SRSF1 and PTBP1 Are trans-Acting Factors That Suppress the Formation of a CD33 Splicing Isoform Linked to Alzheimer’s Disease Risk

Abstract

A single nucleotide polymorphism (SNP) in exon 2 of the CD33 gene is associated with reduced susceptibility to late-onset Alzheimer’s disease (AD) and causal for elevated mRNA lacking exon 2. In contrast to full-length CD33, transcripts lacking exon 2 result in CD33 protein unable to suppress activation responses in myeloid cells, including microglia. Currently, little is known about the regulation of CD33 exon 2 splicing. Using functional genomics and proteomic approaches, we found that SRSF1 and PTBP1 act as splicing enhancers to increase CD33 exon 2 inclusion in mRNA. Binding of PTBP1 to RNA sequences proximal to the intron 1-exon 2 splice junction is altered by the SNP and represents a potential mechanism behind the SNP-genotype dependent alternative splicing. Our studies also reveal that binding of SRSF1 to the CD33 RNA is not altered by the SNP genotype. Instead, a putative SRSF1 binding sequence at the 3′ end of exon 2 directs CD33 exon 2 inclusion into the mRNA, indicating that PTBP1 and SRSF1 promote full-length isoform expression through different mechanisms. Our findings shed light on molecular interactions that regulate CD33 exon 2 splicing, ultimately impacting receptor expression on the cell surface. These data aid in the understanding of CD33’s regulation of microglial signaling underpinning the AD genetic associations.

Multiple Sclerosis: Shall We Target CD33?

“…From a genetic point of view, the common promoter variant CD33 rs3865444, the subject of this study, appears to modify, along with other genetic variants, the function of CD33 and has also been previously associated with AD. More precisely, the CD33 rs3865444 G risk allele for AD has been associated with higher CD33 cell surface expression, while the minor allele (found to be protective against AD) probably leads to an alternatively spliced CD33m isoform, lacking the Ig V-set domain encoded by exon 2 [ 39 , 47 , 48 ]. Therefore, we could assume that the CD33 rs3865444 GG genotype predisposes towards MS by increasing CD33 cell surface expression and decreasing the alternatively spliced CD33 m variant, thus altering myeloid cells function.…”

Splicing alterations in healthy aging and disease

“…These splicing events were enriched in binding sites from 18 RNA binding proteins, including PTBP1, HNRNPC, CPSF7 and ELAVL1 (Raj et al, 2018). Notably, PTBP1 and SRSF1 can also regulate splicing of CD33 , leading to an isoform associated with Alzheimer's risk (van Bergeijk et al, 2019); whereas ELAVL1 has been previously linked with splicing regulation of BIN1 and PICALM in neuronal cells (Scheckel et al, 2016), and hnRNPC with translational regulation of APP mRNA (Borreca et al, 2016). These studies suggest that Alzheimer's disease‐related perturbations in AS are not simply owing to spliceosomal failure but rather that specific genes are reproducibly affected in a specific manner.…”

The effect of splicing MST1R in gastric cancer was enhanced by lncRNA FENDRR

“…SRSF1 is known to serve roles in RNA splicing and genome stability (6,15,16). The RNA recognition motif of SRSF1 for RNA binding can promote spliceosome assembly at adjacent splice sites to facilitate appropriate exon inclusion (17,18). The aberrant spliceosome function of SRSF1 was previously associated with the mis-splicing of multiple genes, including MST1R and enhancer of zeste 2 polycomb repressive complex 2 subunit, which have been implicated in the pathogenesis of myeloid neoplasms (19,20).…”