Deep Visual Proteomics links vascular smooth muscle cell phenotypes to atherosclerotic plaque stability

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Vascular smooth muscle cells (VSMCs) drive atherosclerosis through phenotypic switching, yet their spatial organization and protein signatures within plaques remain poorly characterized. Here, we applied Deep Visual Proteomics (DVP) to dissect more than 500 VSMC neighborhoods across 24 human carotid plaques and profile VSMC plasticity in disease. To functionally interpret these tissue proteomes, we built a reference atlas of primary VSMCs driven toward five phenotypes by TGF-β, PDGF-BB, osteogenic stimuli, IL-1β, or cholesterol, quantifying over 10,000 proteins. We integrated tissue and reference proteomes with a deep-learning framework that assigns functional phenotypes to each neighborhood. This revealed spatially distinct phenotype distributions and a shift toward dedifferentiated states in unstable plaques. Knockdown of four candidates (TNC, TNFAIP2, AEBP1, PLK1) validated operational roles during phenotypic switching. Our approach functionally annotates spatial proteomes and links VSMC plasticity to plaque instability in carotid artery disease.

Authors 16

1. Elena Kratz

   Max Planck Institute of Biochemistry

   Affiliation as printed

   Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany

2. Ankit Sinha

   TUM Klinikum · German Centre for Cardiovascular Research · Max Planck Institute of Biochemistry · Technical University of Munich

   Affiliation as printed

   Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany

   German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Berlin, Germany

   Institute of Molecular Vascular Medicine, TUM University Hospital, Technical University Munich, Munich, Germany

3. Trusha Adeshara

   TUM Klinikum · German Centre for Cardiovascular Research · Technical University of Munich

   Affiliation as printed

   German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Berlin, Germany

   Institute of Molecular Vascular Medicine, TUM University Hospital, Technical University Munich, Munich, Germany

4. Valentina Paloschi

   TUM Klinikum · German Centre for Cardiovascular Research · Technical University of Munich

   Affiliation as printed

   German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Berlin, Germany

   Institute of Molecular Vascular Medicine, TUM University Hospital, Technical University Munich, Munich, Germany

5. Nadja Sachs

   TUM Klinikum · German Centre for Cardiovascular Research · Technical University of Munich

   Affiliation as printed

   Department for Vascular and Endovascular Surgery, TUM University Hospital, Technical University Munich, Munich, Germany

   German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Berlin, Germany

6. Jessica Pauli

   TUM Klinikum · German Centre for Cardiovascular Research · Technical University of Munich

   Affiliation as printed

   German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Berlin, Germany

   Institute of Molecular Vascular Medicine, TUM University Hospital, Technical University Munich, Munich, Germany

7. Nadyia Glukha

   TUM Klinikum · German Centre for Cardiovascular Research · Technical University of Munich

   Affiliation as printed

   German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Berlin, Germany

   Institute of Molecular Vascular Medicine, TUM University Hospital, Technical University Munich, Munich, Germany

8. Annalena Huber

   TUM Klinikum · Technical University of Munich

   Affiliation as printed

   Department for Vascular and Endovascular Surgery, TUM University Hospital, Technical University Munich, Munich, Germany

9. Sara Schanda

   TUM Klinikum · German Centre for Cardiovascular Research · Technical University of Munich

   Affiliation as printed

   German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Berlin, Germany

   Institute of Molecular Vascular Medicine, TUM University Hospital, Technical University Munich, Munich, Germany

10. Andreas Metousis

    Max Planck Institute of Biochemistry

    Affiliation as printed

    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany

11. Tim Heymann

    Max Planck Institute of Biochemistry

    Affiliation as printed

    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany

12. Daniela Branzan

    TUM Klinikum · Technical University of Munich

    Affiliation as printed

    Department for Vascular and Endovascular Surgery, TUM University Hospital, Technical University Munich, Munich, Germany

13. Tore Bleckwehl Aachen Department of Medicine 2

    RWTH Aachen University

    Affiliation as printed

    Department of Medicine 2, RWTH Aachen University, Medical Faculty Aachen, Germany

14. Sikander Hayat Aachen Department of Medicine 2

    RWTH Aachen University · Icahn School of Medicine at Mount Sinai

    Affiliation as printed

    Department of Medicine 2, RWTH Aachen University, Medical Faculty Aachen, Germany

    Icahn School of Medicine at Mount Sinai, New York, USA

15. Lars Mäegdefessel

    TUM Klinikum · Karolinska Institutet · German Centre for Cardiovascular Research · Technical University of Munich

    Affiliation as printed

    Department of Medicine, Karolinska Institutet, Stockholm, Sweden

    German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Berlin, Germany

    Institute of Molecular Vascular Medicine, TUM University Hospital, Technical University Munich, Munich, Germany

16. Matthias Mann corresponding

    Max Planck Institute of Biochemistry

    Affiliation as printed

    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany