Accurate classification of glomerular diseases by hyperspectral imaging and transformer.

BACKGROUND AND OBJECTIVE: In renal disease research, precise glomerular disease diagnosis is crucial for treatment and prognosis. Currently reliant on invasive biopsies, this method bears risks and pathologist-dependent variability, yielding inconsistent results. There is a pressing need for innovative diagnostic tools that enhance traditional methods, streamline processes, and ensure accurate and consistent disease detection. METHODS: In this study, we present an innovative Convolutional Neural Networks-Vision Transformer (CVT) model leveraging Transformer technology to refine glomerular disease diagnosis by fusing spectral and spatial data, surpassing traditional diagnostic limitations. Using interval sampling, preprocessing, and wavelength optimization, we also introduced the Gramian Angular Field (GAF) method for a unified representation of spectral and spatial characteristics. RESULTS: We captured hyperspectral images ranging from 385.18 nm to 1009.47 nm and employed various methods to extract sample features. Initial models based solely on spectral features achieved a accuracy of 85.24 %. However, the CVT model significantly outperformed these, achieving an average accuracy of 94 %. This demonstrates the model's superior capability in utilizing sample data and learning joint feature representations. CONCLUSIONS: The CVT model not only breaks through the limitations of existing diagnostic techniques but also showcases the vast potential of non-invasive, high-precision diagnostic technology in supporting the classification and prognosis of complex glomerular diseases. This innovative approach could significantly impact future diagnostic strategies in renal disease research. CONCISE ABSTRACT: This study introduces a transformative hyperspectral image classification model leveraging a Transformer to significantly improve glomerular disease diagnosis accuracy by synergizing spectral and spatial data, surpassing conventional methods. Through a rigorous comparative analysis, it was determined that while spectral features alone reached a peak accuracy of 85.24 %, the novel Convolutional Neural Network-Transformer (CVT) model's integration of spatial-spectral features via the Gramian Angular Field (GAF) method markedly enhanced diagnostic precision, achieving an average accuracy of 94 %. This methodological innovation not only overcomes traditional diagnostic limitations but also underscores the potential of non-invasive, high-precision technologies in advancing the classification and prognosis of complex renal diseases, setting a new benchmark in the field.

2024 Update on Classification, Etiology, and Typing of Renal Amyloidosis: A Review.

Amyloidosis is a protein folding disease that causes organ injuries and even death. In humans, 42 proteins are now known to cause amyloidosis. Some proteins become amyloidogenic as a result of a pathogenic variant as seen in hereditary amyloidoses. In acquired forms of amyloidosis, the proteins form amyloid in their wild-type state. Four types (serum amyloid A, transthyretin, apolipoprotein A-IV, and ß2-macroglobulin) of amyloid can occur either as acquired or as a mutant. Iatrogenic amyloid from injected protein medications have also been reported and AIL1RAP (anakinra) has been recently found to involve the kidney. Finally, the mechanism of how leukocyte cell-derived chemotaxin 2 (ALECT2) forms amyloid remains unknown. This article reviews the amyloids that involve the kidney and how they are typed.

Spectrum of renal diseases in the elderly, above age 50.

BACKGROUND: The spectrum of kidney diseases varies in the elderly population with frequent inconsistencies between clinical presentation and histopathological diagnosis. The immunofluorescence (IF) may provide additional information in such situations. AIMS: The purpose was to study the spectrum of kidney diseases in patients above 50 years undergoing renal biopsy and utility of light chain (LC) IF in the diagnosis. SETTINGS AND DESIGN: This was a retrospective, crosssectional, singlecenter-based study. MATERIAL AND METHODS: The clinical details, histopathological findings, and LC IF pattern in native renal biopsy of patients above 50 years were noted. STATISTICAL ANALYSIS: Continuous variables were presented as mean ± standard deviation (SD). Categorical variables were expressed as frequencies and percentages. RESULTS: A total of 205 patients were included in the study. The most common clinical presentation was acute kidney injury/rapidly progressive glomerulonephritis (AKI/RPGN) (49%). Glomerular diseases (72%) were more common. Crescentic glomerulonephritis (21%) and membranous nephropathy (MN) (19%) were the most common glomerulopathy. LC restriction was observed in LC cast nephropathy (LCCN), primary amyloidosis, and LC also helped in classifying the cases of MPGN-type morphology. CONCLUSIONS: AKI/RPGN was the most common indication for renal biopsy in patients above 50 years. Crescentic GN and MN were the frequent glomerular pathology. LC IF is a useful adjunctive tool to classify various renal diseases.

