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Fan F, Liu Q, Zee J, Ozeki T, Demeke D, Yang Y, Farris AB, Wang B, Shah M, Jacobs J, Mariani L, Lafata K, Rubin J, Chen Y, Holzman L, Hodgin JB, Madabhushi A, Barisoni L, Janowczyk A. Clinical Relevance of Computationally Derived Tubular Features: Spatial Relationships and the Development of Tubulointerstitial Scarring in MCD/FSGS. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.19.24310619. [PMID: 39072032 PMCID: PMC11275675 DOI: 10.1101/2024.07.19.24310619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background Visual scoring of tubular damage has limitations in capturing the full spectrum of structural changes and prognostic potential. We investigate if computationally quantified tubular features can enhance prognostication and reveal spatial relationships with interstitial fibrosis. Methods Deep-learning and image-processing-based segmentations were employed in N=254/266 PAS-WSIs from the NEPTUNE/CureGN datasets (135/153 focal segmental glomerulosclerosis and 119/113 minimal change disease) for: cortex, tubular lumen (TL), epithelium (TE), nuclei (TN), and basement membrane (TBM). N=104 pathomic features were extracted from these segmented tubular substructures and summarized at the patient level using summary statistics. The tubular features were quantified across the biopsy and in manually segmented regions of mature interstitial fibrosis and tubular atrophy (IFTA), pre-IFTA and non-IFTA in the NEPTUNE dataset. Minimum Redundancy Maximum Relevance was used in the NEPTUNE dataset to select features most associated with disease progression and proteinuria remission. Ridge-penalized Cox models evaluated their predictive discrimination compared to clinical/demographic data and visual-assessment. Models were evaluated in the CureGN dataset. Results N=9 features were predictive of disease progression and/or proteinuria remission. Models with tubular features had high prognostic accuracy in both NEPTUNE and CureGN datasets and increased prognostic accuracy for both outcomes (5.6%-7.7% and 1.6%-4.6% increase for disease progression and proteinuria remission, respectively) compared to conventional parameters alone in the NEPTUNE dataset. TBM thickness/area and TE simplification progressively increased from non- to pre- and mature IFTA. Conclusions Previously under-recognized, quantifiable, and clinically relevant tubular features in the kidney parenchyma can enhance understanding of mechanisms of disease progression and risk stratification.
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Affiliation(s)
- Fan Fan
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Qian Liu
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA
| | - Jarcy Zee
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Takaya Ozeki
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Dawit Demeke
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Yingbao Yang
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Alton B Farris
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Bangcheng Wang
- Department of Pathology, Division of AI & Computational Pathology, Duke University, Durham, NC, United States
| | - Manav Shah
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Jackson Jacobs
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Laura Mariani
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Kyle Lafata
- Department of Radiation Oncology, Duke University, Durham, NC, United States
| | - Jeremy Rubin
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yijiang Chen
- Department of Radiation Oncology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Lawrence Holzman
- Department of Medicine, Division of Nephrology and Hypertension, University of Pennsylvania, Philadelphia, PA, United States
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Anant Madabhushi
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Atlanta Veterans Administration Medical Center, Atlanta, GA, USA
| | - Laura Barisoni
- Department of Pathology, Division of AI & Computational Pathology, Duke University, Durham, NC, United States
- Department of Medicine, Division of Nephrology, Duke University, Durham, NC, USA
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Department of Oncology, Division of Precision Oncology, University Hospital of Geneva, Geneva, Switzerland
- Department of Diagnostics, Division of Clinical Pathology, University Hospital of Geneva, Geneva, Switzerland
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Kozakowski N. The histomorphology of the senescent kidney - the clinical relevance of specimen and biopsy findings in the elderly native kidneys. Curr Opin Urol 2024; 34:170-175. [PMID: 38410848 DOI: 10.1097/mou.0000000000001164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
PURPOSE OF REVIEW Renal pathology is crucial in diagnosing the ageing kidney. Recent technological advances enabled high-resolution molecular investigations into the complex mechanisms of ageing and senescence. RECENT FINDINGS The pathological analysis of large kidney tissue collections coupled with computer-assisted morphometry contributed to the establishment of age-related reference values for glomerular or vascular sclerosis, interstitial fibrosis, and tubular atrophy. Furthermore, new high-throughput proteomic and transcriptomic platforms have entered the field of pathology. When coupled with morphology information, these techniques facilitated the study of extracellular matrix modifications and the senescent immune system in the ageing kidney. Finally, iatrogenic complications are now frequent indications for diagnostic kidney biopsies in older patients, potentially accelerating kidney senescence. SUMMARY Recent pathology literature supports identifying and prognosticating sclerosing processes in ageing kidneys.
