TY - JOUR
T1 - Quantitative assessment of inflammatory infiltrates in kidney transplant biopsies using multiplex tyramide signal amplification and deep learning
AU - Hermsen, Meyke
AU - Volk, Valery
AU - Bräsen, Jan Hinrich
AU - Geijs, Daan J.
AU - Gwinner, Wilfried
AU - Kers, Jesper
AU - Linmans, Jasper
AU - Schaadt, Nadine S.
AU - Schmitz, Jessica
AU - Steenbergen, Eric J.
AU - Swiderska-Chadaj, Zaneta
AU - Smeets, Bart
AU - Hilbrands, Luuk B.
AU - Feuerhake, Friedrich
AU - van der Laak, Jeroen A. W. M.
N1 - Funding Information: Funding This work was supported by the ERACoSysMed initiative (project SysMIFTA) as part of the European Union’s Horizon 2020 Framework Programme offered by ZonMw (grant no. 9003035004), with co-funding by the German Ministry of Research and Education (BMBF), grant no. FKZ031L-0085A (SysMIFTA), FKZ01ZX1710A (MicMode-I2T), and FKZ01ZX1608A (SYSIMIT). JAWML received consultancy fees from Philips (The Netherlands), and grants from ContextVision, Philips (The Netherlands), and Sectra (Sweden), outside of the submitted work. JK received financial support from the Dutch Kidney Foundation (project DEEPGRAFT, Grant No. 17OKG23). Publisher Copyright: © 2021, The Author(s). Copyright: Copyright 2021 Elsevier B.V., All rights reserved.
PY - 2021/8
Y1 - 2021/8
N2 - Delayed graft function (DGF) is a strong risk factor for development of interstitial fibrosis and tubular atrophy (IFTA) in kidney transplants. Quantitative assessment of inflammatory infiltrates in kidney biopsies of DGF patients can reveal predictive markers for IFTA development. In this study, we combined multiplex tyramide signal amplification (mTSA) and convolutional neural networks (CNNs) to assess the inflammatory microenvironment in kidney biopsies of DGF patients (n = 22) taken at 6 weeks post-transplantation. Patients were stratified for IFTA development (<10% versus ≥10%) from 6 weeks to 6 months post-transplantation, based on histopathological assessment by three kidney pathologists. One mTSA panel was developed for visualization of capillaries, T- and B-lymphocytes and macrophages and a second mTSA panel for T-helper cell and macrophage subsets. The slides were multi spectrally imaged and custom-made python scripts enabled conversion to artificial brightfield whole-slide images (WSI). We used an existing CNN for the detection of lymphocytes with cytoplasmatic staining patterns in immunohistochemistry and developed two new CNNs for the detection of macrophages and nuclear-stained lymphocytes. F1-scores were 0.77 (nuclear-stained lymphocytes), 0.81 (cytoplasmatic-stained lymphocytes), and 0.82 (macrophages) on a test set of artificial brightfield WSI. The CNNs were used to detect inflammatory cells, after which we assessed the peritubular capillary extent, cell density, cell ratios, and cell distance in the two patient groups. In this cohort, distance of macrophages to other immune cells and peritubular capillary extent did not vary significantly at 6 weeks post-transplantation between patient groups. CD163 + cell density was higher in patients with ≥10% IFTA development 6 months post-transplantation (p < 0.05). CD3 +CD8 −/CD3 +CD8 + ratios were higher in patients with <10% IFTA development (p < 0.05). We observed a high correlation between CD163 + and CD4 +GATA3 + cell density (R = 0.74, p < 0.001). Our study demonstrates that CNNs can be used to leverage reliable, quantitative results from mTSA-stained, multi spectrally imaged slides of kidney transplant biopsies.
AB - Delayed graft function (DGF) is a strong risk factor for development of interstitial fibrosis and tubular atrophy (IFTA) in kidney transplants. Quantitative assessment of inflammatory infiltrates in kidney biopsies of DGF patients can reveal predictive markers for IFTA development. In this study, we combined multiplex tyramide signal amplification (mTSA) and convolutional neural networks (CNNs) to assess the inflammatory microenvironment in kidney biopsies of DGF patients (n = 22) taken at 6 weeks post-transplantation. Patients were stratified for IFTA development (<10% versus ≥10%) from 6 weeks to 6 months post-transplantation, based on histopathological assessment by three kidney pathologists. One mTSA panel was developed for visualization of capillaries, T- and B-lymphocytes and macrophages and a second mTSA panel for T-helper cell and macrophage subsets. The slides were multi spectrally imaged and custom-made python scripts enabled conversion to artificial brightfield whole-slide images (WSI). We used an existing CNN for the detection of lymphocytes with cytoplasmatic staining patterns in immunohistochemistry and developed two new CNNs for the detection of macrophages and nuclear-stained lymphocytes. F1-scores were 0.77 (nuclear-stained lymphocytes), 0.81 (cytoplasmatic-stained lymphocytes), and 0.82 (macrophages) on a test set of artificial brightfield WSI. The CNNs were used to detect inflammatory cells, after which we assessed the peritubular capillary extent, cell density, cell ratios, and cell distance in the two patient groups. In this cohort, distance of macrophages to other immune cells and peritubular capillary extent did not vary significantly at 6 weeks post-transplantation between patient groups. CD163 + cell density was higher in patients with ≥10% IFTA development 6 months post-transplantation (p < 0.05). CD3 +CD8 −/CD3 +CD8 + ratios were higher in patients with <10% IFTA development (p < 0.05). We observed a high correlation between CD163 + and CD4 +GATA3 + cell density (R = 0.74, p < 0.001). Our study demonstrates that CNNs can be used to leverage reliable, quantitative results from mTSA-stained, multi spectrally imaged slides of kidney transplant biopsies.
UR - http://www.scopus.com/inward/record.url?scp=85106236061&partnerID=8YFLogxK
U2 - https://doi.org/10.1038/s41374-021-00601-w
DO - https://doi.org/10.1038/s41374-021-00601-w
M3 - Article
C2 - 34006891
SN - 0023-6837
VL - 101
SP - 970
EP - 982
JO - Laboratory investigation; a journal of technical methods and pathology
JF - Laboratory investigation; a journal of technical methods and pathology
IS - 8
ER -