Variable expression of eighteen common housekeeping genes in human non-cancerous kidney biopsies.

Housekeeping, or reference genes (RGs) are, by definition, loci with stable expression profiles that are widely used as internal controls to normalize mRNA levels. However, due to specific events, such as pathological changes, or technical procedures, their expression might be altered, failing to fulfil critical normalization pre-requisites. To identify RG genes suitable as internal controls in human non-cancerous kidney tissue, we selected 18 RG candidates based on previous data and screen them in 30 expression datasets (>800 patients), including our own, publicly available or provided by independent groups. Datasets included specimens from patients with hypertensive and diabetic nephropathy, Fabry disease, focal segmental glomerulosclerosis, IgA nephropathy, membranous nephropathy, and minimal change disease. We examined both microdissected and whole section-based datasets. Expression variability of 4 candidate genes (YWHAZ, SLC4A1AP, RPS13 and ACTB) was further examined by qPCR in biopsies from patients with hypertensive nephropathy (n = 11) and healthy controls (n = 5). Only YWHAZ gene expression remained stable in all datasets whereas SLC4A1AP was stable in all but one Fabry dataset. All other RGs were differentially expressed in at least 2 datasets, and in 4.5 datasets on average. No differences in YWHAZ, SLC4A1AP, RPS13 and ACTB gene expression between hypertensive and control biopsies were detected by qPCR. Although RGs suitable to all techniques and tissues are unlikely to exist, our data suggest that in non-cancerous kidney biopsies expression of YWHAZ and SLC4AIAP genes is stable and suitable for normalization purposes.

Coding practice in national and regional kidney biopsy registries.

BACKGROUND: Kidney biopsy registries all over the world benefit research, teaching and health policy. Comparison, aggregation and exchange of data is however greatly dependent on how registration and coding of kidney biopsy diagnoses are performed. This paper gives an overview over kidney biopsy registries, explores how these registries code kidney disease and identifies needs for improvement of coding practice. METHODS: A literature search was undertaken to identify biopsy registries for medical kidney diseases. These data were supplemented with information from personal contacts and from registry websites. A questionnaire was sent to all identified registries, investigating age of registries, scope, method of coding, possible mapping to international terminologies as well as self-reported problems and suggestions for improvement. RESULTS: Sixteen regional or national kidney biopsy registries were identified, of which 11 were older than 10 years. Most registries were located either in Europe (10/16) or in Asia (4/16). Registries most often use a proprietary coding system (12/16). Only a few of these coding systems were mapped to SNOMED CT (1), older SNOMED versions (2) or ERA-EDTA PRD (3). Lack of maintenance and updates of the coding system was the most commonly reported problem. CONCLUSIONS: There were large gaps in the global coverage of kidney biopsy registries. Limited use of international coding systems among existing registries hampers interoperability and exchange of data. The study underlines that the use of a common and uniform coding system is necessary to fully realize the potential of kidney biopsy registries.

Receptor-mediated mitophagy regulates EPO production and protects against renal anemia.

Erythropoietin (EPO) drives erythropoiesis and is secreted mainly by the kidney upon hypoxic or anemic stress. The paucity of EPO production in renal EPO-producing cells (REPs) causes renal anemia, one of the most common complications of chronic nephropathies. Although mitochondrial dysfunction is commonly observed in several renal and hematopoietic disorders, the mechanism by which mitochondrial quality control impacts renal anemia remains elusive. In this study, we showed that FUNDC1, a mitophagy receptor, plays a critical role in EPO-driven erythropoiesis induced by stresses. Mechanistically, EPO production is impaired in REPs in Fundc1-/- mice upon stresses, and the impairment is caused by the accumulation of damaged mitochondria, which consequently leads to the elevation of the reactive oxygen species (ROS) level and triggers inflammatory responses by up-regulating proinflammatory cytokines. These inflammatory factors promote the myofibroblastic transformation of REPs, resulting in the reduction of EPO production. We therefore provide a link between aberrant mitophagy and deficient EPO generation in renal anemia. Our results also suggest that the mitochondrial quality control safeguards REPs under stresses, which may serve as a potential therapeutic strategy for the treatment of renal anemia.

