mRNA editing changes in suicide with major depression.

a Comparison of the relative isoform proportion of PDE8A in control and suicide group within BA24 area. The PDE8A isoforms are depicted in order of significance and abundancy in suicide group. A negative value indicates relative decrease of the isoform whereas an increase in the relative proportion is indicated by a positive value. b Comparison of the relative isoform proportion of PDE8A in control and suicides within the BA9 area. Filled colored bars in (a) and (b) indicate most significant differences between the control and suicide groups. Criteria for the selection are (1) a p-value (FDR) ≤ 0,05 using the one-sample Wilcoxon signed rank test (where null hypothesis H0: median variation = 0) and (2) a median variation ≥ ± 20%. The symbol * indicate a p-value (FDR) ≤ 0.05, ** indicate a p-value (FDR) ≤ 0,01 and *** indicates a p-value (FDR) ≤ 0.001

Fig. 5. Suicide-induced alterations of the relative proportion of PDE8A isoforms in BA24.

a–c Comparison of the relative proportion of ABC, BCEG and ABDE isoforms in control (n = 8) and suicide groups (n = 8). Boxplot represents the distribution of the relative proportion of PDE8A mRNA in BA24 of both groups. d Boxplot representation of mROC combination of relative proportions (%) of ABC + BCEG + ABDE PDE8A isoforms in BA24 of both groups. e Table showing the most significant changes of the relative proportion of PDE8A mRNA isoforms in BA24 of both groups. The symbol * indicates, for Wilcoxon rank-sum test, a p-value ≤ 0.05, ** indicates a p-value ≤ 0.01 and *** indicate a p-value ≤ 0.001

Fig. 6. Suicide-induced alterations of the relative proportion of PDE8A isoforms in BA9.

a–c Comparison of the relative proportion of BD, BCEG and ABF isoforms in control (n = 8) and suicide groups (n = 8). Boxplot represents the distribution of the relative proportion of PDE8A mRNA in BA9 of both groups. d Boxplot representation of mROC combination of relative proportions (%) of BD + BCEG + ABF PDE8A isoforms in BA9 of both groups. e Table showing the most significant changes of the relative proportion of PDE8A mRNA isoforms in BA9 of both groups. The symbol * indicates, for Wilcoxon rank-sum test, a p-value ≤ 0.05, ** indicate a p-value ≤ 0.01 and *** indicate a p-value ≤ 0.001