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Basic Science and Pathogenesis.

Daniel B McClatchy1, Sergio R Labra1, Christine Baal1

  • 1Scripps Research, La Jolla, CA, USA.

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Alzheimer's Disease (AD) disrupts specific protein forms, potentially due to faulty protein transport or degradation. This study analyzed AD brain samples, organoids, and mouse models to understand these spatial protein changes.

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Area of Science:

  • Neuroscience
  • Proteomics
  • Biochemistry

Background:

  • Alzheimer's Disease (AD) research often uses mass spectrometry (MS) but lacks spatial protein information.
  • Proteins exist as spatial isoforms in unique subcellular compartments, crucial for cellular function.
  • Understanding spatial protein changes in AD is vital for identifying new therapeutic targets.

Purpose of the Study:

  • To investigate the spatial distribution and vulnerability of protein isoforms in Alzheimer's Disease pathogenesis.
  • To determine how AD affects protein localization and degradation across different cellular compartments.
  • To identify specific protein perturbations linked to AD progression.

Main Methods:

  • Quantitative MS analysis of human AD and non-demented hippocampi, AD organoids, and AD mouse cortices.
  • Fractionation of samples into distinct biological compartments for spatial proteomic analysis.
  • Utilized tandem mass tags (TMT) and SPS-MS3 acquisition for precise protein quantification.
  • Employed an azidohomoalanine (AHA) pulse-chase strategy in mice to measure protein degradation rates.

Main Results:

  • Significant differences in protein levels were observed across fractions in human AD brains, with many changes being fraction-specific.
  • Protein perturbations were enriched in vesicle transport, including endosomal and nucleo-cytoplasmic trafficking, indicating mislocalization.
  • AD organoid models confirmed vesicle transport dysfunction.
  • AD mouse models showed age-dependent alterations in protein degradation rates, with distinct rates for proteins in different fractions.

Conclusions:

  • Alzheimer's Disease pathogenesis involves the perturbation of specific protein isoforms.
  • Dysfunctional protein trafficking and local degradation pathways are implicated in AD-related spatial protein changes.
  • These findings highlight the importance of spatial proteomic analysis in understanding AD and developing targeted therapies.