Pathology-oriented multiplexing enables integrative disease mapping
Abstract
Abstract The expression and location of proteins in tissues represent key determinants of health and disease. Although recent advances in multiplexed imaging have expanded the number of spatially accessible proteins1–3, the integration of biological layers (that is, cell structure, subcellular domains and signalling activity) remains challenging. This is due to limitations in the compositions of antibody panels and image resolution, which together restrict the scope of image analysis. Here we present pathology-oriented multiplexing (PathoPlex), a scalable, quality-controlled and interpretable framework. It combines highly multiplexed imaging at subcellular resolution with a software package to extract and interpret protein co-expression patterns (clusters) across biological layers. PathoPlex was optimized to map more than 140 commercial antibodies at 80 nm per pixel across 95 iterative imaging cycles and provides pragmatic solutions to enable the simultaneous processing of at least 40 archival biopsy specimens. In a proof-of-concept experiment, we identified epithelial JUN activity as a key switch in immune-mediated kidney disease, thereby demonstrating that clusters can capture relevant pathological features. PathoPlex was then used to analyse human diabetic kidney disease. The framework linked patient-level clusters to organ disfunction and identified disease traits with therapeutic potential (that is, calcium-mediated tubular stress). Finally, PathoPlex was used to reveal renal stress-related clusters in individuals with type 2 diabetes without histological kidney disease. Moreover, tissue-based readouts were generated to assess responses to inhibitors of the glucose cotransporter SGLT2. In summary, PathoPlex paves the way towards democratizing multiplexed imaging and establishing integrative image analysis tools in complex tissues to support the development of next-generation pathology atlases.
Article Details
Authors (75)
Malte Kuehl
Yusuke Okabayashi
Milagros N. Wong
Lukas Gernhold
Gabriele Gut
Nico Kaiser
Maria Schwerk
Stefanie K. Gräfe
Frank Y. Ma
Jovan Tanevski
Philipp S. L. Schäfer
Sam Mezher
Jacobo Sarabia del Castillo
Thiago Goldbeck-Strieder
Olga Zolotareva
Michael Hartung
Fernando M. Delgado Chaves
Lukas Klinkert
Ann-Christin Gnirck
Marc Spehr
David Fleck
Mehdi Joodaki
Victor Parra
Mina Shaigan
Martin Diebold
Marco Prinz
Jennifer Kranz
Johan M. Kux
Fabian Braun
Oliver Kretz
Hui Wu
Florian Grahammer
Sven Heins
Marina Zimmermann
Fabian Haas
Dominik Kylies
Nicola Wanner
Jan Czogalla
Bernhard Dumoulin
Nikolay Zolotarev
Maja Lindenmeyer
Pall Karlson
Jens R. Nyengaard
Marcial Sebode
Sören Weidemann
Thorsten Wiech
Hermann-Josef Groene
Nicola M. Tomas
Catherine Meyer-Schwesinger
Christoph Kuppe
Rafael Kramann
Alexandre Karras
Patrick Bruneval
Pierre-Louis Tharaux
Diego Pastene
Benito Yard
Jennifer A. Schaub
Phillip J. McCown
Laura Pyle
Ye Ji Choi
Takashi Yokoo
Jan Baumbach
Pablo J. Sáez
Ivan Costa
Jan-Eric Turner
Jeffrey B. Hodgin
Julio Saez-Rodríguez
Tobias B. Huber
Petter Bjornstad
Matthias Kretzler
Olivia Lenoir
David J. Nikolic-Paterson
Lucas Pelkmans
Stefan Bonn
Victor G. Puelles