1
|
Cazzaniga G, Rossi M, Eccher A, Girolami I, L'Imperio V, Van Nguyen H, Becker JU, Bueno García MG, Sbaraglia M, Dei Tos AP, Gambaro G, Pagni F. Time for a full digital approach in nephropathology: a systematic review of current artificial intelligence applications and future directions. J Nephrol 2024; 37:65-76. [PMID: 37768550 PMCID: PMC10920416 DOI: 10.1007/s40620-023-01775-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Artificial intelligence (AI) integration in nephropathology has been growing rapidly in recent years, facing several challenges including the wide range of histological techniques used, the low occurrence of certain diseases, and the need for data sharing. This narrative review retraces the history of AI in nephropathology and provides insights into potential future developments. METHODS Electronic searches in PubMed-MEDLINE and Embase were made to extract pertinent articles from the literature. Works about automated image analysis or the application of an AI algorithm on non-neoplastic kidney histological samples were included and analyzed to extract information such as publication year, AI task, and learning type. Prepublication servers and reviews were not included. RESULTS Seventy-six (76) original research articles were selected. Most of the studies were conducted in the United States in the last 7 years. To date, research has been mainly conducted on relatively easy tasks, like single-stain glomerular segmentation. However, there is a trend towards developing more complex tasks such as glomerular multi-stain classification. CONCLUSION Deep learning has been used to identify patterns in complex histopathology data and looks promising for the comprehensive assessment of renal biopsy, through the use of multiple stains and virtual staining techniques. Hybrid and collaborative learning approaches have also been explored to utilize large amounts of unlabeled data. A diverse team of experts, including nephropathologists, computer scientists, and clinicians, is crucial for the development of AI systems for nephropathology. Collaborative efforts among multidisciplinary experts result in clinically relevant and effective AI tools.
Collapse
Affiliation(s)
- Giorgio Cazzaniga
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, Università di Milano-Bicocca, Monza, Italy.
| | - Mattia Rossi
- Division of Nephrology, Department of Medicine, University of Verona, Piazzale Aristide Stefani, 1, 37126, Verona, Italy
| | - Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, P.le Stefani n. 1, 37126, Verona, Italy
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Ilaria Girolami
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, P.le Stefani n. 1, 37126, Verona, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, Università di Milano-Bicocca, Monza, Italy
| | - Hien Van Nguyen
- Department of Electrical and Computer Engineering, University of Houston, Houston, TX, 77004, USA
| | - Jan Ulrich Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - María Gloria Bueno García
- VISILAB Research Group, E.T.S. Ingenieros Industriales, University of Castilla-La Mancha, Ciudad Real, Spain
| | - Marta Sbaraglia
- Department of Pathology, Azienda Ospedale-Università Padova, Padua, Italy
- Department of Medicine, University of Padua School of Medicine, Padua, Italy
| | - Angelo Paolo Dei Tos
- Department of Pathology, Azienda Ospedale-Università Padova, Padua, Italy
- Department of Medicine, University of Padua School of Medicine, Padua, Italy
| | - Giovanni Gambaro
- Division of Nephrology, Department of Medicine, University of Verona, Piazzale Aristide Stefani, 1, 37126, Verona, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, Università di Milano-Bicocca, Monza, Italy
| |
Collapse
|
2
|
Jacq A, Tarris G, Jaugey A, Paindavoine M, Maréchal E, Bard P, Rebibou JM, Ansart M, Calmo D, Bamoulid J, Tinel C, Ducloux D, Crepin T, Chabannes M, Funes de la Vega M, Felix S, Martin L, Legendre M. Automated evaluation with deep learning of total interstitial inflammation and peritubular capillaritis on kidney biopsies. Nephrol Dial Transplant 2023; 38:2786-2798. [PMID: 37197910 DOI: 10.1093/ndt/gfad094] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Interstitial inflammation and peritubular capillaritis are observed in many diseases on native and transplant kidney biopsies. A precise and automated evaluation of these histological criteria could help stratify patients' kidney prognoses and facilitate therapeutic management. METHODS We used a convolutional neural network to evaluate those criteria on kidney biopsies. A total of 423 kidney samples from various diseases were included; 83 kidney samples were used for the neural network training, 106 for comparing manual annotations on limited areas to automated predictions, and 234 to compare automated and visual gradings. RESULTS The precision, recall and F-score for leukocyte detection were, respectively, 81%, 71% and 76%. Regarding peritubular capillaries detection the precision, recall and F-score were, respectively, 82%, 83% and 82%. There was a strong correlation between the predicted and observed grading of total inflammation, as for the grading of capillaritis (r = 0.89 and r = 0.82, respectively, all P < .0001). The areas under the receiver operating characteristics curves for the prediction of pathologists' Banff total inflammation (ti) and peritubular capillaritis (ptc) scores were respectively all above 0.94 and 0.86. The kappa coefficients between the visual and the neural networks' scores were respectively 0.74, 0.78 and 0.68 for ti ≥1, ti ≥2 and ti ≥3, and 0.62, 0.64 and 0.79 for ptc ≥1, ptc ≥2 and ptc ≥3. In a subgroup of patients with immunoglobulin A nephropathy, the inflammation severity was highly correlated to kidney function at biopsy on univariate and multivariate analyses. CONCLUSION We developed a tool using deep learning that scores the total inflammation and capillaritis, demonstrating the potential of artificial intelligence in kidney pathology.
Collapse
Affiliation(s)
- Amélie Jacq
- Department of Nephrology, CHU Dijon, Dijon, France
| | | | - Adrien Jaugey
- ESIREM School, Dijon, France
- LEAD, Laboratoire de l'étude de l'apprentissage et du Développement, Dijon, France
| | - Michel Paindavoine
- LEAD, Laboratoire de l'étude de l'apprentissage et du Développement, Dijon, France
| | | | - Patrick Bard
- ESIREM School, Dijon, France
- LEAD, Laboratoire de l'étude de l'apprentissage et du Développement, Dijon, France
| | - Jean-Michel Rebibou
- Department of Nephrology, CHU Dijon, Dijon, France
- UMR 1098, INCREASE, Besançon, France
| | - Manon Ansart
- ESIREM School, Dijon, France
- LEAD, Laboratoire de l'étude de l'apprentissage et du Développement, Dijon, France
| | - Doris Calmo
- Department of Nephrology, CHU Besançon, Besançon, France
| | - Jamal Bamoulid
- UMR 1098, INCREASE, Besançon, France
- Department of Nephrology, CHU Besançon, Besançon, France
| | - Claire Tinel
- Department of Nephrology, CHU Dijon, Dijon, France
| | - Didier Ducloux
- UMR 1098, INCREASE, Besançon, France
- Department of Nephrology, CHU Besançon, Besançon, France
| | - Thomas Crepin
- UMR 1098, INCREASE, Besançon, France
- Department of Nephrology, CHU Besançon, Besançon, France
| | - Melchior Chabannes
- UMR 1098, INCREASE, Besançon, France
- Department of Nephrology, CHU Besançon, Besançon, France
| | | | - Sophie Felix
- Department of Pathology, CHU Besançon, Besançon, France
| | | | - Mathieu Legendre
- Department of Nephrology, CHU Dijon, Dijon, France
- UMR 1098, INCREASE, Besançon, France
| |
Collapse
|
3
|
Klinkhammer BM, Boor P. Kidney fibrosis: Emerging diagnostic and therapeutic strategies. Mol Aspects Med 2023; 93:101206. [PMID: 37541106 DOI: 10.1016/j.mam.2023.101206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023]
Abstract
An increasing number of patients worldwide suffers from chronic kidney disease (CKD). CKD is accompanied by kidney fibrosis, which affects all compartments of the kidney, i.e., the glomeruli, tubulointerstitium, and vasculature. Fibrosis is the best predictor of progression of kidney diseases. Currently, there is no specific anti-fibrotic therapy for kidney patients and invasive renal biopsy remains the only option for specific detection and quantification of kidney fibrosis. Here we review emerging diagnostic approaches and potential therapeutic options for fibrosis. We discuss how translational research could help to establish fibrosis-specific endpoints for clinical trials, leading to improved patient stratification and potentially companion diagnostics, and facilitating and optimizing development of novel anti-fibrotic therapies for kidney patients.
Collapse
Affiliation(s)
| | - Peter Boor
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany; Electron Microscopy Facility, RWTH Aachen University Hospital, Aachen, Germany; Division of Nephrology and Immunology, RWTH Aachen University Hospital, Aachen, Germany.
| |
Collapse
|
4
|
Denicolò S, Nair V, Leierer J, Rudnicki M, Kretzler M, Mayer G, Ju W, Perco P. Assessment of Fibrinogen-like 2 (FGL2) in Human Chronic Kidney Disease through Transcriptomics Data Analysis. Biomolecules 2022; 13:89. [PMID: 36671474 PMCID: PMC9855364 DOI: 10.3390/biom13010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 01/03/2023] Open
Abstract
Fibrinogen-like 2 (FGL2) was recently found to be associated with fibrosis in a mouse model of kidney damage and was proposed as a potential therapeutic target in chronic kidney disease (CKD). We assessed the association of renal FGL2 mRNA expression with the disease outcome in two independent CKD cohorts (NEPTUNE and Innsbruck CKD cohort) using Kaplan Meier survival analysis. The regulation of FGL2 in kidney biopsies of CKD patients as compared to healthy controls was further assessed in 13 human CKD transcriptomics datasets. The FGL2 protein expression in human renal tissue sections was determined via immunohistochemistry. The regulators of FGL2 mRNA expression in renal tissue were identified in the co-expression and upstream regulator analysis of FGL2-positive renal cells via the use of single-cell RNA sequencing data from the kidney precision medicine project (KPMP). Higher renal FGL2 mRNA expression was positively associated with kidney fibrosis and negatively associated with eGFR. Renal FGL2 mRNA expression was upregulated in CKD as compared with healthy controls and associated with CKD progression in the Innsbruck CKD cohort (p-value = 0.0036) and NEPTUNE cohort (p-value = 0.0048). The highest abundance of FGL2 protein in renal tissue was detected in the thick ascending limb of the loop of Henle and macula densa, proximal tubular cells, as well as in glomerular endothelial cells. The upstream regulator analysis identified TNF, IL1B, IFNG, NFKB1, and SP1 as factors potentially inducing FGL2-co-expressed genes, whereas factors counterbalancing FGL2-co-expressed genes included GLI1, HNF1B, or PPARGC1A. In conclusion, renal FGL2 mRNA expression is elevated in human CKD, and higher FGL2 levels are associated with fibrosis and worse outcomes.
