Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer’s disease

Abstract

Alzheimer’s disease (AD) is characterized by an early, asymptomatic phase (AsymAD) in which individuals exhibit amyloid-beta (Aβ) plaque accumulation in the absence of clinically detectable cognitive decline. Here we report an unbiased multiplex quantitative proteomic and phosphoproteomic analysis using tandem mass tag (TMT) isobaric labeling of human post-mortem cortex (n = 27) across pathology-free controls, AsymAD and symptomatic AD individuals. With off-line high-pH fractionation and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) on an Orbitrap Lumos mass spectrometer, we identified 11,378 protein groups across three TMT 11-plex batches. Immobilized metal affinity chromatography (IMAC) was used to enrich for phosphopeptides from the same TMT-labeled cases and 51,736 phosphopeptides were identified. Of these, 48,992 were quantified by TMT reporter ions representing 33,652 unique phosphosites. Two reference standards in each TMT 11-plex were included to assess intra- and inter-batch variance at the protein and peptide level. This comprehensive human brain proteome and phosphoproteome dataset will serve as a valuable resource for the identification of biochemical, cellular and signaling pathways altered during AD progression.

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

“…Phosphorylation and ubiquitination are PTMs that modulate signaling pathways and pathophysiological mechanisms in AD. Unsurprisingly, these classes of PTMs decorate the MTBR region of tau and are enriched in AD ( Abreha et al, 2018 ; Ping et al, 2018 , 2020 ; Arakhamia et al, 2020 ). Although highly enriched in AD, tau peptides were largely unchanged in AsymAD, demonstrating the late aggregation of tau protein during progression of AD pathology.…”

Quantitative proteomic analysis of the frontal cortex in Alzheimer’s disease

“…The study has several limitations, chief among them being the small sample sizes for discovery and validation. This is unfortunately due to a lack of well curated post‐mortem brain samples and the overwhelming majority of similar studies, with few exceptions being limited by this issue (Ping et al., 2018; Portelius et al., 2017). Another limitation is that the BLSA is a unique cohort of highly educated participants (the mean education is approximately 17 years), so findings may not generalize to the population.…”

Inclusion of African American/Black adults in a pilot brain proteomics study of Alzheimer's disease

“…It is important to note that existing human AD brain proteomics literature includes studies with a variety of sample sizes ( N = 3 50 - ≥ 900 90 ) and brain regions such as frontal lobe, ( Seyfried et al, 2017 ; Ping et al, 2018 ; Zahid et al, 2014 ; McKetney et al, 2019 ; Minjarez et al, 2016 ; Bai et al, 2020 ; Wang et al, 2020 ; Johnson et al, 2020 ; Johnson et al, 2018 ; Zhang et al, 2018 ; Mendonça et al, 2019 ; Adav et al, 2019 ; Bereczki et al, 2018 ; Ping et al, 2020 ) temporal lobe (including hippocampus), ( Xu et al, 2019 ; Manavalan et al, 2013 ; Zahid et al, 2014 ; McKetney et al, 2019 ; Hondius et al, 2016 ; Begcevic et al, 2013 ; Musunuri et al, 2014 ; Andreev et al, 2012 ; Sultana et al, 2007b ; Haytural et al, 2020 ; Johnson et al, 2020 ; Mendonça et al, 2019 ; Xiong et al, 2019 ) and IPL ( McKetney et al, 2019 ). None included nonpathological regions such as GP.…”

“…Most of these studies also do not include racial/ethnic diversity of participants. For example, one report exclusively studied Mexican ( Minjarez et al, 2016 ) and another Japanese ( Manavalan et al, 2013 ) adults, while a few included African American/Black, Hispanic, and Native Hawaiian or other Pacific Islander groups representing 11–13% of study participants ( Seyfried et al, 2017 ; Ping et al, 2018 ; Ping et al, 2020 ). Therefore, these consistent findings increase the confidence of this study.…”