Exploratory classification of clinical phenotypes in Japanese patients with antineutrophil cytoplasmic antibody-associated vasculitis using cluster analysis.

A novel patient cluster in antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) may be identified in Japan. We performed multiple correspondence and cluster analysis regarding 427 clinically diagnosed AAV patients excluding eosinophilic granulomatosis with polyangiitis. Model 1 included the ANCA phenotype, items of the Birmingham Vasculitis Activity Score, and interstitial lung disease; model 2 included serum creatinine (s-Cr) and C-reactive protein (CRP) levels with model 1 components. In seven clusters determined in model 1, the ANCA-negative (n = 8) and proteinase 3-ANCA-positive (n = 41) groups emerged as two distinct clusters. The other five myeloperoxidase-ANCA-positive clusters were characterized by ear, nose, and throat (ENT) (n = 47); cutaneous (n = 36); renal (n = 256), non-renal (n = 33); and both ENT and cutaneous symptoms (n = 6). Four clusters in model 2 were characterized by myeloperoxidase-ANCA negativity (n = 42), without s-Cr elevation (< 1.3 mg/dL) (n = 157), s-Cr elevation (≥ 1.3 mg/dL) with high CRP (> 10 mg/dL) (n = 71), or s-Cr elevation (≥ 1.3 mg/dL) without high CRP (≤ 10 mg/dL) (n = 157). Overall, renal, and relapse-free survival rates were significantly different across the four clusters in model 2. ENT, cutaneous, and renal symptoms may be useful in characterization of Japanese AAV patients with myeloperoxidase-ANCA. The combination of s-Cr and CRP levels may be predictive of prognosis.

A 16-year Survey of Clinicopathological Findings, Electron Microscopy, and Classification of Renal Amyloidosis.

Background: Electron microscopy (EM) is a valuable tool in the diagnosis of renal amyloidosis, particularly in the early stages of the disease. In Iran, studies on EM and the clinical features of renal amyloidosis are scarce. The objective of the present study was to survey EM investigations, pathological classifications, and clinical features of renal amyloidosis. Methods: This cross-sectional study was performed in Shiraz, Iran, during 2001-2016. Out of 2,770 kidney biopsies, 27 cases with a diagnosis of renal amyloidosis were investigated. EM investigation and six staining procedures for light microscopy (LM) were performed. Two pathological classifications based on glomerular, peritubular, perivascular, and interstitial involvement were made. Finally, the association between these classifications and the clinical features was assessed. Chi-square, Fisher's exact, Independent t test, and Multiple logistic regression analysis were used. P values<0.05 were considered statistically significant. Results: In 51.9% of the cases, the clinical diagnosis was nephrotic syndrome. Proteinuria and edema were the most prevalent clinical manifestations. The role of EM investigation for diagnosis was graded "necessary" or "supportive" in 48.2% of the patients. In the classification based on glomerular classes, variables such as the mean blood pressure (P=0.003), history of hypertension (P=0.02), creatinine >1.5 (P=0.03), and severe tubular atrophy (P=0.03) were significantly higher in class B (advanced amyloid depositions). Conclusion: EM plays an important role in the diagnosis of renal amyloidosis. EM in conjunction with LM investigation with Congo red staining is recommended, to prevent misdiagnosis of patients with a clinical suspicion of renal amyloidosis. Among different pathological features of renal amyloidosis, the severity of glomerular amyloid depositions had a clear relationship with clinical presentations.

Recommendations for Preclinical Renal MRI: A Comprehensive Open-Access Protocol Collection to Improve Training, Reproducibility, and Comparability of Studies.

Renal MRI holds incredible promise for making a quantum leap in improving diagnosis and care of patients with a multitude of diseases, by moving beyond the limitations and restrictions of current routine clinical practice. Clinical and preclinical renal MRI is advancing with ever increasing rapidity, and yet, aside from a few examples of renal MRI in routine use, it is still not good enough. Several roadblocks are still delaying the pace of progress, particularly inefficient education of renal MR researchers, and lack of harmonization of approaches that limits the sharing of results among multiple research groups.Here we aim to address these limitations for preclinical renal MRI (predominantly in small animals), by providing a comprehensive collection of more than 40 publications that will serve as a foundational resource for preclinical renal MRI studies. This includes chapters describing the fundamental principles underlying a variety of renal MRI methods, step-by-step protocols for executing renal MRI studies, and detailed guides for data analysis. This collection will serve as a crucial part of a roadmap toward conducting renal MRI studies in a robust and reproducible way, that will promote the standardization and sharing of data.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers.