Collapse
Affiliation(s)
- Sara Denicolò
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Viji Nair
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Johannes Leierer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Michael Rudnicki
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gert Mayer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Wenjun Ju
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul Perco
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020 Innsbruck, Austria
| |
Collapse
|
5
|
ŞAKIR AA, IŞIK AH, ÖZMEN Ö, İPEK V. Analysis and Estimation of Pathological Data and Findings with Deep Learning Methods. MEHMET AKIF ERSOY ÜNIVERSITESI VETERINER FAKÜLTESI DERGISI 2022. [DOI: 10.24880/maeuvfd.1121112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
As in human diseases, rapid diagnosis of animal diseases is of great importance. In order for the disease treatments to be carried out properly, the diagnosis must be of high accuracy, as well as the rapid diagnosis. In this study, the disease types in the data set consisting of the data examined between the years 2000-2020 belonging to the Department of Pathology of the Faculty of Veterinary Medicine of Burdur Mehmet Akif Ersoy University were estimated by using the decision tree classification model and the KNN classification model. Categories such as age, type, city, and gender in the data set were analyzed in graphics. For the estimation and analysis processes to give accurate results, the data set was corrected by going through some pre-processes and the missing data in the data set was completed. It is thought that the results obtained from the estimation and analysis will allow rapid and accurate diagnosis in animal disease diagnoses.
Collapse
|
6
|
Silva J, Souza L, Chagas P, Calumby R, Souza B, Pontes I, Duarte A, Pinheiro N, Santos W, Oliveira L. Boundary-aware glomerulus segmentation: Toward one-to-many stain generalization. Comput Med Imaging Graph 2022; 100:102104. [PMID: 36007483 DOI: 10.1016/j.compmedimag.2022.102104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/28/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022]
Abstract
The growing availability of scanned whole-slide images (WSIs) has allowed nephropathology to open new possibilities for medical decision-making over high-resolution images. Diagnosis of renal WSIs includes locating and identifying specific structures in the tissue. Considering the glomerulus as one of the first structures analyzed by pathologists, we propose here a novel convolutional neural network for glomerulus segmentation. Our end-to-end network, named DS-FNet, combines the strengths of semantic segmentation and semantic boundary detection networks via an attention-aware mechanism. Although we trained the proposed network on periodic acid-Schiff (PAS)-stained WSIs, we found that our network was capable to segment glomeruli on WSIs stained with different techniques, such as periodic acid-methenamine silver (PAMS), hematoxylin-eosin (HE), and Masson trichrome (TRI). To assess the performance of the proposed method, we used three public data sets: HuBMAP (available in a Kaggle competition), a subset of the NEPTUNE data set, and a novel challenging data set, called WSI_Fiocruz. We compared the DS-FNet with six other deep learning networks: original U-Net, our attention version of U-Net called AU-Net, U-Net++, U-Net3Plus, ResU-Net, and DeepLabV3+. Results showed that DS-FNet achieved equivalent or superior results on all data sets: On the HuBMAP data set, it reached a dice score (DSC) of 95.05%, very close to the first place (95.15%); on the NEPTUNE and WSI_Fiocruz data sets, DS-FNet obtained the highest average DSC, whether on PAS-stained images or images stained with other techniques. To the best we know, this is the first work to show consistently high performance in a one-to-many-stain glomerulus segmentation following a thorough protocol on data sets from different medical labs.
Collapse
Affiliation(s)
- Jefferson Silva
- Universidade Federal do Maranhão, Brazil; Universidade Federal da Bahia, Brazil
| | | | | | | | - Bianca Souza
- Universidade Federal da Bahia, Brazil; Fundação Oswaldo Cruz, Brazil
| | | | | | | | - Washington Santos
- Universidade Federal da Bahia, Brazil; Fundação Oswaldo Cruz, Brazil
| | | |
Collapse
|
7
|
Hodgin JB, Mariani LH, Zee J, Liu Q, Smith AR, Eddy S, Hartman J, Hamidi H, Gaut JP, Palmer MB, Nast CC, Chang A, Hewitt S, Gillespie BW, Kretzler M, Holzman LB, Barisoni L. Quantification of Glomerular Structural Lesions: Associations With Clinical Outcomes and Transcriptomic Profiles in Nephrotic Syndrome. Am J Kidney Dis 2022; 79:807-819.e1. [PMID: 34864148 DOI: 10.1053/j.ajkd.2021.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/20/2021] [Indexed: 12/18/2022]
Abstract
RATIONALE & OBJECTIVE The current classification system for focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD) does not fully capture the complex structural changes in kidney biopsies nor the clinical and molecular heterogeneity of these diseases. STUDY DESIGN Prospective observational cohort study. SETTING & PARTICIPANTS 221 MCD and FSGS patients enrolled in the Nephrotic Syndrome Study Network (NEPTUNE). EXPOSURE The NEPTUNE Digital Pathology Scoring System (NDPSS) was applied to generate scores for 37 glomerular descriptors. OUTCOME Time from biopsy to complete proteinuria remission, time from biopsy to kidney disease progression (40% estimated glomerular filtration rate [eGFR] decline or kidney failure), and eGFR over time. ANALYTICAL APPROACH Cluster analysis was used to group patients with similar morphologic characteristics. Glomerular descriptors and patient clusters were assessed for associations with outcomes using adjusted Cox models and linear mixed models. Messenger RNA from glomerular tissue was used to assess differentially expressed genes between clusters and identify genes associated with individual descriptors driving cluster membership. RESULTS Three clusters were identified: X (n = 56), Y (n = 68), and Z (n = 97). Clusters Y and Z had higher probabilities of proteinuria remission (HRs of 1.95 [95% CI, 0.99-3.85] and 3.29 [95% CI, 1.52-7.13], respectively), lower hazards of disease progression (HRs of 0.22 [95% CI, 0.08-0.57] and 0.11 [95% CI, 0.03-0.45], respectively), and lower loss of eGFR over time compared with X. Cluster X had 1,920 genes that were differentially expressed compared with Y+Z; these reflected activation of pathways of immune response and inflammation. Six descriptors driving the clusters individually correlated with clinical outcomes and gene expression. LIMITATIONS Low prevalence of some descriptors and biopsy at a single time point. CONCLUSIONS The NDPSS allows for categorization of FSGS/MCD patients into clinically and biologically relevant subgroups, and uncovers histologic parameters associated with clinical outcomes and molecular signatures not included in current classification systems.
Collapse
Affiliation(s)
- Jeffrey B Hodgin
- Renal Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan.
| | - Laura H Mariani
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jarcy Zee
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania; Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Qian Liu
- Arbor Research Collaborative for Health, Ann Arbor, Michigan, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Abigail R Smith
- Arbor Research Collaborative for Health, Ann Arbor, Michigan, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sean Eddy
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - John Hartman
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Habib Hamidi
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Joseph P Gaut
- Department of Pathology and Immunology, and Internal Medicine, Washington University, St. Louis, Missouri
| | - Matthew B Palmer
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Cynthia C Nast
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Anthony Chang
- Department of Pathology, University of Chicago Medicine, Chicago, Illinois
| | - Stephen Hewitt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Brenda W Gillespie
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Lawrence B Holzman
- Renal-Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Laura Barisoni
- Department of Pathology, Division of AI & Computational Pathology, Duke University, Durham, North Carolina; Department of Medicine, Division of Nephrology, Duke University, Durham, North Carolina.
| |
Collapse
|
8
|
Zee J, Liu Q, Smith AR, Hodgin JB, Rosenberg A, Gillespie BW, Holzman LB, Barisoni L, Mariani LH. Kidney Biopsy Features Most Predictive of Clinical Outcomes in the Spectrum of Minimal Change Disease and Focal Segmental Glomerulosclerosis. J Am Soc Nephrol 2022; 33:1411-1426. [PMID: 35581011 PMCID: PMC9257823 DOI: 10.1681/asn.2021101396] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/01/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Heterogeneity in disease course and treatment response among patients with MCD/FSGS necessitates a granular evaluation of kidney tissue features. This study aimed to identify histologic and ultrastructural descriptors of structural changes most predictive of clinical outcomes in the Nephrotic Syndrome Study Network (NEPTUNE). METHODS Forty-eight histologic (37 glomerular, 9 tubulointerstitial, 2 vascular) and 20 ultrastructural descriptors were quantified by applying the NEPTUNE Digital Pathology Scoring System to NEPTUNE kidney biopsies. Outcomes included time from biopsy to disease progression, first complete remission of proteinuria, and treatment response. Relative importance of pathology and clinical predictors was obtained from random forest models, and predictive discrimination was assessed. RESULTS Among 224 participants (34% Black, 24% Hispanic), model performance was excellent, with predictive discrimination of 0.9 for disease progression, 0.85 for complete remission, and 0.81 for treatment response. The most predictive descriptors of outcomes included both conventional-e.g., global sclerosis or segmental sclerosis and interstitial fibrosis/tubular atrophy-and novel features, including adhesion, interstitial foam cells, deflation, periglomerular fibrosis, mononuclear white blood cells, endothelial cell abnormalities, microvillous transformation, and acute tubular injury. CONCLUSIONS The most predictive descriptors of clinical outcomes among MCD/FSGS patients reflected structural changes in multiple renal compartments. Reporting these descriptors should be standardized to guide prognostication of proteinuric glomerular diseases.
