Proteogenomics Reveals Orthologous Alternatively Spliced Proteoforms in the Same Human and Mouse Brain Regions with Differential Abundance in an Alzheimer’s Disease Mouse Model

Abstract

Alternative splicing (AS) may increase the number of proteoforms produced by a gene. Alzheimer’s disease (AD) is a neurodegenerative disease with well-characterized AS proteoforms. In this study, we used a proteogenomics strategy to build a customized protein sequence database and identify orthologous AS proteoforms between humans and mice on publicly available shotgun proteomics (MS/MS) data of the corpus callosum (CC) and olfactory bulb (OB). Identical proteotypic peptides of six orthologous AS proteoforms were found in both species: PKM1 (gene PKM/Pkm), STXBP1a (gene STXBP1/Stxbp1), Isoform 3 (gene HNRNPK/Hnrnpk), LCRMP-1 (gene CRMP1/Crmp1), SP3 (gene CADM1/Cadm1), and PKCβII (gene PRKCB/Prkcb). These AS variants were also detected at the transcript level by publicly available RNA-Seq data and experimentally validated by RT-qPCR. Additionally, PKM1 and STXBP1a were detected at higher abundances in a publicly available MS/MS dataset of the AD mouse model APP/PS1 than its wild type. These data corroborate other reports, which suggest that PKM1 and STXBP1a AS proteoforms might play a role in amyloid-like aggregate formation. To the best of our knowledge, this report is the first to describe PKM1 and STXBP1a overexpression in the OB of an AD mouse model. We hope that our strategy may be of use in future human neurodegenerative studies using mouse models.

Novel brain-penetrant inhibitor of G9a methylase blocks Alzheimer’s disease proteopathology for precision medication

“…123 HNRNPK, a splicing factor, regulates AD-driving proteoforms. 124 The ribosomal protein interactors RPS14, RPS17, RPS15A, RPL21, RPS8, RPL37A, RPL14, RPS2, RPL26, FAU, RPS13, RPS24 were significantly upregulated in AD patients. 125 The NFT-associated AP2A1 and AP2A2 50 were identified as G9a interactors that are the central hub for AD pathogenesis-associated clathrin-dependent endocytosis and postsynaptic neurotransmitter receptor internalization.…”

dbPepVar: A Novel Cancer Proteogenomics Database

“…In another case, a database of tryptic peptides was created from information found in NCBI's dbSNP [11] by adding to the database only the mutated tryptic peptides and the corresponding reference peptides, an approach distinct from [10], which maintained the complete reference sequence. Applications of such databases include the investigation of neglected tropical diseases [12], Alzheimer's disease [13], and other complex conditions, like cancer.…”