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Transcript isoform switching occurs in the murine synaptic transcriptome during aging

ABSTRACT: Preliminary Summary: In this study, we set to specifically analyze effects of aging on differential splicing in the local synaptic proteome. To this end, we analyzed the RNA extracted from synaptosomes obtained from cerebral cortices of C57BL/6 mice of 3 weeks, 5 months and 19 months of age. Synaptosomes are artificial, membranous sacs that contain synaptic components and are generated by subcellular fractionation of homogenized or ground-up nerve tissue. We employ RNA-seq using paired long-reads to obtain comprehensive sequence information on synaptic transcripts and two different bioinformatic methods (DIEGO and LeafCutter) to quantify differential splicing. Finally, the change in the usage of the selected junctions was validated through RT-qPCR and RT-PCR using an independent set of samples.

ORGANISM(S): Mus musculus

PROVIDER: GSE146636 | GEO | 2024/03/06

REPOSITORIES: GEO

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Project description:Background: Minimal change nephrotic syndrome (MCNS) is considered to be associated with T cell dysfunction, via unknown mechanisms. Experimental observations suggest that some humoral factors alter the permeability of glomerular filtration barrier. However, the nature of such factors remains still uncertain. Methods: Using cDNA microarrays, we performed gene expression profiling of peripheral blood mononuclear cells (PBMC) from three patients with MCNS during nephrosis and remission phases. To confirm the cDNA microarray results, we performed quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) analyses in nephrosis and remission samples from 20 MCNS patients and six patients with nephrotic syndrome due to membranous nephropathy. Results: Out of 24,446 genes screened, 33 genes were up-regulated (at least 1.5-fold) in PBMC from these MCNS patients during the nephrosis phase. Up-regulated genes mainly encoded proteins involved in signal transduction and cytokine response. For further examination, we selected two genes encoding provable secretary proteins, chemokine (C-C) ligand 13 (also known as monocyte chemotactic protein-4) (CCL13) and a novel galectin-related protein (HSPC159). The results of RT-PCR showed that expressions of CCL13 and HSPC159 mRNA in nephrosis PBMC samples are higher than those in remission PBMC samples from all 20 MCNS patients examined. On the other hand, these mRNA expression patterns were variable among six patients with membranous nephropathy. Conclusions: We conclude that CCL13 and HSPC159 mRNA expressions in PBMC is up-regulated in MCNS patients during the nephrosis phase. These expression changes in PBMC might be involved in the pathophysiologic processes of MCNS. Using cDNA microarrays, we performed gene expression profiling of peripheral blood mononuclear cells (PBMC) from three patients with MCNS during nephrosis and remission phases. To confirm the cDNA microarray results, we performed quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) analyses in nephrosis and remission samples from 20 MCNS patients and six patients with nephrotic syndrome due to membranous nephropathy.

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Transcript isoform switching occurs in the murine synaptic transcriptome during aging

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