Targeted Quantification of Detergent-Insoluble RNA-Binding Proteins in Human Brain Reveals Stage and Disease Specific Co-aggregation in Alzheimer's Disease.

Qi Guo,Marla Gearing,Nicholas T Seyfried,Allan I Levey,Maotian Zhou,James J Lah,Sean R Kundinger,Eric B Dammer,Joshua M Shulman

doi:10.3389/fnmol.2021.623659

Qi Guo, Marla Gearing + Show 7 more

Open Access

https://doi.org/10.3389/fnmol.2021.623659

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Abstract

Core spliceosome and related RNA-binding proteins aggregate in Alzheimer’s disease (AD) brain even in early asymptomatic stages (AsymAD) of disease. To assess the specificity of RNA-binding protein aggregation in AD, we developed a targeted mass spectrometry approach to quantify broad classes of RNA-binding proteins with other pathological proteins including tau and amyloid beta (Aβ) in detergent insoluble fractions from control, AsymAD, AD and Parkinson’s disease (PD) brain. Relative levels of specific insoluble RNA-binding proteins across different disease groups correlated with accumulation of Aβ and tau aggregates. RNA-binding proteins, including splicing factors with homology to the basic-acidic dipeptide repeats of U1-70K, preferentially aggregated in AsymAD and AD. In contrast, PD brain aggregates were relatively depleted of many RNA-binding proteins compared to AsymAD and AD groups. Correlation network analyses resolved 29 distinct modules of co-aggregating proteins including modules linked to spliceosome assembly, nuclear speckles and RNA splicing. Modules related to spliceosome assembly and nuclear speckles showed stage-specific enrichment of insoluble RBPs from AsymAD and AD brains, whereas the RNA splicing module was reduced specifically in PD. Collectively, this work identifies classes of RNA-binding proteins that distinctly co-aggregate in detergent-insoluble fractions across the specific neurodegenerative diseases we examined.

Highlights

Protein aggregation in the brain is one of the major pathologic hallmarks of neurodegenerative diseases (Taylor et al, 2002; Ross and Poirier, 2004)
The aggregate enrichment was validated by western blot of pT231-tau, a marker of neurofibrillary tangles, and U1 small ribonucleoprotein kDa (U1-70K) (Figure 1A and Supplementary Figure 1A), counterposed with TDP-43 labeling as a loading control
A large signal increase of insoluble pT231-tau was observed only in Alzheimer’s disease (AD) cases (Supplementary Figure 1B), while U1-70K was enriched in the insoluble fraction of both AsymAD and AD (Supplementary Figure 1C), with little to no enrichment of either hallmark observed in Parkinson’s disease (PD)

Summary

Introduction

Protein aggregation in the brain is one of the major pathologic hallmarks of neurodegenerative diseases (Taylor et al, 2002; Ross and Poirier, 2004). U1-70K does not coaggregate with extracellular Aβ plaques in AD brains, yet in neurons mis-localizes from the nucleus to the cytoplasm were it co-aggregates with NFTs (Diner et al, 2014; Hales et al, 2016; Bishof et al, 2018; Hsieh et al, 2019) These co-aggregates between related U1 snRNP proteins and tau appear to be specific to AD as they are not observed in other tauopathies (Bai et al, 2013; Diner et al, 2014; Hales et al, 2016; Bishof et al, 2018). This supports a hypothesis that the cytoplasmic aggregation of U1-70K and functionally related RBPs provide a biological link between Aβ deposition and tau aggregation in AD

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