Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics

Carlyle, Becky C.; Kandigian, Savannah E.; Kreuzer, Johannes; Das, Sudeshna; Trombetta, Bianca A.; Kuo, Yikai; Bennett, David A.; Schneider, Julie A.; Petyuk, Vladislav; Kitchen, Robert; Morris, Robert T.; Nairn, Angus C.; Hyman, Bradley T.; Haas, Wilhelm; Arnold, Steven E.

doi:10.1016/j.neurobiolaging.2021.04.012

Cited by 47 publications

(47 citation statements)

References 87 publications

(122 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To confirm that our dataset profiled an enriched synaptic proteome, we performed several alignment and enrichment analyses. Firstly, we aligned our filtered dataset with two recent human brain and synapse proteome studies [33,34]. This revealed >99% of our dataset matched recently published data (Figure 1B).…”

Section: Resultsmentioning

confidence: 56%

Synaptic proteomics reveal distinct molecular signatures of cognitive change andC9ORF72repeat expansion in the human ALS cortex

László

Hindley

Avila

et al. 2022

Preprint

View full text Add to dashboard Cite

The two major hypotheses of Amyotrophic Lateral Sclerosis (ALS) pathogenesis (dying-forward and dying-back) have synapses at their core. Furthermore, increasing evidence suggests synaptic dysfunction is a central and possibly triggering factor in ALS. Despite this, we still know very little about the molecular profile of an ALS synapse. To address this gap, we designed a synaptic proteomics experiment to perform an unbiased assessment of the synaptic proteome in the ALS brain. We isolated synaptoneurosomes from fresh-frozen post-mortem human cortex (11 controls and 18 ALS) and stratified the ALS group based on cognitive profile (Edinburgh Cognitive and Behavioural ALS Screen (ECAS score)) and presence of a C9ORF72 hexanucleotide repeat expansion (C9ORF72-RE). This allowed us to assess regional differences and the impact of phenotype and genotype on the synaptic proteome, using Tandem Mass Tagging-based proteomics. We identified over 6000 proteins in our synaptoneurosomes and using robust bioinformatics analysis we validated the strong enrichment of synapses. We found more than 30 ALS-associated proteins at the synapse, including TDP-43, FUS, SOD1 and C9ORF72. We identified almost 500 proteins with altered expression levels in ALS synapses, with region-specific changes highlighting proteins and pathways with intriguing links to neurophysiology and pathology. Stratifying the ALS cohort by cognitive status revealed almost 150 specific alterations in cognitively impaired ALS synapses, highlighting novel synaptic proteins that may underlie the synaptic vulnerability in these patients. Stratifying by C9ORF72-RE status revealed 330 protein alterations in the C9ORF72-RE+ve group, with KEGG pathway analysis highlighting strong enrichment for postsynaptic dysfunction, related to glutamatergic receptor signalling. We have validated some of these changes by western blot and at a single synapse level using array tomography imaging. In summary, we have generated the first unbiased map of the human ALS synaptic proteome, revealing novel insight into this key compartment in ALS pathophysiology and highlighting the influence of cognitive decline and C9ORF72-RE on synaptic composition.

show abstract

Section: Resultsmentioning

confidence: 56%

Synaptic proteomics reveal distinct molecular signatures of cognitive change andC9ORF72repeat expansion in the human ALS cortex

László

Hindley

Avila

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“… 13 and added pre- and post-synaptic terms from an inclusion list generated in Carlyle et al . 4 ( Supplementary Table 4 ). We generated an organelle marker map by performing a PCA on all proteins across all samples.…”

Section: Resultsmentioning

confidence: 99%

“… 8 recently showed that enrichment of mitochondrial, myelin sheath and synaptosomal fractions from transgenic Alzheimer’s disease mouse model tissue was able to identify compartment-specific alterations in disease-relevant pathways such as metabolism and synaptic dysfunction. Carlyle et al 4 furthermore showed that enrichment of synaptosomes from post-mortem human brain tissue revealed a number of targets selectively associated with cognitive impairment in older individuals that were not revealed by whole-tissue studies. These studies indicate the potential value of broader subcellular profiling of the Alzheimer’s disease brain.…”

Section: Introductionmentioning

confidence: 99%

Proteomic characterization of post-mortem human brain tissue following ultracentrifugation-based subcellular fractionation

Kandigian

Ethier

Kitchen

et al. 2022

Brain Communications

Self Cite

View full text Add to dashboard Cite

Proteomic characterization of human brain tissue is increasingly utilized to identify potential novel biomarker and drug targets for a variety of neurological diseases. In whole tissue studies, results may be driven by changes in the proportion of the largest and most abundant organelles or tissue cell-type composition. Spatial proteomics approaches enhance our knowledge of disease mechanisms and changing signaling pathways at the subcellular level by taking into account the importance of cellular localization, which critically influences protein function. Density gradient-based ultracentrifugation methods allow for subcellular fractionation and have been utilized in cell lines, mouse, and human brain tissue to quantify thousands of proteins in specific enriched organelles such as the pre- and post-synapse. Serial ultra-centrifugation methods allow for the analysis of multiple cellular organelles from the same biological sample, and to our knowledge have not been previously applied to frozen post-mortem human brain tissue. The use of frozen human tissue for tissue fractionation faces two major challenges, the post-mortem interval, during which proteins may leach from their usual location into the cytosol, and freezing, which results in membrane breakdown. Despite these challenges, in this proof-of-concept study, we show that the majority of proteins segregate reproducibly into crude density-based centrifugation fractions, that the fractions are enriched for the appropriate organellar markers, and that significant differences in protein localization can be observed between tissue from individuals with Alzheimer’s Disease and control individuals.

show abstract

“…Change in brain protein expression in AD versus controls was determined using our in-house developed database—NeuroPro—which combines results from 33 previous studies that used proteomics to identify consistent protein differences between AD and control human brain tissue [ 11 , 12 , 41 , 44 – 73 ].…”

Section: Methodsmentioning

confidence: 99%

The amyloid plaque proteome in early onset Alzheimer’s disease and Down syndrome

Drummond

Kavanagh

Pires

et al. 2022

acta neuropathol commun

View full text Add to dashboard Cite

Amyloid plaques contain many proteins in addition to beta amyloid (Aβ). Previous studies examining plaque-associated proteins have shown these additional proteins are important; they provide insight into the factors that drive amyloid plaque development and are potential biomarkers or therapeutic targets for Alzheimer’s disease (AD). The aim of this study was to comprehensively identify proteins that are enriched in amyloid plaques using unbiased proteomics in two subtypes of early onset AD: sporadic early onset AD (EOAD) and Down Syndrome (DS) with AD. We focused our study on early onset AD as the drivers of the more aggressive pathology development in these cases is unknown and it is unclear whether amyloid-plaque enriched proteins differ between subtypes of early onset AD. Amyloid plaques and neighbouring non-plaque tissue were microdissected from human brain sections using laser capture microdissection and label-free LC–MS was used to quantify the proteins present. 48 proteins were consistently enriched in amyloid plaques in EOAD and DS. Many of these proteins were more significantly enriched in amyloid plaques than Aβ. The most enriched proteins in amyloid plaques in both EOAD and DS were: COL25A1, SMOC1, MDK, NTN1, OLFML3 and HTRA1. Endosomal/lysosomal proteins were particularly highly enriched in amyloid plaques. Fluorescent immunohistochemistry was used to validate the enrichment of four proteins in amyloid plaques (moesin, ezrin, ARL8B and SMOC1) and to compare the amount of total Aβ, Aβ40, Aβ42, phosphorylated Aβ, pyroglutamate Aβ species and oligomeric species in EOAD and DS. These studies showed that phosphorylated Aβ, pyroglutamate Aβ species and SMOC1 were significantly higher in DS plaques, while oligomers were significantly higher in EOAD. Overall, we observed that amyloid plaques in EOAD and DS largely contained the same proteins, however the amount of enrichment of some proteins was different in EOAD and DS. Our study highlights the significant enrichment of many proteins in amyloid plaques, many of which may be potential therapeutic targets and/or biomarkers for AD.

show abstract

Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics

Cited by 47 publications

References 87 publications

Synaptic proteomics reveal distinct molecular signatures of cognitive change andC9ORF72repeat expansion in the human ALS cortex

Synaptic proteomics reveal distinct molecular signatures of cognitive change andC9ORF72repeat expansion in the human ALS cortex

Proteomic characterization of post-mortem human brain tissue following ultracentrifugation-based subcellular fractionation

The amyloid plaque proteome in early onset Alzheimer’s disease and Down syndrome

Contact Info

Product

Resources

About