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Affiliation(s)
- Nicolas Kozakowski
- Medical University of Vienna, Department of Pathology, Vienna, Austria; General Hospital, Waehringer Guertel, Vienna, Austria
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Xu T, Herkens L, Jia T, Klinkhammer BM, Kant S, Krusche CA, Buhl EM, Hayat S, Floege J, Strnad P, Kramann R, Djudjaj S, Boor P. The role of desmoglein-2 in kidney disease. Kidney Int 2024; 105:1035-1048. [PMID: 38395410 DOI: 10.1016/j.kint.2024.01.037] [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: 11/08/2022] [Revised: 12/07/2023] [Accepted: 01/09/2024] [Indexed: 02/25/2024]
Abstract
Desmosomes are multi-protein cell-cell adhesion structures supporting cell stability and mechanical stress resilience of tissues, best described in skin and heart. The kidney is exposed to various mechanical stimuli and stress, yet little is known about kidney desmosomes. In healthy kidneys, we found desmosomal proteins located at the apical-junctional complex in tubular epithelial cells. In four different animal models and patient biopsies with various kidney diseases, desmosomal components were significantly upregulated and partly miss-localized outside of the apical-junctional complexes along the whole lateral tubular epithelial cell membrane. The most upregulated component was desmoglein-2 (Dsg2). Mice with constitutive tubular epithelial cell-specific deletion of Dsg2 developed normally, and other desmosomal components were not altered in these mice. When challenged with different types of tubular epithelial cell injury (unilateral ureteral obstruction, ischemia-reperfusion, and 2,8-dihydroxyadenine crystal nephropathy), we found increased tubular epithelial cell apoptosis, proliferation, tubular atrophy, and inflammation compared to wild-type mice in all models and time points. In vitro, silencing DSG2 via siRNA weakened cell-cell adhesion in HK-2 cells and increased cell death. Thus, our data show a prominent upregulation of desmosomal components in tubular cells across species and diseases and suggest a protective role of Dsg2 against various injurious stimuli.
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Affiliation(s)
- Tong Xu
- Institute of Pathology, RWTH Aachen University, Aachen, Germany; Department of Urology, the First Affiliated Hospital of Airforce Medical University, Xi'an, China
| | - Lea Herkens
- Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - Ting Jia
- Institute of Pathology, RWTH Aachen University, Aachen, Germany; Department of Nephrology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | | | - Sebastian Kant
- Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany
| | - Claudia A Krusche
- Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany
| | - Eva M Buhl
- Electron Microscopy Facility, RWTH Aachen University, Aachen, Germany
| | - Sikander Hayat
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Pavel Strnad
- Department of Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, RWTH Aachen University, Aachen, Germany
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany; Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Sonja Djudjaj
- Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - Peter Boor
- Institute of Pathology, RWTH Aachen University, Aachen, Germany; Electron Microscopy Facility, RWTH Aachen University, Aachen, Germany; Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany.
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Farhat I, Maréchal E, Calmo D, Ansart M, Paindavoine M, Bard P, Tarris G, Ducloux D, Felix SA, Martin L, Tinel C, Gibier JB, Funes de la Vega M, Rebibou JM, Bamoulid J, Legendre M. Recognition of intraglomerular histological features with deep learning in protocol transplant biopsies and their association with kidney function and prognosis. Clin Kidney J 2024; 17:sfae019. [PMID: 38370429 PMCID: PMC10873504 DOI: 10.1093/ckj/sfae019] [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: 10/31/2023] [Indexed: 02/20/2024] Open
Abstract
Background The Banff Classification may not adequately address protocol transplant biopsies categorized as normal in patients experiencing unexplained graft function deterioration. This study seeks to employ convolutional neural networks to automate the segmentation of glomerular cells and capillaries and assess their correlation with transplant function. Methods A total of 215 patients were categorized into three groups. In the Training cohort, glomerular cells and capillaries from 37 patients were manually annotated to train the networks. The Test cohort (24 patients) compared manual annotations vs automated predictions, while the Application cohort (154 protocol transplant biopsies) examined predicted factors in relation to kidney function and prognosis. Results In the Test cohort, the networks recognized histological structures with Precision, Recall, F-score and Intersection Over Union exceeding 0.92, 0.85, 0.89 and 0.74, respectively. Univariate analysis revealed associations between the estimated glomerular filtration rate (eGFR) at biopsy and relative endothelial area (r = 0.19, P = .027), endothelial cell density (r = 0.20, P = .017), mean parietal epithelial cell area (r = -0.38, P < .001), parietal epithelial cell density (r = 0.29, P < .001) and mesangial cell density (r = 0.22, P = .010). Multivariate analysis retained only endothelial cell density as associated with eGFR (Beta = 0.13, P = .040). Endothelial cell density (r = -0.22, P = .010) and mean podocyte area (r = 0.21, P = .016) were linked to proteinuria at biopsy. Over 44 ± 29 months, 25 patients (16%) reached the primary composite endpoint (dialysis initiation, or 30% eGFR sustained decline), with relative endothelial area, mean endothelial cell area and parietal epithelial cell density below medians linked to this endpoint [hazard ratios, respectively, of 2.63 (P = .048), 2.60 (P = .039) and 3.23 (P = .019)]. Conclusion This study automated the measurement of intraglomerular cells and capillaries. Our results suggest that the precise segmentation of endothelial and epithelial cells may serve as a potential future marker for the risk of graft loss.
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Affiliation(s)
- Imane Farhat
- Department of Nephrology, CHU Dijon, Dijon, France
| | | | - Doris Calmo
- Department of Nephrology, CHU Besançon, Besançon, France
| | - Manon Ansart
- LEAD-CNRS, UMR 5022, Université de Bourgogne, Dijon, France
| | | | - Patrick Bard
- LEAD-CNRS, UMR 5022, Université de Bourgogne, Dijon, France
| | | | - Didier Ducloux
- Department of Nephrology, CHU Besançon, Besançon, France
- Etablissement Français du sang, Besançon, France
| | | | | | - Claire Tinel
- Department of Nephrology, CHU Dijon, Dijon, France
- Etablissement Français du sang, Besançon, France
| | | | | | - Jean-Michel Rebibou
- Department of Nephrology, CHU Dijon, Dijon, France
- Etablissement Français du sang, Besançon, France
| | - Jamal Bamoulid
- Department of Nephrology, CHU Besançon, Besançon, France
- Etablissement Français du sang, Besançon, France
| | - Mathieu Legendre
- Department of Nephrology, CHU Dijon, Dijon, France
- LEAD-CNRS, UMR 5022, Université de Bourgogne, Dijon, France
- Etablissement Français du sang, Besançon, France
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Asghar MS, Denic A, Rule AD. Morphometric analysis of chronicity on kidney biopsy: a useful prognostic exercise. Clin Kidney J 2024; 17:sfad226. [PMID: 38327281 PMCID: PMC10849190 DOI: 10.1093/ckj/sfad226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Indexed: 02/09/2024] Open
Abstract
Chronic changes on kidney biopsy specimens include increasing amounts of arteriosclerosis, glomerulosclerosis, interstitial fibrosis and tubular atrophy, enlarged nephron size, and reduced nephron number. These chronic changes are difficult to accurately assess by visual inspection but are reasonably quantified using morphometry. This review describes the various patient populations that have undergone morphometric analysis of kidney biopsies. The common approaches to morphometric analysis are described. The chronic kidney disease outcomes associated with various chronic changes by morphometry are also summarized. Morphometry enriches the characterization of chronicity on a kidney biopsy and this can supplement the pathologist's diagnosis. Artificial intelligence image processing tools are needed to automate the annotations needed for practical morphometric analysis of kidney biopsy specimens in routine clinical care.
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Affiliation(s)
- Muhammad S Asghar
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Aleksandar Denic
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Andrew D Rule
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
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Erratum: Tubular and Glomerular Size by Cortex Depth as Predictors for Progressive Chronic Kidney Disease after Radical Nephrectomy for Tumor. J Am Soc Nephrol 2023; 34:2057. [PMID: 37855717 PMCID: PMC10703076 DOI: 10.1681/asn.0000000000000228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
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Denic A, Fnu A, Mahesh K, Rule AD. Authors' Reply: Morphometric Approach to Different Nephron Segments. J Am Soc Nephrol 2023; 34:2054-2056. [PMID: 38039092 PMCID: PMC10881185 DOI: 10.1681/asn.0000000000000234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2023] Open
Affiliation(s)
- Aleksandar Denic
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Aperna Fnu
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Kumar Mahesh
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Andrew D. Rule
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
- Division of Epidemiology, Mayo Clinic, Rochester, Minnesota
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Sasaki T, Tsuboi N. Morphometric Approach to Different Nephron Segments. J Am Soc Nephrol 2023; 34:2053. [PMID: 38039091 PMCID: PMC10881183 DOI: 10.1681/asn.0000000000000236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2023] Open
Affiliation(s)
- Takaya Sasaki
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
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