Broad‐ranging effects of APOE4 on cellular protein expression in neural precursors

Abstract

AbstractBackgroundIt is increasingly becoming evident that ApoE4 isoform contributes to AD risk over the life course of individuals. Much remains unknown about the biological pathways that connect APOE4 genotype with the development of pathology that eventually leads to AD, nor do we know how early in life these cellular alterations begin. To answer these questions, we derived neural precursor cells (NPCs) from induced pluripotent stem cells (IPSCs) that were CRISPR‐edited at APOE locus (Ramakrishna et al. 2021; Schmid et al. 2019). We intended to characterize the protein expression landscape in the NPCs subsequent to targeted deletion of E4 from a parent IPSC line of APOE3/4 genotype.MethodsProtein isolates from NPCs were analyzed on the Thermo Scientific‐ Orbitrap Fusion instrument and the resulting Mass Spectrometer data was searched against a reference human protein database using Proteome Discoverer 2.2. Differentially expressed proteins (DEP) were determined from the protein abundance fold change values obtained for each protein. Proteins which showed >1.2‐fold difference with FDR adjusted P‐value < 0.05 were considered differentially expressed. DEPs were mapped to STRING database (v11.5) for retrieval of interacting proteins and functional enrichment.ResultsCRISPR‐editing of E4 from the parent line revealed 105 differential expressed proteins. Of these, 62 were upregulated, and 43 were downregulated. Further analysis of the DEPs via STRING database showed that these changes primarily affect pathways linked to RNA processing, plasma membrane repair, and cytoskeleton organization.ConclusionsOur primary motivation was to determine proteomic alterations with targeted deletion of E4. And indeed, we find the effects of E4 extend beyond proteins considered central to AD pathology. Knowing more about the protein interactions regulated by ApoE, in an isoform‐specific manner, has the potential to reveal novel drug targets. In future experiments, we intend to follow the DEPs identified here and the associated pathways through the course of neural differentiation.