Animal Models of Renal Pathophysiology and Disease.

Renal diseases remain devastating illnesses with unacceptably high rates of mortality and morbidity worldwide. Animal models are essential tools to better understand the pathomechanisms of kidney-related illnesses and to develop new, successful therapeutic strategies. Magnetic resonance imaging (MRI) has been actively explored in the last decades for assessing renal function, perfusion, tissue oxygenation as well as the degree of fibrosis and inflammation. This chapter aims to provide a comprehensive overview of animal models of acute and chronic kidney diseases, highlighting MRI-specific considerations, advantages, and pitfalls, and thus assisting the researcher in experiment planning.This publication is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers.

COVID-19 and the kidney.

COVID-19 is primarily considered a respiratory illness, but the kidney may be one of the targets of SARS-CoV-2 infection, since the virus enters cells through the angiotensin-converting enzyme 2 receptor, which is found in abundance in the kidney. Information on kidney involvement in COVID-19 is limited but is evolving rapidly. This article discusses the pathogenesis of acute kidney injury (AKI) in COVID-19, its optimal management, and the impact of COVID-19 on patients with chronic kidney disease, patients with end-stage kidney disease on dialysis, and kidney transplant recipients.

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project.

An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative efforts such as the Kidney Precision Medicine Project are working towards this goal through the collection and integration of large, disparate clinical, biological and imaging data from patients with kidney disease. Ontologies are powerful tools that facilitate these efforts by enabling researchers to organize and make sense of different data elements and the relationships between them. Ontologies are critical to support the types of big data analysis necessary for kidney precision medicine, where heterogeneous clinical, imaging and biopsy data from diverse sources must be combined to define a patient's phenotype. The development of two new ontologies - the Kidney Tissue Atlas Ontology and the Ontology of Precision Medicine and Investigation - will support the creation of the Kidney Tissue Atlas, which aims to provide a comprehensive molecular, cellular and anatomical map of the kidney. These ontologies will improve the annotation of kidney-relevant data, and eventually lead to new definitions of kidney disease in support of precision medicine.

The revised version 2018 of the nationwide web-based registry system for kidney diseases in Japan: Japan Renal Biopsy Registry and Japan Kidney Disease Registry.

BACKGROUND: The Japan Renal Biopsy Registry (J-RBR), the first nation-wide registry of renal biopsies in Japan, was established in 2007, and expanded to include non-biopsy cases as the Japan Kidney Disease Registry (J-KDR) in 2009. The J-RBR/J-KDR is one of the biggest registries for kidney diseases. It has revealed the prevalence and distribution of kidney diseases in Japan. This registry system was meant to be revised after 10 years. METHODS: In 2017, the Committees of the Japanese Society of Nephrology started a project for the revision of the J-RBR/J-KDR. The revised system was designed in such a way that the diagnoses of the patients could be selected from the Diagnosis Panel, a list covering almost all known kidney diseases, and focusing on their pathogenesis rather than morphological classification. The Diagnosis Panel consists of 22 categories (18 glomerular, 1 tubulointerstitial, 1 congenital/genetical, 1 transplant related, and 1 other) and includes 123 diagnostic names. The items for clinical diagnosis and laboratory data were also renewed, with the addition of the information on immunosuppressive treatment. RESULTS: The revised version of J-RBR/J-KDR came into use in January 2018. The number of cases registered under the revised system was 2748 in the first year. The total number of cases has reached to 43,813 since 2007. CONCLUSION: The revised version 2018 J-RBR/J-KDR system attempts to cover all kidney diseases by focusing on their pathogenesis. It will be a new platform for the standardized registration of kidney biopsy cases that provides more systemized data of higher quality.

Preoperative Intravenous Iron and Erythropoietin to Treat Severe Anemia in Patient With Stage 4 Kidney Disease Before Oncologic Surgery: A Case Report.

