A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease
Authors: Boeddrich Annett , Haenig Christian , Neuendorf Nancy , Blanc Eric , Ivanov Andranik , Kirchner Marieluise , Schleumann Philipp , Bayraktaroğlu Irem , Richter Matthias , Molenda Christine Mirjam , Sporbert Anje , Zenkner Martina , Schnoegl Sigrid , Suenkel Christin , Schneider Luisa-Sophie , Rybak-Wolf Agnieszka , Kochnowsky Bianca , Byrne Lauren M. , Wild Edward J. , Nielsen Jørgen E. , Dittmar Gunnar , Peters Oliver , Beule Dieter , Wanker Erich E. 
Published: January 2023

AbstractBackgroundAlzheimer’s disease (AD) is characterized by the accumulation of amyloid-β (Aβ) peptides in intra- and extracellular deposits. How Aβ aggregates perturb the proteome in brains of patients and AD transgenic mouse models, however, remains largely unclear. State-of-the-art mass spectrometry (MS) methods can comprehensively detect proteomic alterations in neurodegenerative disorders, providing relevant insights unobtainable with transcriptomics investigations. Analyses of the relationship between progressive Aβ aggregation and protein abundance changes in brains of 5xFAD transgenic mice have not been reported previously.MethodsWe quantified progressive Aβ aggregation in hippocampus and cortex of 5xFAD mice and controls with immunohistochemistry and biochemical membrane filter assays. Protein changes in different mouse tissues were analysed by MS-based proteomics using label-free quantification (LFQ); resulting MS data were processed using an established pipeline. Results were contrasted with existing proteomic data sets from postmortem AD patient brains. Finally, abundance changes in the candidate marker Arl8b were validated in CSF from AD patients and controls using ELISAs.Results:Experiments revealed a more rapid accumulation of Aβ42 peptides in hippocampus than in cortex of 5xFAD mice, accompanied by many more protein abundance changes in hippocampus than in cortex, indicating that Aβ42 aggregate deposition is associated with brain region-specific proteome perturbations. Generating time-resolved data sets, we defined Aβ aggregate-correlated and anticorrelated proteome changes, a fraction of which was conserved in postmortem AD patient brain tissue, suggesting that proteome changes in 5xFAD mice mimic disease relevant changes in human AD. We detected a positive correlation between Aβ42 aggregate deposition in the hippocampus of 5xFAD mice and the abundance of the lysosome-associated small GTPase Arl8b, which accumulated together with axonal lysosomal membranes in close proximity of extracellular Aβ plaques in 5xFAD brains. Abnormal aggregation of Arl8b was observed in AD brain tissue. Arl8b protein levels were significantly increased in cerebrospinal fluid (CSF) of AD patients, a clinically accessible body fluid.ConclusionsWe report a comprehensive biochemical and proteomic investigation of hippocampal and cortical brain tissue derived from 5xFAD transgenic mice, providing a valuable resource to the neuroscientific community. We identified Arl8b, with significant abundance changes in 5xFAD and AD patient brains. Arl8b might enable the measurement of progressive lysosome accumulation in AD patients and have clinical utility as a candidate biomarker.Data are available via ProteomeXchange with identifier PXD030348.