Collapse
Affiliation(s)
- Jarcy Zee
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, and Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Qian Liu
- Arbor Research Collaborative for Health, Ann Arbor, Michigan
| | - Abigail R Smith
- Arbor Research Collaborative for Health, Ann Arbor, Michigan
| | - Jeffrey B Hodgin
- Renal Pathology, Department of Pathology and Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan
| | - Avi Rosenberg
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland and Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Brenda W Gillespie
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Lawrence B Holzman
- Renal-Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Laura Barisoni
- Department of Pathology, Division of AI and Computational Pathology, and Department of Medicine, Division of Nephrology, Duke University, Durham, North Carolina
| | | | | |
Collapse
|
9
|
Lee J, Warner E, Shaikhouni S, Bitzer M, Kretzler M, Gipson D, Pennathur S, Bellovich K, Bhat Z, Gadegbeku C, Massengill S, Perumal K, Saha J, Yang Y, Luo J, Zhang X, Mariani L, Hodgin JB, Rao A. Unsupervised machine learning for identifying important visual features through bag-of-words using histopathology data from chronic kidney disease. Sci Rep 2022; 12:4832. [PMID: 35318420 PMCID: PMC8941143 DOI: 10.1038/s41598-022-08974-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 12/22/2022] Open
Abstract
Pathologists use visual classification to assess patient kidney biopsy samples when diagnosing the underlying cause of kidney disease. However, the assessment is qualitative, or semi-quantitative at best, and reproducibility is challenging. To discover previously unknown features which predict patient outcomes and overcome substantial interobserver variability, we developed an unsupervised bag-of-words model. Our study applied to the C-PROBE cohort of patients with chronic kidney disease (CKD). 107,471 histopathology images were obtained from 161 biopsy cores and identified important morphological features in biopsy tissue that are highly predictive of the presence of CKD both at the time of biopsy and in one year. To evaluate the performance of our model, we estimated the AUC and its 95% confidence interval. We show that this method is reliable and reproducible and can achieve 0.93 AUC at predicting glomerular filtration rate at the time of biopsy as well as predicting a loss of function at one year. Additionally, with this method, we ranked the identified morphological features according to their importance as diagnostic markers for chronic kidney disease. In this study, we have demonstrated the feasibility of using an unsupervised machine learning method without human input in order to predict the level of kidney function in CKD. The results from our study indicate that the visual dictionary, or visual image pattern, obtained from unsupervised machine learning can predict outcomes using machine-derived values that correspond to both known and unknown clinically relevant features.
Collapse
Affiliation(s)
- Joonsang Lee
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Elisa Warner
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Salma Shaikhouni
- Department of Internal Medicine, Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Markus Bitzer
- Department of Internal Medicine, Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Matthias Kretzler
- Department of Internal Medicine, Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Debbie Gipson
- Department of Pediatrics, Pediatric Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Subramaniam Pennathur
- Department of Internal Medicine, Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Keith Bellovich
- Department of Internal Medicine, Nephrology, St. Clair Nephrology Research, Detroit, MI, USA
| | - Zeenat Bhat
- Department of Internal Medicine, Nephrology, Wayne State University, Detroit, MI, USA
| | - Crystal Gadegbeku
- Department of Internal Medicine, Nephrology, Cleveland Clinic, Cleveland, OH, USA
| | - Susan Massengill
- Department of Pediatrics, Pediatric Nephrology, Levine Children's Hospital, Charlotte, NC, USA
| | - Kalyani Perumal
- Department of Internal Medicine, Nephrology, Department of JH Stroger Hospital, Chicago, IL, USA
| | - Jharna Saha
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yingbao Yang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jinghui Luo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Laura Mariani
- Department of Internal Medicine, Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
10
|
Impact of Consensus Definitions on Identification of Glomerular Lesions by Light and Electron Microscopy. Kidney Int Rep 2022; 7:78-86. [PMID: 35005316 PMCID: PMC8720667 DOI: 10.1016/j.ekir.2021.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 10/11/2021] [Indexed: 12/04/2022] Open
Abstract
Introduction In 2020, a working group of 13 renal pathologists published consensus definitions for 47 individual glomerular lesions found on light microscopy (LM) and 47 glomerular lesions and 9 normal structures found on electron microscopy (EM). Methods To test the impact of these definitions on identification of these lesions and structures, 2 surveys were circulated to all members of the Renal Pathology Society (RPS), each having 32 images (19 LM, 13 EM) and accompanying questions with 5 multiple-choice answers, one being the consensus choice of the working group. The first survey (survey 1 [S1]), answered by 297 RPS members, was sent in September 2020, before publication of the consensus definitions. The second (survey 2 [S2]), with images of the same lesions and structures (but not the same images) and the same questions and multiple choices in different order, was sent in April 2020, 5 months after the publication of the definitions. Results S2 was taken by 181 RPS members; 64% also took S1 and 61% reported having read the definitions paper (def. paper). Mean agreement with the consensus answers increased modestly between the 2 surveys (65.2% vs. 72.0%, P = 0.097); the increase was greater and significant when only respondents to S2 who read the def. paper were considered (65.2% vs. 74.8%, P = 0.026). Furthermore, in S2 agreement with consensus answers was greater among respondents who read this paper versus those who did not (66.9% vs. 74.8%, P < 0.0001). Conclusions Publication of the consensus definitions modestly improved interobserver agreement in identification of glomerular lesions.
Collapse
|
11
|
Kline A, Chung HJ, Rahmani W, Chun J. Semi-Supervised Segmentation of Renal Pathology: An Alternative to Manual Segmentation and Input to Deep Learning Training. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021; 2021:2688-2691. [PMID: 34891805 DOI: 10.1109/embc46164.2021.9630248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Kidney biopsy interpretation is the gold standard for the diagnosis and prognosis for kidney disease. Pathognomonic diagnosis hinges on the correct assessment of different structures within a biopsy that is manually visualized and interpreted by a renal pathologist. This laborious undertaking has spurred attempts to automate the process, offloading the consumption of temporal resources. Segmentation of kidney structures, specifically, the glomeruli, tubules, and interstitium, is a precursory step for disease classification problems. Translating renal disease decision making into a deep learning model for diagnostic and prognostic classification also relies on adequate segmentation of structures within the kidney biopsy. This study showcases a semi-automated segmentation technique where the user defines starting points for glomeruli in kidney biopsy images of both healthy normal and diabetic kidney disease stained with Nile Red that are subsequently partitioned into four areas: background, glomeruli, tubules and interstitium. Five of 30 biopsies that were segmented using the semi-automated method were randomly selected and the regions of interest were compared to the manual segmentation of the same images. Dice Similarity Coefficients (DSC) between the methods showed excellent agreement; Healthy (glomeruli: 0.92, tubules: 0.86, intersititium: 0.78) and diabetic nephropathy: (glomeruli: 0.94, tubules: 0.80, intersititium: 0.80). To our knowledge this is the first semi-automated segmentation algorithm performed with human renal biopsies stained with Nile Red. Utility of this methodology includes further image processing within structures across disease states based on biological morphological structures. It can also be used as input into a deep learning network to train semantic segmentation and input into a deep learning algorithm for classification of disease states.
Collapse
|
12
|
Lao Q, Xia W, Jin J, Jia Y, Feng J. Modified Look-Locker Inverse-Recovery (MOLLI) Sequence of Quantitative Imaging in Dirty Magnetic Resonance Longitudinal Relaxation Time Diagnostic Value of GE Combined with Longitudinal Relaxation Time Quantitative Imaging for Myocardial Amyloidosis. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:2800891. [PMID: 34712458 PMCID: PMC8548173 DOI: 10.1155/2021/2800891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/15/2021] [Accepted: 09/18/2021] [Indexed: 11/17/2022]
Abstract
The pathological changes of myocarditis include degeneration and necrosis of myocardial cells and infiltration of inflammatory cells in the myocardial interstitium, accompanied by obvious myocardial fibrosis. Myocardial fibrosis is a determinant of ventricular remodeling and an important indicator of the classification of clinical risk factors and has an important value in evaluating the prognosis of heart disease. Cardiac magnetic resonance (CMR) is the "gold standard" for evaluating the shape and function of the heart, and it can show the characteristic pathological changes of myocardial tissue. The traditional gadolinium imaging agent delays the enhanced sequence images to visually show the extent of the affected myocardial fibrosis, but it cannot effectively identify small focal fibrosis or widespread diffuse fibrosis. The CMR longitudinal relaxation time quantitative technique can directly measure the relaxation time (T1) determined by the myocardial tissue and does not depend on the signal strength of the reference tissue and can quantitatively analyze the affected myocardium. In this study, the initial and enhanced quantitative imaging techniques of CMR were used to measure the magnetic value of the myocardium in patients with myocarditis, to explore the diagnostic value of myocardial fibrosis, and to analyze the correlation between cardiac fibrosis and cardiac function.
Collapse
Affiliation(s)
- Qun Lao
- Department of Radiology, Hangzhou Children's Hospital, Hangzhou, Zhejiang 310014, China
| | - Wenping Xia
- Department of Radiology, Yin Zhou Second Hospital, Ningbo, Zhejiang 315040, China
| | - Jing Jin
- Department of Radiology, Yin Zhou Second Hospital, Ningbo, Zhejiang 315040, China
| | - Yuzhu Jia
- Department of Radiology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang 310012, China
| | - Jianju Feng
- Departments of Radiology, Zhuji Affiliated Hospital of Shaoxing University, Zhuji People's Hospital, Zhuji, Zhejiang 311800, China
| |
Collapse
|
13
|
APOL1 genotype-associated morphologic changes among patients with focal segmental glomerulosclerosis. Pediatr Nephrol 2021; 36:2747-2757. [PMID: 33646395 PMCID: PMC8524347 DOI: 10.1007/s00467-021-04990-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/25/2021] [Accepted: 02/05/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND The G1 and G2 alleles of apolipoprotein L1 (APOL1) are common in the Black population and associated with increased risk of focal segmental glomerulosclerosis (FSGS). The molecular mechanisms linking APOL1 risk variants with FSGS are not clearly understood, and APOL1's natural absence in laboratory animals makes studying its pathobiology challenging. METHODS In a cohort of 90 Black patients with either FSGS or minimal change disease (MCD) enrolled in the Nephrotic Syndrome Study Network (58% pediatric onset), we used kidney biopsy traits as an intermediate outcome to help illuminate tissue-based consequences of APOL1 risk variants and expression. We tested associations between APOL1 risk alleles or glomerular APOL1 mRNA expression and 83 light- or electron-microscopy traits measuring structural and cellular kidney changes. RESULTS Under both recessive and dominant models in the FSGS patient subgroup (61%), APOL1 risk variants were significantly correlated (defined as FDR <0.1) with decreased global mesangial hypercellularity, decreased condensation of cytoskeleton, and increased tubular microcysts. No significant correlations were detected in MCD cohort. Independent of risk alleles, glomerular APOL1 expression in FSGS patients was not correlated with morphologic features. CONCLUSIONS While APOL1-associated FSGS is associated with two risk alleles, both one and two risk alleles are associated with cellular/tissue changes in this study of FSGS patients. Our lack of discovery of a large group of tissue differences in FSGS and no significant difference in MCD may be due to the lack of power but also supports investigating whether machine learning methods may more sensitively detect APOL1-associated changes.
