Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens

Nature Nanotechnology, vol. 18, pp. 336–342

Abstract

Abstract Expansion microscopy physically enlarges biological specimens to achieve nanoscale resolution using diffraction-limited microscopy systems 1 . However, optimal performance is usually reached using laser-based systems (for example, confocal microscopy), restricting its broad applicability in clinical pathology, as most centres have access only to light-emitting diode (LED)-based widefield systems. As a possible alternative, a computational method for image resolution enhancement, namely, super-resolution radial fluctuations (SRRF) 2,3 , has recently been developed. However, this method has not been explored in pathology specimens to date, because on its own, it does not achieve sufficient resolution for routine clinical use. Here, we report expansion-enhanced super-resolution radial fluctuations (ExSRRF), a simple, robust, scalable and accessible workflow that provides a resolution of up to 25 nm using LED-based widefield microscopy. ExSRRF enables molecular profiling of subcellular structures from archival formalin-fixed paraffin-embedded tissues in complex clinical and experimental specimens, including ischaemic, degenerative, neoplastic, genetic and immune-mediated disorders. Furthermore, as examples of its potential application to experimental and clinical pathology, we show that ExSRRF can be used to identify and quantify classical features of endoplasmic reticulum stress in the murine ischaemic kidney and diagnostic ultrastructural features in human kidney biopsies.

Authors 37

1. Dominik Kylies

   Universitätsklinikum Erlangen · University Medical Center Hamburg-Eppendorf

   Affiliation as printed

   Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

   III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

   Research Center On Rare Kidney Diseases (RECORD), University Hospital Erlangen, Erlangen, Germany

2. Marina Zimmermann

   Universität Hamburg · University Medical Center Hamburg-Eppendorf

   Affiliation as printed

   Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

   III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

   Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

3. Fabian Haas

   University Medical Center Hamburg-Eppendorf

   Affiliation as printed

   Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

   III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

4. Maria Schwerk

   University Medical Center Hamburg-Eppendorf

   Affiliation as printed

   Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

   III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

5. Malte B. Kuehl

   Universität Hamburg · University Medical Center Hamburg-Eppendorf

   Affiliation as printed

   Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

   III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

   Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

6. Michael Brehler

   Universität Hamburg · University Medical Center Hamburg-Eppendorf

   Affiliation as printed

   Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

7. Jan Czogalla

   University Medical Center Hamburg-Eppendorf

   Affiliation as printed

   Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

   III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

8. Lola C. Hernandez

   Universität Hamburg

   Affiliation as printed

   Cell Communication and Migration Laboratory, Department of Biochemistry and Molecular Cell Biology (IBMZ), Center for Experimental Medicine, Hamburg, Germany

9. Leonie Konczalla

   Universität Hamburg · University Medical Center Hamburg-Eppendorf

   Affiliation as printed

   Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

   Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

10. Yusuke Okabayashi

    Jikei University School of Medicine · University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

11. Julia Menzel
    Affiliation as printed

    Abberior Instruments GmbH, Göttingen, Germany

12. Ilka Edenhofer

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

13. Sam Mezher

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

14. Hande Aypek

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

15. Bernhard Dumoulin

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

16. Hui Min Wu

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

17. Smilla Hofmann

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

18. Oliver Kretz

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

19. Nicola Wanner

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

20. Nicola M. Tomas

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

21. Susanne Krasemann

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

22. Markus Glatzel

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

23. Christoph Kuppe Aachen Institute of Experimental Medicine and Systems Biology Division of Nephrology and Clinical Immunology

    RWTH Aachen University

    Affiliation as printed

    Institute of Experimental Medicine and Systems Biology and Division of Nephrology and Clinical Immunology, RWTH Aachen University Medical Faculty, Aachen, Germany

24. Rafael Kramann Aachen Institute of Experimental Medicine and Systems Biology Division of Nephrology and Clinical Immunology

    RWTH Aachen University

    Affiliation as printed

    Institute of Experimental Medicine and Systems Biology and Division of Nephrology and Clinical Immunology, RWTH Aachen University Medical Faculty, Aachen, Germany

25. Bella Banjanin

    Erasmus MC · Erasmus MC Cancer Institute

    Affiliation as printed

    Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands

    Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands

26. Rebekka K. Schneider Aachen Institute for Cell and Tumor Biology

    Erasmus MC · Erasmus MC Cancer Institute · RWTH Aachen University

    Affiliation as printed

    Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands

    Institute for Cell and Tumor Biology, RWTH Aachen University, Aachen, Germany

    Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands

27. Christopher Urbschat

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Department of Obstetrics and Fetal Medicine, Division of Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

28. Petra Arck

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Department of Obstetrics and Fetal Medicine, Division of Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

29. Nicola Gagliani

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

30. Marc A.M.J. van Zandvoort Aachen Institute for Molecular Cardiovascular Research (IMCAR)

    Maastricht University · RWTH Aachen University

    Affiliation as printed

    Department of Genetics and Cell Biology, Maastricht University, School for Oncology and Reproduction GROW, School for Mental Health and Neuroscience MHeNS, and School for Cardiovascular Diseases CARIM, Maastricht University, Maastricht, The Netherlands

    Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, Aachen, Germany

31. Thorsten Wiech

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

32. Florian Grahammer

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

33. Pablo José Sáez

    Universität Hamburg

    Affiliation as printed

    Cell Communication and Migration Laboratory, Department of Biochemistry and Molecular Cell Biology (IBMZ), Center for Experimental Medicine, Hamburg, Germany

34. Milagros N. Wong

    Aarhus University · Aarhus University Hospital · University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Department of Clinical Medicine, Aarhus University, Aarhus, Denmark

    Department of Pathology, Aarhus University Hospital, Aarhus, Denmark

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

35. Stefan Bonn

    Universität Hamburg · University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

36. Tobias Bruno Huber

    University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

37. Victor G. Puelles corresponding

    Aarhus University · Aarhus University Hospital · University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Department of Clinical Medicine, Aarhus University, Aarhus, Denmark. v.puelles@uke.de

    Department of Pathology, Aarhus University Hospital, Aarhus, Denmark. v.puelles@uke.de

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany. v.puelles@uke.de

    III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. v.puelles@uke.de

    Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany