Isoform-level brain expression profiling of the spermidine/spermine N1-Acetyltransferase1 ( SAT1 ) gene in major depression and suicide

Abstract

Low brain expression of the spermidine/spermine N-1 acetyltransferase (SAT1) gene, the rate-limiting enzyme involved in catabolism of polyamines that mediate the polyamine stress response (PSR), has been reported in depressed suicides. However, it is unknown whether this effect is associated with depression or with suicide and whether all or only specific isoforms expressed by SAT1, such as the primary 171 amino acid protein-encoding transcript (SSAT), or an alternative splice variant (SSATX) that is involved in SAT1 regulated unproductive splicing and transcription (RUST), are involved. We applied next generation sequencing (RNA-seq) to assess gene-level, isoform-level, and exon-level SAT1 expression differences between healthy controls (HC, N = 29), DSM-IV major depressive disorder suicides (MDD-S, N = 21) and MDD non-suicides (MDD, N = 9) in the dorsal lateral prefrontal cortex (Brodmann Area 9, BA9) of medication-free individuals postmortem. Using small RNA-seq, we also examined miRNA species putatively involved in SAT1 post-transcriptional regulation. A DSM-IV diagnosis was made by structured interview. Toxicology and history ruled out recent psychotropic medication. At the gene-level, we found low SAT1 expression in both MDD-S (vs. HC, p = 0.002) and MDD (vs. HC, p = 0.002). At the isoform-level, reductions in MDD-S (vs. HC) were most pronounced in four transcripts including SSAT and SSATX, while reductions in MDD (vs. HC) were pronounced in three transcripts, one of which was reduced in MDD relative to MDD-S (all p < 0.1 FDR corrected). We did not observe evidence for differential exon-usage (i.e. splicing) nor differences in miRNA expression. Results replicate the finding of low SAT1 brain expression in depressed suicides in an independent sample and implicate low SAT1 brain expression in MDD independent of suicide. Low expressions of both SSAT and SATX isoforms suggest that shared transcriptional mechanisms involved in RUST may account for low SAT1 brain expression in depressed suicides. Future studies are required to understand the functions and regulation of SAT1 isoforms, and how they relate to the pathogenesis of MDD and suicide.

Targets of polyamine dysregulation in major depression and suicide: Activity-dependent feedback, excitability, and neurotransmission

“…The first study suggesting a dysregulation of the polyamine system in MDD-suicides showed significant decreases in gene and protein expression of SAT1 in the precentral gyrus (BA4) and cortical frontal lobe areas (BA11 and BA8,9) in both non-depressed suicides and MDD-suicides compared to controls (Sequeira et al, 2006). This finding has been confirmed by our group and several others across brain regions and several population groups (Fiori et al, 2011; Guipponi et al, 2009b; Klempan et al, 2009a; Klempan et al, 2009b; Pantazatos et al, 2015; Sequeira et al, 2007). It was also demonstrated that the rs6526342 SNP, located in the promoter regulatory region of SAT1, had a significant effect on gene expression and that this SNP was associated with suicide in a French-Canadian sample (Sequeira et al, 2006), known to have a founder population effect (Scriver, 2001).…”

A pilot integrative genomics study of GABA and glutamate neurotransmitter systems in suicide, suicidal behavior, and major depressive disorder

“…Procedures for brain collection and psychological autopsy, psychiatric diagnosis, inclusion and exclusion criteria are as described above for the genotyped postmortem sample. Postmortem intervals (PMI), RIN scores, and pH for the postmortem samples were within acceptable ranges and are reported elsewhere [Galfalvy et al, 2015; Pantazatos et al, 2015]. …”

“…For a detailed description of the RNA-seq methodology as previously described [Pantazatos et al, 2015]. Briefly, RNA was extracted from dorsal prefrontal cortex (BA9) using previously established protocols [Sibille et al, 2004] and conducted according to NIH Roadmap Epigenomics Mapping Consortium (REMC) guidelines.…”

“…Preprocessing and differential expression analyses used Tophat and Cufflinks (v.2.2.0) software [Trapnell et al, 2012] Briefly, for each clinical sample, raw RNA-seq reads were aligned and mapped to the human reference genome and assembled using Tophat v2.0.9. These assemblies were then merged together to provide a uniform basis for calculating gene and transcript expression in each sample using Cufflinks v2.2.0 (see Pantazatos et al [2015] Supplementary Table SII for read mapping statistics). Cuffquant v2.2.1 (4237) was then used to quantify gene and isoform-level expression values, and the output CXB files were then input to Cuffnorm v2.2.1 (4237), which produced normalized expression values for each sample.…”

Glucocorticoid Receptor-Related Genes: Genotype and Brain Gene Expression Relationships to Suicide and Major Depressive Disorder

“…Details of the RNA sequencing methodology have been previously reported 40 . Briefly, RNA was extracted from dorsal prefrontal cortex (BA9) using previously established protocols 33 and conducted according to the guidelines recommended by the NIH Roadmap Epigenomics Mapping Consortium (REMC).…”