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Pathology-oriented multiplexing enables integrative disease mapping.

Malte Kuehl1,2,3,4,5, Yusuke Okabayashi6,7,8, Milagros N Wong9,10,11,12

  • 1Department of Clinical Medicine, Aarhus University, Aarhus, Denmark. malte.kuehl@clin.au.dk.

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|July 18, 2025
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Summary
This summary is machine-generated.

Pathology-oriented multiplexing (PathoPlex) enables detailed protein analysis in tissues, revealing disease mechanisms and therapeutic targets in kidney disease and diabetes. This advanced imaging framework integrates multiple biological layers for comprehensive pathological insights.

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Area of Science:

  • Biomedical Imaging
  • Molecular Pathology
  • Computational Biology

Background:

  • Protein expression and localization are crucial for understanding health and disease.
  • Current multiplexed imaging techniques face limitations in integrating cellular and subcellular biological layers due to antibody panel composition and image resolution.
  • Analyzing complex protein interactions across different biological scales remains a significant challenge in pathology.

Purpose of the Study:

  • To introduce PathoPlex, a scalable, quality-controlled, and interpretable framework for highly multiplexed imaging at subcellular resolution.
  • To develop a software package for extracting and interpreting protein co-expression patterns across biological layers.
  • To demonstrate the utility of PathoPlex in identifying pathological features and therapeutic targets in kidney disease and diabetes.

Main Methods:

  • PathoPlex combines highly multiplexed imaging (over 140 antibodies at 80 nm/pixel, 95 cycles) with specialized software.
  • The framework was optimized for processing archival biopsy specimens, enabling simultaneous analysis of at least 40 samples.
  • Protein co-expression patterns (clusters) were extracted and analyzed across cellular and subcellular domains.

Main Results:

  • PathoPlex identified epithelial JUN activity as a key factor in immune-mediated kidney disease.
  • Analysis of human diabetic kidney disease linked patient-level protein clusters to organ dysfunction and identified calcium-mediated tubular stress as a therapeutic target.
  • Renal stress-related clusters were identified in individuals with type 2 diabetes lacking histological kidney disease, and responses to SGLT2 inhibitors were assessed.

Conclusions:

  • PathoPlex provides a powerful and scalable solution for integrative image analysis in complex tissues.
  • The framework facilitates the democratization of multiplexed imaging, enabling deeper insights into disease mechanisms.
  • PathoPlex supports the development of next-generation pathology atlases and aids in identifying novel therapeutic strategies.