Computational analysis of 3′UTR region of CASP3 with respect to miRSNPs and SNPs in targetting miRNAs

• We identified miRSNPs in the CASP3 gene and SNPs in miRNAs genes targeting 3′UTR of CASP3.
• We assessed the impact of these miRSNPs and SNPs of miRNA genes with respect to apoptosis. We found 89 different miRNA binding sites for 43 different miRNAs and 16 different SNPs in binding sites.
• MiR-4802-3p’s binding site has a SNP on CASP3 3′UTR and its genomic sequence has a SNP at the same nucleotide.
• We report a strong association between miR-4802-3p and apoptosis upon computational targetting analysis.

Apoptosis is a strictly organized course which keeps the healthy survival/death equilibrium. Disregulation in apoptosis may lead autoimmunity or cancer, but increased apoptosis can lead degenerative diseases. Studies during the last several years have identified numerous affected miRNAs in association with apoptosis, their target genes and biological functions, and possible drug interventions. Polymorphisms in miRNA genes or miRNA target sites (miRSNPs) can modify miRNA action. While polymorphisms in miRNA genes are relatively rare, SNPs in miRNA-binding sites in target genes are more frequent. Several studies have shown that SNPs in miRNA target sites enhance or weaken the interaction between miRNA and its target transcripts and are associated with cancers and other diseases. We aimed to identify miRSNPs on executioner caspase, CASP3 gene (caspase-3) and SNPs in miRNA genes targeting 3′UTR of CASP3 and assessing the impact of these miRSNPs and SNPs of miRNA genes targeting 3′UTR of CASP3 with respect to apoptosis. We identified 89 different miRNA binding sites (for 43 different miRNAs) and 16 different SNPs in binding sites of miRNA in the 3′UTR of the CASP3 gene. Also, 2 SNPs (rs372435266 and rs190144655) were found on this miRNA′ genomic sequence. One of them crossmatched with a SNP in the 3′UTR of CASP3 that we found formerly. This miRNA was miR-4802-3p. Besides, miR-4802-3p targets three other apoptosis related genes, XIAP, IL1A and SOX2. This means that miR-4802-3p may also have a critical effect on apoptosis via different pathways other than caspase-3. We can therefore conclude that this is the first study proving a strong association between miR-4802-3p and apoptosis upon computational targetting analysis.

Apoptotic signaling pathways. Three main caspases-dependent apoptotic signaling pathways were schematized here. (a) Cytokines/Fas-mediated extrinsic pathway: the Fas receptor binds the Fas ligand (FasL), a transmembrane protein part of the TNF family. The interaction between Fas and FasL results in the formation of the death-inducing signaling complex (DISC), which contains the FADD, caspase-8 and caspase-10. In some types of cells (type I), processed caspase-8 directly activates caspase-3, and triggers the execution of apoptosis of the cell. In other types of cells (type II), the Fas-FADD starts a feedback loop that spirals into increasing release of proapoptotic factors from mitochondria and the amplified activation of caspase-8. (b) Mitochondrial-mediated intrinsic pathway: permeabilisation of the mitochondria and release of cytochrome c into the cytoplasm are realized. Cytochrome c then forms a multi-protein complex known as the ‘apoptosome’ and initiates activation of the caspase cascade through caspase-9. (c) Endoplasmik reticulum (ER)/Ca-mediated pathway: caspase-12 is localized to the ER and activated by ER stress, including disruption of ER calcium homeostasis and accumulation of excess proteins in ER, but not by membrane- or mitochondrial-targeted apoptotic signals.SNPs in the miR-4802-3p and in the binding site with 3′UTR of CASP3. MiR-4802-3p’s binding site has a SNP (rs386513603, T/C) in the CASP3 3’UTR and its genomic sequence has a SNP (rs372435266, A/T) at the same nucleotide with rs386513603 and another SNP (rs190144655, C/T) at another site of the binding region. MiRSNP (rs386513603) at the CASP3 3′UTR and SNP (rs372435266) at miR-4802-3p genomic sequence cross-matches at the same site of binding region.Figure optionsDownload as PowerPoint slide