Collapse
|
14
|
Huo Y, Deng R, Liu Q, Fogo AB, Yang H. AI applications in renal pathology. Kidney Int 2021; 99:1309-1320. [PMID: 33581198 PMCID: PMC8154730 DOI: 10.1016/j.kint.2021.01.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/09/2021] [Accepted: 01/13/2021] [Indexed: 12/20/2022]
Abstract
The explosive growth of artificial intelligence (AI) technologies, especially deep learning methods, has been translated at revolutionary speed to efforts in AI-assisted healthcare. New applications of AI to renal pathology have recently become available, driven by the successful AI deployments in digital pathology. However, synergetic developments of renal pathology and AI require close interdisciplinary collaborations between computer scientists and renal pathologists. Computer scientists should understand that not every AI innovation is translatable to renal pathology, while renal pathologists should capture high-level principles of the relevant AI technologies. Herein, we provide an integrated review on current and possible future applications in AI-assisted renal pathology, by including perspectives from computer scientists and renal pathologists. First, the standard stages, from data collection to analysis, in full-stack AI-assisted renal pathology studies are reviewed. Second, representative renal pathology-optimized AI techniques are introduced. Last, we review current clinical AI applications, as well as promising future applications with the recent advances in AI.
Collapse
Affiliation(s)
- Yuankai Huo
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Ruining Deng
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Quan Liu
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Agnes B Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Haichun Yang
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
| |
Collapse
|
15
|
Lujan G, Quigley JC, Hartman D, Parwani A, Roehmholdt B, Meter BV, Ardon O, Hanna MG, Kelly D, Sowards C, Montalto M, Bui M, Zarella MD, LaRosa V, Slootweg G, Retamero JA, Lloyd MC, Madory J, Bowman D. Dissecting the Business Case for Adoption and Implementation of Digital Pathology: A White Paper from the Digital Pathology Association. J Pathol Inform 2021; 12:17. [PMID: 34221633 PMCID: PMC8240548 DOI: 10.4103/jpi.jpi_67_20] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/20/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022] Open
Abstract
We believe the switch to a digital pathology (DP) workflow is imminent and it is essential to understand the economic implications of conversion. Many aspects of the adoption of DP will be disruptive and have a direct financial impact, both in short term costs, such as investment in equipment and personnel, and long term revenue potential, such as improved productivity and novel tests. The focus of this whitepaper is to educate pathologists, laboratorians and other stakeholders about the business and monetary considerations of converting to a digital pathology workflow. The components of a DP business plan will be thoroughly summarized, and guidance will be provided on how to build a case for adoption and implementation as well as a roadmap for transitioning from an analog to a digital pathology workflow in various laboratory settings. It is important to clarify that this publication is not intended to list prices although some financials will be mentioned as examples. The authors encourage readers who are evaluating conversion to a DP workflow to use this paper as a foundational guide for conducting a thorough and complete assessment while incorporating in current market pricing. Contributors to this paper analyzed peer-reviewed literature and data collected from various institutions, some of which are mentioned. Digital pathology will change the way we practice through facilitating patient access to expert pathology services and enabling image analysis tools and assays to aid in diagnosis, prognosis, risk stratification and therapeutic selection. Together, they will result in the delivery of valuable information from which to make better decisions and improve the health of patients.
Collapse
Affiliation(s)
- Giovanni Lujan
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - Douglas Hartman
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Anil Parwani
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Brian Roehmholdt
- Department of Pathology, Southern California Permanente Medical Group, La Canada Flintridge, CA, USA
| | | | - Orly Ardon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew G. Hanna
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Marilyn Bui
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Mark D. Zarella
- Johns Hopkins Medicine Pathology Informatics, Baltimore, MD 21287, USA
| | - Victoria LaRosa
- Education Services Department, Oracle Corp, Austin, Texas, USA
| | | | | | | | - James Madory
- Department of Pathology, Medical University of South Carolina, Charleston, SC, USA
| | | |
Collapse
|
16
|
Towards harmony in defining and reporting glomerular diseases on kidney biopsy. Curr Opin Nephrol Hypertens 2021; 30:280-286. [PMID: 33767056 DOI: 10.1097/mnh.0000000000000701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW To review recent efforts to develop uniformity and precision in defining individual glomerular histologic and ultrastructural lesions and proposals for developing greater uniformity in reporting of glomerular diseases. RECENT FINDINGS Over the past 2 decades, scoring systems for multiple glomerular diseases have emerged, as have several consortia for the study of glomerular diseases. However, one important limitation faced by renal pathologists and nephrologists has been a lack of uniformity and precision in defining the morphologic lesions seen by light and electron microscopy on which the scoring systems are based. In response to this, the Renal Pathology Society organized a working group that over 4 years arrived at consensus definitions for many such lesions. These definitions can be applied within the context of scoring systems for different glomerular diseases, and recently proposed reporting systems based on pathogenic categories and for defining the overall severity of chronic changes. SUMMARY From extensive discussions a panel of 13 renal pathologists reached consensus in defining 47 individual glomerular lesions seen on light microscopy and 56 glomerular lesions and key normal structures seen by electron microscopy. Validation of the impact of these consensus definitions on interobserver agreement in lesion identification is currently underway.
Collapse
|
17
|
Gillespie BW, Laurin LP, Zinsser D, Lafayette R, Marasa M, Wenderfer SE, Vento S, Poulton C, Barisoni L, Zee J, Helmuth M, Lugani F, Kamel M, Hill-Callahan P, Hewitt SM, Mariani LH, Smoyer WE, Greenbaum LA, Gipson DS, Robinson BM, Gharavi AG, Guay-Woodford LM, Trachtman H. Improving data quality in observational research studies: Report of the Cure Glomerulonephropathy (CureGN) network. Contemp Clin Trials Commun 2021; 22:100749. [PMID: 33851061 PMCID: PMC8039553 DOI: 10.1016/j.conctc.2021.100749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 01/16/2021] [Accepted: 02/09/2021] [Indexed: 12/21/2022] Open
Abstract
Background High data quality is of crucial importance to the integrity of research projects. In the conduct of multi-center observational cohort studies with increasing types and quantities of data, maintaining data quality is challenging, with few published guidelines. Methods The Cure Glomerulonephropathy (CureGN) Network has established numerous quality control procedures to manage the 70 participating sites in the United States, Canada, and Europe. This effort is supported and guided by the activities of several committees, including Data Quality, Recruitment and Retention, and Central Review, that work in tandem with the Data Coordinating Center to monitor the study. We have implemented coordinator training and feedback channels, data queries of questionable or missing data, and developed performance metrics for recruitment, retention, visit completion, data entry, recording of patient-reported outcomes, collection, shipping and accessing of biological samples and pathology materials, and processing, cataloging and accessing genetic data and materials. Results We describe the development of data queries and site Report Cards, and their use in monitoring and encouraging excellence in site performance. We demonstrate improvements in data quality and completeness over 4 years after implementing these activities. We describe quality initiatives addressing specific challenges in collecting and cataloging whole slide images and other kidney pathology data, and novel methods of data quality assessment. Conclusions This paper reports the CureGN experience in optimizing data quality and underscores the importance of general and study-specific data quality initiatives to maintain excellence in the research measures of a multi-center observational study.
Collapse
Affiliation(s)
- Brenda W Gillespie
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Louis-Philippe Laurin
- Division of Nephrology, Maisonneuve-Rosemont Hospital, Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Dawn Zinsser
- Arbor Research Collaborative for Health, Ann Arbor, MI, 48104, USA
| | | | - Maddalena Marasa
- Department of Medicine, Division of Nephrology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | | | - Suzanne Vento
- NYU Langone Health, Department of Pediatrics, Division of Nephrology, New York, NY, USA
| | - Caroline Poulton
- Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura Barisoni
- Department of Pathology, Division of AI and Computational Pathology, Department of Medicine, Division of Nephrology, Duke University, Durham, NC, USA
| | - Jarcy Zee
- Arbor Research Collaborative for Health, Ann Arbor, MI, 48104, USA
| | - Margaret Helmuth
- Arbor Research Collaborative for Health, Ann Arbor, MI, 48104, USA
| | - Francesca Lugani
- Laboratory of Molecular Nephrology, Istituto Giannina Gaslini, IRCCS, Genoa, Italy
| | - Margret Kamel
- Emory University, Department of Pediatrics, Division of Nephrology, Atlanta, GA, USA
| | | | - Stephen M Hewitt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura H Mariani
- University of Michigan, Division of Nephrology, Ann Arbor, MI, USA
| | - William E Smoyer
- Center for Clinical and Translational Research, the Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Larry A Greenbaum
- Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Debbie S Gipson
- University of Michigan, Division of Nephrology, Department of Pediatrics, Ann Arbor, MI, USA
| | | | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lisa M Guay-Woodford
- Center for Translational Research, Children's National Hospital, Washington, DC, USA
| | - Howard Trachtman
- NYU Langone Health, Department of Pediatrics, Division of Nephrology, New York, NY, USA
| |
Collapse
|
18
|
Abstract
PURPOSE OF REVIEW Successful integration of artificial intelligence into extant clinical workflows is contingent upon a number of factors including clinician comprehension and interpretation of computer vision. This article discusses how image analysis and machine learning have enabled comprehensive characterization of kidney morphology for development of automated diagnostic and prognostic renal pathology applications. RECENT FINDINGS The primordial digital pathology informatics work employed classical image analysis and machine learning to prognosticate renal disease. Although this classical approach demonstrated tremendous potential, subsequent advancements in hardware technology rendered artificial neural networks '(ANNs) the method of choice for machine vision in computational pathology'. Offering rapid and reproducible detection, characterization and classification of kidney morphology, ANNs have facilitated the development of diagnostic and prognostic applications. In addition, modern machine learning with ANNs has revealed novel biomarkers in kidney disease, demonstrating the potential for machine vision to elucidate novel pathologic mechanisms beyond extant clinical knowledge. SUMMARY Despite the revolutionary developments potentiated by modern machine learning, several challenges remain, including data quality control and curation, image annotation and ontology, integration of multimodal data and interpretation of machine vision or 'opening the black box'. Resolution of these challenges will not only revolutionize diagnostic pathology but also pave the way for precision medicine and integration of artificial intelligence in the process of care.
