The proteomic landscape of proteotoxic stress in a fibrogenic liver disease

ABSTRACT: Protein misfolding diseases, including alpha-1 antitrypsin deficiency (AATD), pose significant health challenges, yet their progression at the cellular level remains poorly understood. Here, we employ spatial proteomics by mass spectrometry and machine learning to map the molecular landscape of AATD in human liver tissue at high resolution. Our approach, combining Deep Visual Proteomics with single-cell analysis in a patient cohort, characterized early and late responses to protein aggregation across fibrosis stages. We achieved a remarkable quantitative depth of 2,800 proteins per single hepatocyte shape, providing detailed insights into cellular heterogeneity. This comprehensive biological dataset revealed an unexpected early integrated peroxisomal upregulation, preceding the canonical unfolded protein response. Our single-cell data demonstrate that alpha-1 antitrypsin accumulation is largely cell-intrinsic, with minimal stress propagation between neighboring hepatocytes. By integrating proteomic data with AI-guided image analysis across multiple disease stages, we identify a terminal hepatocyte phenotype, marked by globular protein aggregates and distinct proteomic signatures including elevated TNFSF10/TRAIL expression. This phenotype may represent a critical stage in disease progression. Our study unveils novel insights into AATD pathogenesis and introduces a powerful methodology for high-resolution, in situ proteomic analysis of complex tissues. This approach holds potential to unravel molecular mechanisms in various protein misfolding disorders and beyond, setting a new standard for understanding disease progression at the single-cell level in human tissue.

INSTRUMENT(S): Orbitrap Astral

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hepatocyte, Liver

DISEASE(S): Alpha 1-antitrypsin Deficiency

SUBMITTER: Mario Oroshi  

LAB HEAD: Matthias Mann

PROVIDER: PXD054440 | Pride | 2025-02-19

REPOSITORIES: pride