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

Dominik Kylies; Marina Zimmermann; Fabian Haas; Maria Schwerk; Malte Kuehl; Michael Brehler; Jan Czogalla; Lola C. Hernandez; Leonie Konczalla; Yusuke Okabayashi; Julia Menzel; Ilka Edenhofer; Sam Mezher; Hande Aypek; Bernhard Dumoulin; Hui Wu; Smilla Hofmann; Oliver Kretz; Nicola Wanner; Nicola M. Tomas; Susanne Krasemann; Markus Glatzel; Christoph Kuppe; Rafael Kramann; Bella Banjanin; Rebekka K. Schneider; Christopher Urbschat; Petra Arck; Nicola Gagliani; Marc van Zandvoort; Thorsten Wiech; Florian Grahammer; Pablo J. Sáez; Milagros N. Wong; Stefan Bonn; Tobias B. Huber; Victor G. Puelles

doi:10.1038/s41565-023-01328-z

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

Dominik Kylies, Marina Zimmermann, Fabian Haas, Maria Schwerk, Malte Kuehl, Michael Brehler, Jan Czogalla, Lola C. Hernandez, Leonie Konczalla, Yusuke Okabayashi, Julia Menzel, Ilka Edenhofer, Sam Mezher, Hande Aypek, Bernhard Dumoulin, Hui Wu, Smilla Hofmann, Oliver Kretz, Nicola Wanner, Nicola M. TomasSusanne Krasemann, Markus Glatzel, Christoph Kuppe, Rafael Kramann, Bella Banjanin, Rebekka K. Schneider, Christopher Urbschat, Petra Arck, Nicola Gagliani, Marc van Zandvoort, Thorsten Wiech, Florian Grahammer, Pablo J. Sáez, Milagros N. Wong, Stefan Bonn, Tobias B. Huber, Victor G. Puelles^*

^*Corresponding author for this work

Developmental Biology

Research output: Contribution to journal › Article › Academic › peer-review

19 Citations (Scopus)

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Abstract

Expansion microscopy physically enlarges biological specimens to achieve nanoscale resolution using diffraction-limited microscopy systems¹. 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.

Original language	English
Pages (from-to)	336-342
Number of pages	7
Journal	Nature Nanotechnology
Volume	18
Issue number	4
DOIs	https://doi.org/10.1038/s41565-023-01328-z
Publication status	Published - 10 Apr 2023

Bibliographical note

Funding:
Open access funding provided by Universitätsklinikum
Hamburg-Eppendorf (UKE).

Publisher Copyright:
© 2023, The Author(s).

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Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimensFinal published version, 13.6 MBLicence: CC BY

Cite this

Kylies, D., Zimmermann, M., Haas, F., Schwerk, M., Kuehl, M., Brehler, M., Czogalla, J., Hernandez, L. C., Konczalla, L., Okabayashi, Y., Menzel, J., Edenhofer, I., Mezher, S., Aypek, H., Dumoulin, B., Wu, H., Hofmann, S., Kretz, O., Wanner, N., ... Puelles, V. G. (2023). Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens. Nature Nanotechnology, 18(4), 336-342. https://doi.org/10.1038/s41565-023-01328-z

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title = "Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens",

abstract = "Expansion microscopy physically enlarges biological specimens to achieve nanoscale resolution using diffraction-limited microscopy systems1. 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.",

author = "Dominik Kylies and Marina Zimmermann and Fabian Haas and Maria Schwerk and Malte Kuehl and Michael Brehler and Jan Czogalla and Hernandez, {Lola C.} and Leonie Konczalla and Yusuke Okabayashi and Julia Menzel and Ilka Edenhofer and Sam Mezher and Hande Aypek and Bernhard Dumoulin and Hui Wu and Smilla Hofmann and Oliver Kretz and Nicola Wanner and Tomas, {Nicola M.} and Susanne Krasemann and Markus Glatzel and Christoph Kuppe and Rafael Kramann and Bella Banjanin and Schneider, {Rebekka K.} and Christopher Urbschat and Petra Arck and Nicola Gagliani and {van Zandvoort}, Marc and Thorsten Wiech and Florian Grahammer and S{\'a}ez, {Pablo J.} and Wong, {Milagros N.} and Stefan Bonn and Huber, {Tobias B.} and Puelles, {Victor G.}",

note = "Funding: Open access funding provided by Universit{\"a}tsklinikum Hamburg-Eppendorf (UKE). Publisher Copyright: {\textcopyright} 2023, The Author(s).",

year = "2023",

month = apr,

day = "10",

doi = "10.1038/s41565-023-01328-z",

language = "English",

volume = "18",

pages = "336--342",

journal = "Nature Nanotechnology",

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Kylies, D, Zimmermann, M, Haas, F, Schwerk, M, Kuehl, M, Brehler, M, Czogalla, J, Hernandez, LC, Konczalla, L, Okabayashi, Y, Menzel, J, Edenhofer, I, Mezher, S, Aypek, H, Dumoulin, B, Wu, H, Hofmann, S, Kretz, O, Wanner, N, Tomas, NM, Krasemann, S, Glatzel, M, Kuppe, C, Kramann, R, Banjanin, B , Schneider, RK, Urbschat, C, Arck, P, Gagliani, N, van Zandvoort, M, Wiech, T, Grahammer, F, Sáez, PJ, Wong, MN, Bonn, S, Huber, TB & Puelles, VG 2023, 'Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens', Nature Nanotechnology, vol. 18, no. 4, pp. 336-342. https://doi.org/10.1038/s41565-023-01328-z

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T1 - Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens

AU - Kylies, Dominik

AU - Zimmermann, Marina

AU - Haas, Fabian

AU - Schwerk, Maria

AU - Kuehl, Malte

AU - Brehler, Michael

AU - Czogalla, Jan

AU - Hernandez, Lola C.

AU - Konczalla, Leonie

AU - Okabayashi, Yusuke

AU - Menzel, Julia

AU - Edenhofer, Ilka

AU - Mezher, Sam

AU - Aypek, Hande

AU - Dumoulin, Bernhard

AU - Wu, Hui

AU - Hofmann, Smilla

AU - Kretz, Oliver

AU - Wanner, Nicola

AU - Tomas, Nicola M.

AU - Krasemann, Susanne

AU - Glatzel, Markus

AU - Kuppe, Christoph

AU - Kramann, Rafael

AU - Banjanin, Bella

AU - Schneider, Rebekka K.

AU - Urbschat, Christopher

AU - Arck, Petra

AU - Gagliani, Nicola

AU - van Zandvoort, Marc

AU - Wiech, Thorsten

AU - Grahammer, Florian

AU - Sáez, Pablo J.

AU - Wong, Milagros N.

AU - Bonn, Stefan

AU - Huber, Tobias B.

AU - Puelles, Victor G.

PY - 2023/4/10

Y1 - 2023/4/10

N2 - Expansion microscopy physically enlarges biological specimens to achieve nanoscale resolution using diffraction-limited microscopy systems1. 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.

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

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