Collapse
|
19
|
Chen Y, Zee J, Smith A, Jayapandian C, Hodgin J, Howell D, Palmer M, Thomas D, Cassol C, Farris AB, Perkinson K, Madabhushi A, Barisoni L, Janowczyk A. Assessment of a computerized quantitative quality control tool for whole slide images of kidney biopsies. J Pathol 2021; 253:268-278. [PMID: 33197281 DOI: 10.1002/path.5590] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/30/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022]
Abstract
Inconsistencies in the preparation of histology slides and whole-slide images (WSIs) may lead to challenges with subsequent image analysis and machine learning approaches for interrogating the WSI. These variabilities are especially pronounced in multicenter cohorts, where batch effects (i.e. systematic technical artifacts unrelated to biological variability) may introduce biases to machine learning algorithms. To date, manual quality control (QC) has been the de facto standard for dataset curation, but remains highly subjective and is too laborious in light of the increasing scale of tissue slide digitization efforts. This study aimed to evaluate a computer-aided QC pipeline for facilitating a reproducible QC process of WSI datasets. An open source tool, HistoQC, was employed to identify image artifacts and compute quantitative metrics describing visual attributes of WSIs to the Nephrotic Syndrome Study Network (NEPTUNE) digital pathology repository. A comparison in inter-reader concordance between HistoQC aided and unaided curation was performed to quantify improvements in curation reproducibility. HistoQC metrics were additionally employed to quantify the presence of batch effects within NEPTUNE WSIs. Of the 1814 WSIs (458 H&E, 470 PAS, 438 silver, 448 trichrome) from n = 512 cases considered in this study, approximately 9% (163) were identified as unsuitable for subsequent computational analysis. The concordance in the identification of these WSIs among computational pathologists rose from moderate (Gwet's AC1 range 0.43 to 0.59 across stains) to excellent (Gwet's AC1 range 0.79 to 0.93 across stains) agreement when aided by HistoQC. Furthermore, statistically significant batch effects (p < 0.001) in the NEPTUNE WSI dataset were discovered. Taken together, our findings strongly suggest that quantitative QC is a necessary step in the curation of digital pathology cohorts. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Yijiang Chen
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Jarcy Zee
- Arbor Research Collaborative for Health, Ann Arbor, MI, USA
| | - Abigail Smith
- Arbor Research Collaborative for Health, Ann Arbor, MI, USA
| | - Catherine Jayapandian
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Jeffrey Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - David Howell
- Department of Pathology, Duke University, Durham, NC, USA
| | - Matthew Palmer
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA
| | - David Thomas
- Department of Pathology, Duke University, Durham, NC, USA.,Nephrocor, Memphis, TN, USA
| | - Clarissa Cassol
- Renal Pathology Division, Arkana Laboratories, Little Rock, AK, USA.,Department of Pathology - Renal Pathology Division, Ohio State University Medical Center, Columbus, OH, USA
| | - Alton B Farris
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | | | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.,Louis Stokes VA Medical Center, Cleveland, OH, USA
| | - Laura Barisoni
- Department of Pathology, Duke University, Durham, NC, USA.,Department of Medicine, Division of Nephrology, Duke University, Durham, NC, USA
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.,Precision Oncology Center, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
20
|
Barisoni L, Lafata KJ, Hewitt SM, Madabhushi A, Balis UGJ. Digital pathology and computational image analysis in nephropathology. Nat Rev Nephrol 2020; 16:669-685. [PMID: 32848206 PMCID: PMC7447970 DOI: 10.1038/s41581-020-0321-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2020] [Indexed: 12/17/2022]
Abstract
The emergence of digital pathology - an image-based environment for the acquisition, management and interpretation of pathology information supported by computational techniques for data extraction and analysis - is changing the pathology ecosystem. In particular, by virtue of our new-found ability to generate and curate digital libraries, the field of machine vision can now be effectively applied to histopathological subject matter by individuals who do not have deep expertise in machine vision techniques. Although these novel approaches have already advanced the detection, classification, and prognostication of diseases in the fields of radiology and oncology, renal pathology is just entering the digital era, with the establishment of consortia and digital pathology repositories for the collection, analysis and integration of pathology data with other domains. The development of machine-learning approaches for the extraction of information from image data, allows for tissue interrogation in a way that was not previously possible. The application of these novel tools are placing pathology centre stage in the process of defining new, integrated, biologically and clinically homogeneous disease categories, to identify patients at risk of progression, and shifting current paradigms for the treatment and prevention of kidney diseases.
Collapse
Affiliation(s)
- Laura Barisoni
- Department of Pathology, Duke University, Durham, NC, USA.
- Department of Medicine, Division of Nephrology, Duke University, Durham, NC, USA.
| | - Kyle J Lafata
- Department of Radiology, Duke University, Durham, NC, USA
- Department of Radiation Oncology, Duke University, Durham, NC, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
- Louis Stokes Veterans Administration Medical Center, Cleveland, OH, USA
| | | |
Collapse
|
21
|
Haas M, Seshan SV, Barisoni L, Amann K, Bajema IM, Becker JU, Joh K, Ljubanovic D, Roberts ISD, Roelofs JJ, Sethi S, Zeng C, Jennette JC. Consensus definitions for glomerular lesions by light and electron microscopy: recommendations from a working group of the Renal Pathology Society. Kidney Int 2020; 98:1120-1134. [PMID: 32866505 DOI: 10.1016/j.kint.2020.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 01/10/2023]
Abstract
Over the past 2 decades, scoring systems for multiple glomerular diseases have emerged, as have consortia of pathologists and nephrologists for the study of glomerular diseases, including correlation of pathologic findings with clinical features and outcomes. However, one important limitation faced by members of these consortia and other renal pathologists and nephrologists in both investigative work and routine practice remains a lack of uniformity and precision in clearly defining the morphologic lesions on which the scoring systems are based. In response to this issue, the Renal Pathology Society organized a working group to identify the most frequently identified glomerular lesions observed by light microscopy and electron microscopy, review the literature to capture the published definitions most often used for each, and determine consensus terms and definitions for each lesion in a series of online and in-person meetings. The defined lesions or abnormal findings are not specific for any individual disease or subset of diseases, but rather can be applied across the full spectrum of glomerular diseases and within the context of the different scoring systems used for evaluating and reporting these diseases. In addition to facilitating glomerular disease research, standardized terms and definitions should help harmonize reporting of medical kidney diseases worldwide and lead to more-precise diagnoses and improved patient care.
Collapse
Affiliation(s)
- Mark Haas
- Department of Pathology & Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA.
| | - Surya V Seshan
- Department of Pathology, Weill Cornell Medical College, New York, New York, USA
| | - Laura Barisoni
- Department of Pathology, Duke University, Durham, North Carolina, USA
| | - Kerstin Amann
- Department of Nephropathology, Friedrich-Alexander University, Erlangen-Nürnberg, Germany
| | - Ingeborg M Bajema
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Ulrich Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Kensuke Joh
- Department of Pathology, The Jikei University School of Medicine, Tokyo, Japan
| | - Danica Ljubanovic
- Department of Pathology, Dubrava University Hospital, Zagreb Medical School, Zagreb, Croatia
| | - Ian S D Roberts
- Department of Cellular Pathology, Oxford University Hospitals, Oxford, UK
| | - Joris J Roelofs
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sanjeev Sethi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Caihong Zeng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - J Charles Jennette
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| |
Collapse
|
22
|
Lapedis CJ, Mariani LH, Jang BJ, Hodgin J, Hicken MT. Understanding the Link between Neighborhoods and Kidney Disease. ACTA ACUST UNITED AC 2020; 1:845-854. [PMID: 33367284 DOI: 10.34067/kid.0001202019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Neighborhoods are where we live, learn, work, pray, and play. Growing evidence indicates that neighborhoods are an important determinant of health. The built features of our neighborhoods, such as the ways in which the streets are designed and connected and the availability of green spaces and transit stops, as well as the social features, such as the trust among neighbors and the perceptions of safety, may influence health through multiple pathways, such as access to important resources, psychosocial stress, and health behaviors. In particular, the extant literature consistently documents an association between neighborhood features and renal-associated conditions, such as cardiovascular disease, hypertension, diabetes, and obesity. There is also some evidence suggesting an association between neighborhood poverty and ESKD. The link between neighborhood and earlier stages of CKD, however, has been less clear, with most studies documenting no association. It may be that the neighborhood measures used in previous studies do not capture features of the neighborhood important for earlier stages of disease development and progression. It may also be that our current biomarkers (e.g., eGFR) and urine protein are not able to pick up very early forms of renal damage because of the kidney's overall high reserve capacity. This paper critically reviews the state of the literature on neighborhood and renal disease, with recommendations for neighborhood measures in future research. Neighborhoods are designed, built, and informed by policy, and thus, they are amenable to intervention, making them a potentially powerful way to improve renal health and reduce health inequalities at the population level.
Collapse
Affiliation(s)
- Cathryn J Lapedis
- Department of Veterans Affairs, Ann Arbor Health System, Ann Arbor, Michigan.,National Clinical Scholar Program, Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, Michigan Medicine, Ann Arbor, Michigan
| | - Laura H Mariani
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan
| | - Bohyun Joy Jang
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey Hodgin
- Department of Pathology, Michigan Medicine, Ann Arbor, Michigan
| | - Margaret T Hicken
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan.,Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
23
|
Kang E, Kim Y, Kim YC, Kim E, Lee N, Kim Y, Lee S, Han S, Choe M, Hwang JH, Lee S, Park JI, Park JT, Lim BJ, Lee JP, An JN, Ryu DR, Kim JH, Kang HG, Lee HS, Moon KC, Joo KW, Oh KH, Han SS, Lee H, Kim DK. Biobanking for glomerular diseases: a study design and protocol for KOrea Renal biobank NEtwoRk System TOward NExt-generation analysis (KORNERSTONE). BMC Nephrol 2020; 21:367. [PMID: 32842999 PMCID: PMC7448429 DOI: 10.1186/s12882-020-02016-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 08/12/2020] [Indexed: 11/24/2022] Open
Abstract
Backgrounds Glomerular diseases, a set of debilitating and complex disease entities, are related to mortality and morbidity. To gain insight into pathophysiology and novel treatment targets of glomerular disease, various types of biospecimens linked to deep clinical phenotyping including clinical information, digital pathology, and well-defined outcomes are required. We provide the rationale and design of the KOrea Renal biobank NEtwoRk System TOward Next-generation analysis (KORNERSTONE). Methods The KORNERSTONE, which has been initiated by Korea Centres for Disease Control and Prevention, is designed as a multi-centre, prospective cohort study and biobank for glomerular diseases. Clinical data, questionnaires will be collected at the time of kidney biopsy and subsequently every 1 year after kidney biopsy. All of the clinical data will be extracted from the electrical health record and automatically uploaded to the web-based database. High-quality digital pathologies are obtained and connected in the database. Various types of biospecimens are collected at baseline and during follow-up: serum, urine, buffy coat, stool, glomerular complementary DNA (cDNA), tubulointerstitial cDNA. All data and biospecimens are processed and stored in a standardised manner. The primary outcomes are mortality and end-stage renal disease. The secondary outcomes will be deterioration renal function, remission of proteinuria, cardiovascular events and quality of life. Discussion Ethical approval has been obtained from the institutional review board of each participating centre and ethics oversight committee. The KORNERSTONE is designed to deliver pioneer insights into glomerular diseases. The study design allows comprehensive, integrated and high-quality data collection on baseline laboratory findings, clinical outcomes including administrative data and digital pathologic images. This may provide various biospecimens and information to many researchers, establish the rationale for future more individualised treatment strategies for glomerular diseases. Trial registration NCT03929887.
Collapse
Affiliation(s)
- Eunjeong Kang
- Department of Internal Medicine, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, Seoul, South Korea
| | - Yaerim Kim
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, South Korea
| | - Yong Chul Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Eunyoung Kim
- Seoul National University Hospital Clinical Trial Centre, Seoul, South Korea
| | - Nankyoung Lee
- Seoul National University Hospital Human Biobank, Seoul, South Korea
| | - Yeonghui Kim
- Division of Nephrology, Department of Internal Medicine, Keimyung University Dongsan Hospital, Daegu, South Korea
| | - Soojin Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Seungyeup Han
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, South Korea
| | - Misun Choe
- Department of Pathology, Keimyung University School of Medicine, Daegu, South Korea
| | - Jin Ho Hwang
- Department of Internal Medicine, Chung-Ang University Hospital, Seoul, South Korea
| | - Sunhwa Lee
- Division of Nephrology, Department of Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, Gangwon-do, South Korea
| | - Ji In Park
- Division of Nephrology, Department of Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, Gangwon-do, South Korea
| | - Jung Tak Park
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, South Korea
| | - Beom Jin Lim
- Department of Pathology, Yonsei University College of Medicine, Seoul, South Korea
| | - Jung Pyo Lee
- Department of Internal Medicine Seoul National University Boramae Medical Center, Seoul National University College of Medicine, Seoul, South Korea
| | - Jung Nam An
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang, South Korea
| | - Dong-Ryeol Ryu
- Department of Internal Medicine, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, Seoul, South Korea
| | - Jung-Hyun Kim
- Department of Home Economics Education, Major of Food and Nutrition, Pai Chai University, Daejeon, South Korea
| | - Hee Gyung Kang
- Department of Paediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyun Soon Lee
- Department of Pathology, Hankook Renal Pathology Lab, Seoul, South Korea
| | - Kyung Chul Moon
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Kwon Wook Joo
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Kook-Hwan Oh
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Seung Seok Han
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Hajeong Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong Ki Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea.
| | | |
Collapse
|
24
|
Jayapandian CP, Chen Y, Janowczyk AR, Palmer MB, Cassol CA, Sekulic M, Hodgin JB, Zee J, Hewitt SM, O'Toole J, Toro P, Sedor JR, Barisoni L, Madabhushi A. Development and evaluation of deep learning-based segmentation of histologic structures in the kidney cortex with multiple histologic stains. Kidney Int 2020; 99:86-101. [PMID: 32835732 PMCID: PMC8414393 DOI: 10.1016/j.kint.2020.07.044] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 06/29/2020] [Accepted: 07/24/2020] [Indexed: 12/21/2022]
Abstract
The application of deep learning for automated segmentation (delineation of boundaries) of histologic primitives (structures) from whole slide images can facilitate the establishment of novel protocols for kidney biopsy assessment. Here, we developed and validated deep learning networks for the segmentation of histologic structures on kidney biopsies and nephrectomies. For development, we examined 125 biopsies for Minimal Change Disease collected across 29 NEPTUNE enrolling centers along with 459 whole slide images stained with Hematoxylin & Eosin (125), Periodic Acid Schiff (125), Silver (102), and Trichrome (107) divided into training, validation and testing sets (ratio 6:1:3). Histologic structures were manually segmented (30048 total annotations) by five nephropathologists. Twenty deep learning models were trained with optimal digital magnification across the structures and stains. Periodic Acid Schiff-stained whole slide images yielded the best concordance between pathologists and deep learning segmentation across all structures (F-scores: 0.93 for glomerular tufts, 0.94 for glomerular tuft plus Bowman’s capsule, 0.91 for proximal tubules, 0.93 for distal tubular segments, 0.81 for peritubular capillaries, and 0.85 for arteries and afferent arterioles). Optimal digital magnifications were 5X for glomerular tuft/tuft plus Bowman’s capsule, 10X for proximal/distal tubule, arteries and afferent arterioles, and 40X for peritubular capillaries. Silver stained whole slide images yielded the worst deep learning performance. Thus, this largest study to date adapted deep learning for the segmentation of kidney histologic structures across multiple stains and pathology laboratories. All data used for training and testing and a detailed online tutorial will be publicly available.
Collapse
Affiliation(s)
- Catherine P Jayapandian
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA.
| | - Yijiang Chen
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Andrew R Janowczyk
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA; Precision Oncology Center, Lausanne University Hospital, Vaud, Switzerland
| | - Matthew B Palmer
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Miroslav Sekulic
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA; Department of Pathology, University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jarcy Zee
- Department of Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, National Institutes of Health, National Cancer Institute, Bethesda, Maryland, USA
| | - John O'Toole
- Lerner Research and Glickman Urology and Kidney Institutes, Cleveland Clinic, Cleveland, Ohio, USA
| | - Paula Toro
- Department of Pathology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - John R Sedor
- Lerner Research and Glickman Urology and Kidney Institutes, Cleveland Clinic, Cleveland, Ohio, USA; Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Laura Barisoni
- Department of Pathology and Medicine, Division of Nephrology, Duke University, Durham, North Carolina, USA
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA; Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, Ohio, USA
| | | |
Collapse
|
25
|
Bueno G, Gonzalez-Lopez L, Garcia-Rojo M, Laurinavicius A, Deniz O. Data for glomeruli characterization in histopathological images. Data Brief 2020; 29:105314. [PMID: 32154349 PMCID: PMC7058889 DOI: 10.1016/j.dib.2020.105314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/13/2020] [Indexed: 11/16/2022] Open
Abstract
The data presented in this article is part of the whole slide imaging (WSI) datasets generated in European project AIDPATH This data is also related to the research paper entitle "Glomerulosclerosis Identification in Whole Slide Images using Semantic Segmentation", published in Computer Methods and Programs in Biomedicine Journal [1]. In that article, different methods based on deep learning for glomeruli segmentation and their classification into normal and sclerotic glomerulous are presented and discussed. The raw data used is described and provided here. In addition, the detected glomeruli are also provided as individual image files. These data will encourage research on artificial intelligence (AI) methods, create and compare fresh algorithms, and measure their usability in quantitative nephropathology.
Collapse
Affiliation(s)
- Gloria Bueno
- VISILAB, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | | | | | | | - Oscar Deniz
- VISILAB, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| |
Collapse
|
26
|
Royal V, Zee J, Liu Q, Avila-Casado C, Smith AR, Liu G, Mariani LH, Hewitt S, Holzman LB, Gillespie BW, Hodgin JB, Barisoni L. Ultrastructural Characterization of Proteinuric Patients Predicts Clinical Outcomes. J Am Soc Nephrol 2020; 31:841-854. [PMID: 32086276 DOI: 10.1681/asn.2019080825] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/31/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The analysis and reporting of glomerular features ascertained by electron microscopy are limited to few parameters with minimal predictive value, despite some contributions to disease diagnoses. METHODS We investigated the prognostic value of 12 electron microscopy histologic and ultrastructural changes (descriptors) from the Nephrotic Syndrome Study Network (NEPTUNE) Digital Pathology Scoring System. Study pathologists scored 12 descriptors in NEPTUNE renal biopsies from 242 patients with minimal change disease or FSGS, with duplicate readings to evaluate reproducibility. We performed consensus clustering of patients to identify unique electron microscopy profiles. For both individual descriptors and clusters, we used Cox regression models to assess associations with time from biopsy to proteinuria remission and time to a composite progression outcome (≥40% decline in eGFR, with eGFR<60 ml/min per 1.73 m2, or ESKD), and linear mixed models for longitudinal eGFR measures. RESULTS Intrarater and interrater reproducibility was >0.60 for 12 out of 12 and seven out of 12 descriptors, respectively. Individual podocyte descriptors such as effacement and microvillous transformation were associated with complete remission, whereas endothelial cell and glomerular basement membrane abnormalities were associated with progression. We identified six descriptor-based clusters with distinct electron microscopy profiles and clinical outcomes. Patients in a cluster with more prominent foot process effacement and microvillous transformation had the highest rates of complete proteinuria remission, whereas patients in clusters with extensive loss of primary processes and endothelial cell damage had the highest rates of the composite progression outcome. CONCLUSIONS Systematic analysis of electron microscopic findings reveals clusters of findings associated with either proteinuria remission or disease progression.
Collapse
Affiliation(s)
- Virginie Royal
- Department of Pathology, Hôpital Maisonneuve-Rosemont, Université de Montréal, Montréal, Québec, Canada;
| | - Jarcy Zee
- Arbor Research Collaborative for Health, Ann Arbor, Michigan
| | - Qian Liu
- Arbor Research Collaborative for Health, Ann Arbor, Michigan
| | - Carmen Avila-Casado
- Department of Laboratory Medicine, University of Toronto, Scarborough, Ontario, Canada
| | - Abigail R Smith
- Arbor Research Collaborative for Health, Ann Arbor, Michigan
| | - Gang Liu
- Arbor Research Collaborative for Health, Ann Arbor, Michigan
| | - Laura H Mariani
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Stephen Hewitt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lawrence B Holzman
- Renal-Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Brenda W Gillespie
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey B Hodgin
- Renal Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Laura Barisoni
- Department of Pathology, Duke University, Durham, North Carolina
| |
Collapse
|
27
|
Schaub JA, Hamidi H, Subramanian L, Kretzler M. Systems Biology and Kidney Disease. Clin J Am Soc Nephrol 2020; 15:695-703. [PMID: 31992571 PMCID: PMC7269226 DOI: 10.2215/cjn.09990819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The kidney is a complex organ responsible for maintaining multiple aspects of homeostasis in the human body. The combination of distinct, yet interrelated, molecular functions across different cell types make the delineation of factors associated with loss or decline in kidney function challenging. Consequently, there has been a paucity of new diagnostic markers and treatment options becoming available to clinicians and patients in managing kidney diseases. A systems biology approach to understanding the kidney leverages recent advances in computational technology and methods to integrate diverse sets of data. It has the potential to unravel the interplay of multiple genes, proteins, and molecular mechanisms that drive key functions in kidney health and disease. The emergence of large, detailed, multilevel biologic and clinical data from national databases, cohort studies, and trials now provide the critical pieces needed for meaningful application of systems biology approaches in nephrology. The purpose of this review is to provide an overview of the current state in the evolution of the field. Recent successes of systems biology to identify targeted therapies linked to mechanistic biomarkers in the kidney are described to emphasize the relevance to clinical care and the outlook for improving outcomes for patients with kidney diseases.
Collapse
Affiliation(s)
- Jennifer A Schaub
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Habib Hamidi
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Lalita Subramanian
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
28
|
Abstract
Emergent coronaviruses such as MERS-CoV and SARS-CoV can cause significant morbidity and mortality in infected individuals. Lung infection is a common clinical feature and contributes to disease severity as well as viral transmission. Animal models are often required to study viral infections and therapies, especially during an initial outbreak. Histopathology studies allow for identification of lesions and affected cell types to better understand viral pathogenesis and clarify effective therapies. Use of immunostaining allows detection of presumed viral receptors and viral tropism for cells can be evaluated to correlate with lesions. In the lung, lesions and immunostaining can be qualitatively described to define the cell types, microanatomic location, and type of changes seen. These features are important and necessary, but this approach can have limitations when comparing treatment groups. Semiquantitative and quantitative tissue scores are more rigorous as these provide the ability to statistically compare groups and increase the reproducibility and rigor of the study. This review describes principles, approaches, and resources that can be useful to evaluate coronavirus lung infection, focusing on MER-CoV infection as the principal example.
Collapse
Affiliation(s)
- David K Meyerholz
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
| | - Amanda P Beck
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| |
Collapse
|
29
|
Perco P, Ju W, Kerschbaum J, Leierer J, Menon R, Zhu C, Kretzler M, Mayer G, Rudnicki M. Identification of dicarbonyl and L-xylulose reductase as a therapeutic target in human chronic kidney disease. JCI Insight 2019; 4:128120. [PMID: 31217356 PMCID: PMC6629103 DOI: 10.1172/jci.insight.128120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/16/2019] [Indexed: 12/18/2022] Open
Abstract
An imbalance of nephroprotective factors and renal damaging molecules contributes to development and progression of chronic kidney disease (CKD). We investigated associations of renoprotective factor gene expression patterns with CKD severity and outcome. Gene expression profiles of 197 previously reported renoprotective factors were analyzed in a discovery cohort in renal biopsies of 63 CKD patients. Downregulation of dicarbonyl and L-xylulose reductase (DCXR) showed the strongest association with disease progression. This significant association was validated in an independent set of 225 patients with nephrotic syndrome from the multicenter NEPTUNE cohort. Reduced expression of DCXR was significantly associated with degree of histological damage as well as with lower estimated glomerular filtration rate and increased urinary protein levels. DCXR downregulation in CKD was confirmed in 3 publicly available transcriptomics data sets in the context of CKD. Expression of DCXR showed positive correlations to enzymes that are involved in dicarbonyl stress detoxification based on transcriptomics profiles. The sodium glucose cotransporter-2 (SGLT2) inhibitors canagliflozin and empagliflozin showed a beneficial effect on renal proximal tubular cells under diabetic stimuli-enhanced DCXR gene expression. In summary, lower expression of the renoprotective factor DCXR in renal tissue is associated with more severe disease and worse outcome in human CKD.
Collapse
Affiliation(s)
- Paul Perco
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Wenjun Ju
- Department of Internal Medicine, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Julia Kerschbaum
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Johannes Leierer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Rajasree Menon
- Department of Internal Medicine, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Catherine Zhu
- Department of Internal Medicine, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthias Kretzler
- Department of Internal Medicine, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Gert Mayer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Michael Rudnicki
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | | |
Collapse
|
30
|
Nauhria S, Hangfu L. Virtual microscopy enhances the reliability and validity in histopathology curriculum: Practical guidelines. MEDEDPUBLISH 2019; 8:28. [PMID: 38089371 PMCID: PMC10712629 DOI: 10.15694/mep.2019.000028.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
This article was migrated. The article was marked as recommended. Digital pathology innovation and application in medical education have paved the path for a significant shift in the advancement of the medical curriculum. The new technology of virtual microscopy is a proven reliable and valid pedagogy method for histopathology learning objectives, and assessments. The current transformation has brought educators around the globe nearer towards the goal of achieving competence in Curriculum Inventory in the medical curriculum. This paper emphasises the practical tips and guidelines for cost-effective implementation and the successful use of Virtual Microscope technology to enhance the histopathology curriculum in a medical school.
Collapse
|
31
|
Bülow RD, Boor P. Extracellular Matrix in Kidney Fibrosis: More Than Just a Scaffold. J Histochem Cytochem 2019; 67:643-661. [PMID: 31116062 DOI: 10.1369/0022155419849388] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Kidney fibrosis is the common histological end-point of progressive, chronic kidney diseases (CKDs) regardless of the underlying etiology. The hallmark of renal fibrosis, similar to all other organs, is pathological deposition of extracellular matrix (ECM). Renal ECM is a complex network of collagens, elastin, and several glycoproteins and proteoglycans forming basal membranes and interstitial space. Several ECM functions beyond providing a scaffold and organ stability are being increasingly recognized, for example, in inflammation. ECM composition is determined by the function of each of the histological compartments of the kidney, that is, glomeruli, tubulo-interstitium, and vessels. Renal ECM is a dynamic structure undergoing remodeling, particularly during fibrosis. From a clinical perspective, ECM proteins are directly involved in several rare renal diseases and indirectly in CKD progression during renal fibrosis. ECM proteins could serve as specific non-invasive biomarkers of fibrosis and scaffolds in regenerative medicine. The gold standard and currently only specific means to measure renal fibrosis is renal biopsy, but new diagnostic approaches are appearing. Here, we discuss the localization, function, and remodeling of major renal ECM components in healthy and diseased, fibrotic kidneys and the potential use of ECM in diagnostics of renal fibrosis and in tissue engineering.
Collapse
Affiliation(s)
- Roman David Bülow
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Peter Boor
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany.,Department of Nephrology and Immunology, RWTH Aachen University Hospital, Aachen, Germany
| |
Collapse
|
32
|
Mariani LH, Bomback AS, Canetta PA, Flessner MF, Helmuth M, Hladunewich MA, Hogan JJ, Kiryluk K, Nachman PH, Nast CC, Rheault MN, Rizk DV, Trachtman H, Wenderfer SE, Bowers C, Hill-Callahan P, Marasa M, Poulton CJ, Revell A, Vento S, Barisoni L, Cattran D, D'Agati V, Jennette JC, Klein JB, Laurin LP, Twombley K, Falk RJ, Gharavi AG, Gillespie BW, Gipson DS, Greenbaum LA, Holzman LB, Kretzler M, Robinson B, Smoyer WE, Guay-Woodford LM. CureGN Study Rationale, Design, and Methods: Establishing a Large Prospective Observational Study of Glomerular Disease. Am J Kidney Dis 2018; 73:218-229. [PMID: 30420158 PMCID: PMC6348011 DOI: 10.1053/j.ajkd.2018.07.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/31/2018] [Indexed: 01/01/2023]
Abstract
RATIONALE & OBJECTIVES Glomerular diseases, including minimal change disease, focal segmental glomerulosclerosis, membranous nephropathy, and immunoglobulin A (IgA) nephropathy, share clinical presentations, yet result from multiple biological mechanisms. Challenges to identifying underlying mechanisms, biomarkers, and new therapies include the rarity of each diagnosis and slow progression, often requiring decades to measure the effectiveness of interventions to prevent end-stage kidney disease (ESKD) or death. STUDY DESIGN Multicenter prospective cohort study. SETTING & PARTICIPANTS Cure Glomerulonephropathy (CureGN) will enroll 2,400 children and adults with minimal change disease, focal segmental glomerulosclerosis, membranous nephropathy, or IgA nephropathy (including IgA vasculitis) and a first diagnostic kidney biopsy within 5 years. Patients with ESKD and those with secondary causes of glomerular disease are excluded. EXPOSURES Clinical data, including medical history, medications, family history, and patient-reported outcomes, are obtained, along with a digital archive of kidney biopsy images and blood and urine specimens at study visits aligned with clinical care 1 to 4 times per year. OUTCOMES Patients are followed up for changes in estimated glomerular filtration rate, disease activity, ESKD, and death and for nonrenal complications of disease and treatment, including infection, malignancy, cardiovascular, and thromboembolic events. ANALYTICAL APPROACH The study design supports multiple longitudinal analyses leveraging the diverse data domains of CureGN and its ancillary program. At 2,400 patients and an average of 2 years' initial follow-up, CureGN has 80% power to detect an HR of 1.4 to 1.9 for proteinuria remission and a mean difference of 2.1 to 3.0mL/min/1.73m2 in estimated glomerular filtration rate per year. LIMITATIONS Current follow-up can only detect large differences in ESKD and death outcomes. CONCLUSIONS Study infrastructure will support a broad range of scientific approaches to identify mechanistically distinct subgroups, identify accurate biomarkers of disease activity and progression, delineate disease-specific treatment targets, and inform future therapeutic trials. CureGN is expected to be among the largest prospective studies of children and adults with glomerular disease, with a broad goal to lessen disease burden and improve outcomes.
