Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics

Hadley, Kevin C.; Rakhit, Rishi; Guo, Hongbo; Sun, Yulong; Jonkman, James; McLaurin, JoAnne; Hazrati, Lili‐Naz; Emili, Andrew; Chakrabartty, Avijit

doi:10.7554/elife.09579

Cited by 41 publications

(57 citation statements)

References 51 publications

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“…Immunohistochemistry results showed that the increased presence of synaptic proteins was not simply a result of increased numbers of plaque associated neurites in rpAD. Previous immunohistochemistry studies have confirmed that many synaptic proteins can be found dispersed throughout plaques[32, 65], therefore, this may be the case in rpAD plaques also. Aβ oligomers are known to accumulate in synapses, particularly in synapses near plaques[60].…”

Section: Discussionmentioning

confidence: 69%

“…This database combined the results from studies that identified proteins in neurofibrillary tangles[50, 66, 82], proteins enriched in plaques[32, 43], proteins that had significantly altered expression in various regions and/or fractions of AD brains in comparison to control brains and proteins that contained the keyword “Alzheimer” in the Uniprot human database[1, 2, 4, 11, 13, 14, 22, 31–33, 36, 37, 45, 54, 55, 77, 78, 89, 90, 96]. Protein groups identified in rpAD and sAD plaques were screened against this database to determine how many of the proteins identified in this study have been previously associated with AD pathology.…”

Section: Methodsmentioning

confidence: 99%

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Proteomic differences in amyloid plaques in rapidly progressive and sporadic Alzheimer’s disease

Nayak²,

et al. 2017

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Rapidly progressive Alzheimer’s disease (rpAD) is a particularly aggressive form of Alzheimer’s disease, with a median survival time of 7–10 months after diagnosis. Why these patients have such a rapid progression of Alzheimer’s disease is currently unknown. To further understand pathological differences between rpAD and typical sporadic Alzheimer’s disease (sAD) we used localized proteomics to analyze the protein differences in amyloid plaques in rpAD and sAD. Label-free quantitative LC-MS/MS was performed on amyloid plaques microdissected from rpAD and sAD patients (n=22 for each patient group) and protein expression differences were quantified. On average, 913±30 (mean±SEM) proteins were quantified in plaques from each patient and 279 of these proteins were consistently found in plaques from every patient. We found significant differences in protein composition between rpAD and sAD plaques. We found that rpAD plaques contained significantly higher levels of neuronal proteins (p=0.0017) and significantly lower levels of astrocyte proteins (p=1.08x10−6). Unexpectedly, cumulative protein differences in rpAD plaques did not suggest accelerated typical sAD. Plaques from patients with rpAD were particularly abundant in synaptic proteins, especially those involved in synaptic vesicle release, highlighting the potential importance of synaptic dysfunction in the accelerated development of plaque pathology in rpAD. Combined, our data provides new direct evidence that amyloid plaques do not all have the same protein composition and that the proteomic differences in plaques could provide important insight into the factors that contribute to plaque development. The cumulative protein differences in rpAD plaques suggest rpAD may be a novel subtype of Alzheimer’s disease.

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Section: Discussionmentioning

confidence: 69%

Section: Methodsmentioning

confidence: 99%

Proteomic differences in amyloid plaques in rapidly progressive and sporadic Alzheimer’s disease

Nayak²,

et al. 2017

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“…In addition, matrix-assisted laser desorption/ionization (MALDI) could be applied to determine gradient changes at defined tissue interphases (41). A limitation to this study is that H&E staining relies on pattern recognition rather than staining for specific proteins, however, our approach could be combined with spatially targeted optical microproteomics (STOMP) which combines antibodies and fluorescence to identify regions of interest (42).…”

Section: Discussionmentioning

confidence: 99%

Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues

Herrera

Mallikarjun

Rosini

et al. 2019

Preprint

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Haematoxylin and eosin (H&E)which respectively stain nuclei blue and other cellular and stromal material pinkare routinely used for clinical diagnosis based on the identification of morphological features. A richer characterization can be achieved by laser capture microdissection coupled to mass spectrometry (LCM-MS), giving an unbiased assay of the proteins that make up the tissue. However, the process of fixing, and H&E staining of tissues is poorly compatible with standard sample preparation methods for mass spectrometry, resulting in low protein yield. Here we describe a microproteomics technique optimized to analyze H&E-stained, formalin-fixed paraffin-embedded (FFPE) tissues. We advance our methodology by combining 3 techniques shown to individually enhance protein yields (heat extraction, physical disruption, and in column digestion) into one optimized pipeline for the analysis of H&E stained FFPE tissues. Micro-dissected morphologically normal human lung alveoli (0.082 mm 3 ) and human lung blood vessels (0.094 mm 3 ) from FFPE fixed section from Idiopathic Pulmonary Fibrosis (IPF) specimens were then subject to comparative proteomics using this methodology. This approach yielded 1252 differentially expressed proteins including 137 extracellular matrix (ECM) proteins. In addition, we offer proof of principal that MS can identify distinct, characteristic proteomic compositions of anatomical features within complex tissues.

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“…A substantial mass of the amyloid plaque core is composed of a complex mixture of glycoproteins, glycolipids, lipids and proteins other than APP/Aβ [142,143]. Among the best characterized molecules are a variety of glycosaminoglycans, gangliosides, cholesterol, fatty acids, triglycerides, α1-antichymotrypsin and apolipoprotein E [144–152] and a large number of proteins identified by mass spectrometry [143,153]. Approximately 35% of the mass of AD amyloid cores is composed of non-Aβ molecules [32] enmeshed within an array of 10 nm fibrillar Aβ peptides.…”

Section: The Complicated Catalog Of App/aβ-related Peptides and Ad Ammentioning

confidence: 99%

APP/Aβ structural diversity and Alzheimer's disease pathogenesis

Roher

Kokjohn

Clarke

et al. 2017

Neurochemistry International

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The amyloid cascade hypothesis of Alzheimer’s disease (AD) proposes amyloid-β (Aβ) is a chief pathological element of dementia. AD therapies have targeted monomeric and oligomeric Aβ 1-40 and 1-42 peptides. However, alternative APP proteolytic processing produces a complex roster of Aβ species. In addition, Aβ peptides are subject to extensive posttranslational modification (PTM). We propose that amplified production of some APP/Aβ species, perhaps exacerbated by differential gene expression and reduced peptide degradation, creates a diverse spectrum of modified species which disrupt brain homeostasis and accelerate AD neurodegeneration. We surveyed the literature to catalog Aβ PTM including species with isoAsp at positions 7 and 23 which may phenocopy the Tottori and Iowa Aβ mutations that result in early onset AD. We speculate that accumulation of these alterations induce changes in secondary and tertiary structure of Aβ that favor increased toxicity, and seeding and propagation in sporadic AD. Additionally, amyloid-β peptides with a pyroglutamate modification at position 3 and oxidation of Met35 make up a substantial portion of sporadic AD amyloid deposits. The intrinsic physical properties of these species, including resistance to degradation, an enhanced aggregation rate, increased neurotoxicity, and association with behavioral deficits, suggest their emergence is linked to dementia. The generation of specific 3D-molecular conformations of Aβ impart unique biophysical properties and a capacity to seed the prion-like global transmission of amyloid through the brain. The accumulation of rogue Aβ ultimately contributes to the destruction of vascular walls, neurons and glial cells culminating in dementia. A systematic examination of Aβ PTM and the analysis of the toxicity that they induced may help create essential biomarkers to more precisely stage AD pathology, design countermeasures and gauge the impacts of interventions.

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Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics

Cited by 41 publications

References 51 publications

Proteomic differences in amyloid plaques in rapidly progressive and sporadic Alzheimer’s disease

Proteomic differences in amyloid plaques in rapidly progressive and sporadic Alzheimer’s disease

Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues

APP/Aβ structural diversity and Alzheimer's disease pathogenesis

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