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Deep learning for dual detection of microsatellite instability and POLE mutations in colorectal cancer histopathology

In the spectrum of colorectal tumors, microsatellite-stable (MSS) tumors with DNA polymerase ε (POLE) mutations exhibit a hypermutated profile, holding the potential to respond to immunotherapy similarly to their microsatellite-instable (MSI) counterparts. Yet, due to their rarity and the associated...

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Main Authors: Gustav, Marco (Author) , Reitsam, Nic Gabriel (Author) , Carrero, Zunamys I. (Author) , Loeffler, Chiara M. L. (Author) , van Treeck, Marko (Author) , Yuan, Tanwei (Author) , West, Nicholas P. (Author) , Quirke, Philip (Author) , Brinker, Titus Josef (Author) , Brenner, Hermann (Author) , Favre, Loëtitia (Author) , Märkl, Bruno (Author) , Stenzinger, Albrecht (Author) , Brobeil, Alexander (Author) , Hoffmeister, Michael (Author) , Calderaro, Julien (Author) , Pujals, Anaïs (Author) , Kather, Jakob Nikolas (Author)
Format: Article (Journal)
Language:English
Published: 23 May 2024
In: npj precision oncology
Year: 2024, Volume: 8, Pages: 1-11
ISSN:2397-768X
DOI:10.1038/s41698-024-00592-z
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.1038/s41698-024-00592-z
Verlag, kostenfrei, Volltext: https://www.nature.com/articles/s41698-024-00592-z
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Author Notes:Marco Gustav, Nic Gabriel Reitsam, Zunamys I. Carrero, Chiara M.L. Loeffler, Marko van Treeck, Tanwei Yuan, Nicholas P. West, Philip Quirke, Titus J. Brinker, Hermann Brenner, Loëtitia Favre, Bruno Märkl, Albrecht Stenzinger, Alexander Brobeil, Michael Hoffmeister, Julien Calderaro, Anaïs Pujals & Jakob Nikolas Kather
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Summary:In the spectrum of colorectal tumors, microsatellite-stable (MSS) tumors with DNA polymerase ε (POLE) mutations exhibit a hypermutated profile, holding the potential to respond to immunotherapy similarly to their microsatellite-instable (MSI) counterparts. Yet, due to their rarity and the associated testing costs, systematic screening for these mutations is not commonly pursued. Notably, the histopathological phenotype resulting from POLE mutations is theorized to resemble that of MSI. This resemblance not only could facilitate their detection by a transformer-based Deep Learning (DL) system trained on MSI pathology slides, but also indicates the possibility for MSS patients with POLE mutations to access enhanced treatment options, which might otherwise be overlooked. To harness this potential, we trained a Deep Learning classifier on a large dataset with the ground truth for microsatellite status and subsequently validated its capabilities for MSI and POLE detection across three external cohorts. Our model accurately identified MSI status in both the internal and external resection cohorts using pathology images alone. Notably, with a classification threshold of 0.5, over 75% of POLE driver mutant patients in the external resection cohorts were flagged as “positive” by a DL system trained on MSI status. In a clinical setting, deploying this DL model as a preliminary screening tool could facilitate the efficient identification of clinically relevant MSI and POLE mutations in colorectal tumors, in one go.
Item Description:Gesehen am 25.11.2024
Physical Description:Online Resource
ISSN:2397-768X
DOI:10.1038/s41698-024-00592-z

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