Collapse
Affiliation(s)
- Laura H Mariani
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, MI; Arbor Research Collaborative for Health, Ann Arbor, MI.
| | - Andrew S Bomback
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Pietro A Canetta
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Michael F Flessner
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | | | - Michelle A Hladunewich
- Division of Nephrology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Jonathan J Hogan
- Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Patrick H Nachman
- Division of Renal Diseases and Hypertension, Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Cynthia C Nast
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Michelle N Rheault
- Division of Nephrology, Department of Pediatrics, University of Minnesota Masonic Children's Hospital, Minneapolis, MN
| | - Dana V Rizk
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Howard Trachtman
- Division of Nephrology, Department of Pediatrics, New York University Langone Medical Center, New York, NY
| | - Scott E Wenderfer
- Renal Section, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Corinna Bowers
- Center for Clinical and Translational Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | | | - Maddalena Marasa
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Caroline J Poulton
- Division of Nephrology and Hypertension, Kidney Center, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Adelaide Revell
- Center for Clinical and Translational Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Suzanne Vento
- Division of Nephrology, Department of Pediatrics, New York University Langone Medical Center, New York, NY
| | | | - Dan Cattran
- Division of Nephrology, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Vivette D'Agati
- Department of Pathology, Columbia University Medical Center, New York, NY
| | - J Charles Jennette
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC
| | - Jon B Klein
- Department of Medicine, The University of Louisville School of Medicine, and Robley Rex VA Medical Center, Louisville, KY
| | | | - Katherine Twombley
- Pediatric Nephrology, Medical University of South Carolina, Charleston, SC
| | - Ronald J Falk
- Division of Nephrology and Hypertension, Kidney Center, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Brenda W Gillespie
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Debbie S Gipson
- Division of Nephrology, Department of Pediatrics, University of Michigan, Ann Arbor, MI
| | | | - Lawrence B Holzman
- Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Matthias Kretzler
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Bruce Robinson
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, MI; Arbor Research Collaborative for Health, Ann Arbor, MI
| | - William E Smoyer
- Center for Clinical and Translational Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Lisa M Guay-Woodford
- Center for Translational Science, Children's National Health System, Washington, DC
| | | |
Collapse
|
33
|
Digital pathology in nephrology clinical trials, research, and pathology practice. Curr Opin Nephrol Hypertens 2018; 26:450-459. [PMID: 28858910 DOI: 10.1097/mnh.0000000000000360] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW In this review, we will discuss (i) how the recent advancements in digital technology and computational engineering are currently applied to nephropathology in the setting of clinical research, trials, and practice; (ii) the benefits of the new digital environment; (iii) how recognizing its challenges provides opportunities for transformation; and (iv) nephropathology in the upcoming era of kidney precision and predictive medicine. RECENT FINDINGS Recent studies highlighted how new standardized protocols facilitate the harmonization of digital pathology database infrastructure and morphologic, morphometric, and computer-aided quantitative analyses. Digital pathology enables robust protocols for clinical trials and research, with the potential to identify previously underused or unrecognized clinically useful parameters. The integration of digital pathology with molecular signatures is leading the way to establishing clinically relevant morpho-omic taxonomies of renal diseases. SUMMARY The introduction of digital pathology in clinical research and trials, and the progressive implementation of the modern software ecosystem, opens opportunities for the development of new predictive diagnostic paradigms and computer-aided algorithms, transforming the practice of renal disease into a modern computational science.
Collapse
|
34
|
Zee J, Hodgin JB, Mariani LH, Gaut JP, Palmer MB, Bagnasco SM, Rosenberg AZ, Hewitt SM, Holzman LB, Gillespie BW, Barisoni L. Reproducibility and Feasibility of Strategies for Morphologic Assessment of Renal Biopsies Using the Nephrotic Syndrome Study Network Digital Pathology Scoring System. Arch Pathol Lab Med 2018; 142:613-625. [PMID: 29457738 DOI: 10.5858/arpa.2017-0181-oa] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Context Testing reproducibility is critical for the development of methodologies for morphologic assessment. Our previous study using the descriptor-based Nephrotic Syndrome Study Network Digital Pathology Scoring System (NDPSS) on glomerular images revealed variable reproducibility. Objective To test reproducibility and feasibility of alternative scoring strategies for digital morphologic assessment of glomeruli and explore use of alternative agreement statistics. Design The original NDPSS was modified (NDPSS1 and NDPSS2) to evaluate (1) independent scoring of each individual biopsy level, (2) use of continuous measures, (3) groupings of individual descriptors into classes and subclasses prior to scoring, and (4) indication of pathologists' confidence/uncertainty for any given score. Three and 5 pathologists scored 157 and 79 glomeruli using the NDPSS1 and NDPSS2, respectively. Agreement was tested using conventional (Cohen κ) and alternative (Gwet agreement coefficient 1 [AC1]) agreement statistics and compared with previously published data (original NDPSS). Results Overall, pathologists' uncertainty was low, favoring application of the Gwet AC1. Greater agreement was achieved using the Gwet AC1 compared with the Cohen κ across all scoring methodologies. Mean (standard deviation) differences in agreement estimates using the NDPSS1 and NDPSS2 compared with the single-level original NDPSS were -0.09 (0.17) and -0.17 (0.17), respectively. Using the Gwet AC1, 79% of the original NDPSS descriptors had good or excellent agreement. Pathologist feedback indicated the NDPSS1 and NDPSS2 were time-consuming. Conclusions The NDPSS1 and NDPSS2 increased pathologists' scoring burden without improving reproducibility. Use of alternative agreement statistics was strongly supported. We suggest using the original NDPSS on whole slide images for glomerular morphology assessment and for guiding future automated technologies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Laura Barisoni
- From Biostatistics, Arbor Research Collaborative for Health, Ann Arbor, Michigan (Dr Zee); the Departments of Pathology (Dr Hodgin), Internal Medicine (Dr Mariani), and Biostatistics (Dr Gillespie), University of Michigan, Ann Arbor; Arbor Research Collaborative for Health, Ann Arbor, Michigan (Dr Mariani); the Department of Pathology & Immunology, Washington University, St Louis, Missouri (Dr Gaut); the Departments of Pathology and Laboratory Medicine (Dr Palmer) and Medicine (Dr. Holzman), University of Pennsylvania, Philadelphia; the Department of Pathology, Johns Hopkins University, Baltimore, Maryland (Drs Bagnasco and Rosenberg); the Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland (Dr Rosenberg); the Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland (Dr Hewitt); and the Department of Pathology, University of Miami, Miami, Florida (Dr Barisoni)
| |
Collapse
|
35
|
|
36
|
van de Lest NA, Zandbergen M, IJpelaar DHT, Wolterbeek R, Bruijn JA, Bajema IM, Scharpfenecker M. Nephrin Loss Can Be Used to Predict Remission and Long-term Renal Outcome in Patients With Minimal Change Disease. Kidney Int Rep 2017; 3:168-177. [PMID: 29340328 PMCID: PMC5762955 DOI: 10.1016/j.ekir.2017.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/30/2017] [Accepted: 09/18/2017] [Indexed: 11/16/2022] Open
Abstract
Introduction Minimal change disease is a common cause of nephrotic syndrome. In general, patients with minimal change disease respond to corticosteroids and have excellent long-term renal survival. However, some patients have less favorable outcome. These patients are often thought to have progressed to focal segmental glomerulosclerosis. We previously reported that a segmental loss of podocyte markers is present before the development of focal segmental glomerulosclerosis in a rat model. Here, we investigated whether loss of podocyte marker nephrin can serve as a biomarker for predicting poor outcome in patients with minimal change disease. Methods We obtained 47 kidney biopsy samples from patients diagnosed with minimal change disease and stained sections with periodic acid−Schiff and for nephrin. Nephrin loss was scored by 2 independent researchers who were blinded to clinical outcome. Clinical data were collected retrospectively, and nephrin loss was correlated with clinical follow-up data. Results Nephrin loss was present in 34% of the biopsy samples. During follow-up, patients with nephrin loss achieved remission less frequently (61%) compared to patients without (96%) (P = 0.002). Moreover, 5-year eGFR was lower in the patients with renal nephrin loss. The risk of eGFR decreasing to < 60 ml/min per 1.73m2 increased with each percentage of glomeruli with nephrin loss (hazard ratio = 1.044, 95% confidence interval = 1.02−1.07). Conclusion These results indicate that nephrin loss in patients with minimal change disease can help predict both remission and long-term renal outcome.
Collapse
Affiliation(s)
- Nina A van de Lest
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Malu Zandbergen
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Daphne H T IJpelaar
- Department of Nephrology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ron Wolterbeek
- Department of Medical Statistics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jan A Bruijn
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ingeborg M Bajema
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | | |
Collapse
|
37
|
Lindenmeyer MT, Kretzler M. Renal biopsy-driven molecular target identification in glomerular disease. Pflugers Arch 2017; 469:1021-1028. [PMID: 28664406 DOI: 10.1007/s00424-017-2006-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 05/25/2017] [Indexed: 12/12/2022]
Abstract
Chronic kidney disease has severe impacts on the patient and represents a major burden to the health care systems worldwide. Despite an increased knowledge of pathophysiological processes involved in kidney diseases, the progress in defining novel treatment strategies has been limited. One reason is the descriptive disease categorization used in nephrology based on clinical findings or histopathological categories irrespective of potential different molecular disease mechanisms. To accelerate progress toward a targeted treatment, a definition of human disease extending from phenotypic disease classification to mechanism-based disease definitions is needed. In recent years, we have witnessed a major transition in biomedical research from a single gene research to an information rich and collaborative science. Tissue-based analysis in renal disease allows to link structure to molecular function. In our review, we introduce the concept of precision medicine in nephrology, describe several large cohort studies established for molecular analysis of kidney diseases, and highlight examples of renal biopsy-driven target identification by integrative systems biology approaches. Furthermore, we give an outlook on how the new disease definitions can be used for patient stratification in clinical trial design. Finally, we introduce the concept of an informational commons of renal precision medicine for joint analyses of large-scale data sets in renal failure.
Collapse
Affiliation(s)
- Maja T Lindenmeyer
- Nephrological Center, Medical Clinic and Policlinic IV, University of Munich, Munich, Germany
| | - Matthias Kretzler
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA.
- Internal Medicine - Nephrology, University of Michigan, 1150 W. Medical Center Dr. 1560 MSRB II, Ann Arbor, MI, 48109-5676, USA.
| |
Collapse
|