Automated Prediction of Kidney Failure in IgA Nephropathy with Deep Learning from Biopsy Images
Francesca Testa, Francesco Fontana, Federico Pollastri, Johanna Chester, Marco Leonelli, Francesco Giaroni, F. Gualtieri, Federico Bolelli, Elena Mancini, Maurizio Nordio, Paolo Sacco, Giulia Ligabue, Silvia Giovanella, Maria Ferri, Gaetano Alfano, Loreto Gesualdo, Simonetta Cimino, Gabriele Donati, Costantino Grana, Riccardo Magistroni
Abstract
Background and objectives Digital pathology and artificial intelligence offer new opportunities for automatic histologic scoring. We applied a deep learning approach to IgA nephropathy biopsy images to develop an automatic histologic prognostic score, assessed against ground truth (kidney failure) among patients with IgA nephropathy who were treated over 39 years. We assessed noninferiority in comparison with the histologic component of currently validated predictive tools. We correlated additional histologic features with our deep learning predictive score to identify potential additional predictive features. Design, setting, participants, & measurements Training for deep learning was performed with randomly selected, digitalized, cortical Periodic acid–Schiff–stained sections images (363 kidney biopsy specimens) to develop our deep learning predictive score. We estimated noninferiority using the area under the receiver operating characteristic curve (AUC) in a randomly selected group (95 biopsy specimens) against the gold standard Oxford classification (MEST-C) scores used by the International IgA Nephropathy Prediction Tool and the clinical decision supporting system for estimating the risk of kidney failure in IgA nephropathy. We assessed additional potential predictive histologic features against a subset (20 kidney biopsy specimens) with the strongest and weakest deep learning predictive scores. Results We enrolled 442 patients; the 10-year kidney survival was 78%, and the study median follow-up was 6.7 years. Manual MEST-C showed no prognostic relationship for the endocapillary parameter only. The deep learning predictive score was not inferior to MEST-C applied using the International IgA Nephropathy Prediction Tool and the clinical decision supporting system (AUC of 0.84 versus 0.77 and 0.74, respectively) and confirmed a good correlation with the tubolointerstitial score (r=0.41, P <0.01). We observed no correlations between the deep learning prognostic score and the mesangial, endocapillary, segmental sclerosis, and crescent parameters. Additional potential predictive histopathologic features incorporated by the deep learning predictive score included ( 1 ) inflammation within areas of interstitial fibrosis and tubular atrophy and ( 2 ) hyaline casts. Conclusions The deep learning approach was noninferior to manual histopathologic reporting and considered prognostic features not currently included in MEST-C assessment. Podcast This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2022_07_26_CJN01760222.mp3.