Preoperative treatment of anemia with intravenous iron is inconsistent despite known risks of anemia and allogeneic blood transfusions. Limited research exists on the effectiveness of preoperative intravenous iron for chronic kidney disease (CKD) patients. We discuss a patient with severe anemia from advanced CKD, endometrial cancer, and menometrorrhagia. Her hemoglobin increased more than 2 g/dL after erythropoietin and two 750-mg ferric carboxymaltose infusions 5 weeks before a total abdominal hysterectomy and avoided blood transfusions perioperatively. By raising hemoglobin, preoperative intravenous iron and erythropoietin reduce blood transfusions and consequent risk of future allograft rejection and alloimmunization in potential transplant recipients.

[Inflammation in kidney diseases].

The term "inflammation" is certainly one of the oldest medical terms still in use. However, its meaning has changed over the centuries. This work gives a historical and critical review of the concept of inflammation, with special reference to kidney diseases. Over time the definition of inflammation has shifted from a pure collection of symptoms to a histopathological definition, characterized by the tissue "inflammatory infiltrates" and different subcategories according to the cell type involved. The advantages of this classification are the generally good response to corticosteroids (with only a few exceptions) and the availability of specific drugs for each inflammatory infiltrate. Finally, a "molecular" definition of inflammation has arisen, where the inflammatory infiltrates make room to a plethora of plasma mediators. The authors show that the use of plasma biomarkers as a tool to define inflammatory state leads to net inflation of the number of "inflammatory" diseases - an effect that shows clearly in the field of nephrology.

Classification of glomerular hypercellularity using convolutional features and support vector machine.

Glomeruli are histological structures of the kidney cortex formed by interwoven blood capillaries, and are responsible for blood filtration. Glomerular lesions impair kidney filtration capability, leading to protein loss and metabolic waste retention. An example of lesion is the glomerular hypercellularity, which is characterized by an increase in the number of cell nuclei in different areas of the glomeruli. Glomerular hypercellularity is a frequent lesion present in different kidney diseases. Automatic detection of glomerular hypercellularity would accelerate the screening of scanned histological slides for the lesion, enhancing clinical diagnosis. Having this in mind, we propose a new approach for classification of hypercellularity in human kidney images. Our proposed method introduces a novel architecture of a convolutional neural network (CNN) along with a support vector machine, achieving near perfect average results on FIOCRUZ data set in a binary classification (lesion or normal). Additionally, classification of hypercellularity sub-lesions was also evaluated, considering mesangial, endocapilar and both lesions, reaching an average accuracy of 82%. Either in binary task or in the multi-classification one, our proposed method outperformed Xception, ResNet50 and InceptionV3 networks, as well as a traditional handcrafted-based method. To the best of our knowledge, this is the first study on deep learning over a data set of glomerular hypercellularity images of human kidney.

Pattern of renal amyloidosis in South Africa.

BACKGROUND: Kidney disease is a serious manifestation of systemic amyloidosis and a major cause of morbidity and mortality. Tuberculosis (TB) occurs up to 27 times more commonly in human immunodeficiency virus (HIV) infected patients and is also an important cause of renal amyloid; there are however no reports of renal amyloidosis in South Africa in the HIV era. METHODS: This was a retrospective record review of cases of amyloidosis diagnosed on renal biopsies at our tertiary referral hospital between January 1985 and December 2016. RESULTS: Forty-six cases of amyloidosis were identified over the study period. The calculated biopsy prevalence was 1.38 per 100 non-transplant renal biopsies (95% Confidence Interval 1.02-1.86). AL amyloidosis was identified in 26 (57%) cases and AA in 20 (43%). The median age at presentation was 51 years and 52% of cases were female. Patients with AA amyloidosis were significantly younger compared to their AL counterparts (age 42 years vs. 58 years, p = < 0.001) and were all significantly non-white. The main clinical presentation was nephrotic syndrome (85%) and 52% of cases also had a serum creatinine value of greater than 120 µmol/L. Of the 20 cases of AA amyloidosis, 12 (60%) were associated with tuberculosis. HIV infection was noted in only two (10%) of the 20 AA cases. Median survival after diagnosis was 2 months. CONCLUSION: Amyloidosis is a rare cause of kidney disease and typically presents with nephrotic syndrome. A similar number of AA and AL types were observed, and outcomes are worse in cases of AA amyloid. While TB remains the major underlying disease in this type, HIV infection was infrequent in cases of AA renal amyloidosis.