A position paper on standardizing the nonneoplastic kidney biopsy report

Standardized Protocols for Clinical and Histopathological Characterization of Hidradenitis Suppurativa Tissue Specimens

Methods for describing and reporting the clinical and histologic characteristics of cutaneous tissue samples from patients with hidradenitis suppurativa (HS) are not currently standardized, limiting clinicians' and scientists' ability to uniformly record, report, and communicate about the characteristics of tissue used in translational experiments. A recently published consensus statement outlined morphological definitions of typical HS lesions, but no consensus has been reached regarding clinical characterization and examination of HS tissue samples. In this study, we aimed to establish a protocol for reporting histopathologic and clinical characteristics of HS tissue specimens. This study was conducted from May 2023 to August 2023. Experts in clinical care, dermatopathology, and translational research were recruited, and a modified Delphi technique was used to develop a protocol for histologic reporting and clinical characterization of submitted tissue specimens from patients with HS. A total of 27 experts participated (14 dermatologists, 3 fellowship-trained dermatopathologists, 3 plastic surgeons, 3 general surgeons, and 4 research scientists) in creating and reviewing protocols for the clinical and histopathological examination of HS tissue specimens. The protocols were formatted as a synoptic report and will help to consistently classify specimens in biobanks on the basis of histologic features and more accurately report and select samples used in translational research projects.

The compositional and functional imbalance of the gut microbiota in CKD linked to disease patterns

BACKGROUND

The prevalence of chronic kidney disease (CKD) is on the rise, posing a significant public health challenge. Although gut microbiome dysbiosis has been implicated in the impairment of kidney functions, the existence of pathological subtypes-linked differences remains largely unknown. We aimed to characterize the intestinal microbiota in patients with membranous nephropathy (MN), IgA nephropathy (IgAN), minimal change disease (MCD), and ischemic renal injury (IRI) in order to investigate the intricate relationship between intestinal microbiota and CKD across different subtypes.

METHODS

We conducted a cross-sectional study involving 94 patients with various pathological patterns of CKD and 54 healthy controls (HCs). The clinical parameters were collected, and stool samples were obtained from each participant. Gut microbial features were analyzed using 16S rRNA sequencing and taxon annotation to compare the HC, CKD, MN, IgAN, MCD, and IRI groups.

RESULTS

The CKD subjects exhibited significantly reduced alpha diversity, modified community structures, and disrupted microbial composition and potential functions compared to the control group. The opportunistic pathogen Klebsiella exhibited a significant enrichment in patients with CKD, whereas Akkermansia showed higher abundance in HCs. The study further revealed the presence of heterogeneity in intestinal microbial signatures across diverse CKD pathological types, including MN, IgAN, MCD, and IRI. The depression of the family Lachnospiraceae and the genus Bilophila was prominently observed exclusively in patients with MN, while suppressed Streptococcus was detected only in individuals with MCD, and a remarkable expansion of the genus Escherichia was uniquely found in cases of IRI. The study also encompassed the development of classifiers employing gut microbial diagnostic markers to accurately discriminate between distinct subtypes of CKD.

CONCLUSIONS

The dysregulation of gut microbiome was strongly correlated with CKD, exhibiting further specificity towards distinct pathological patterns. Our study emphasizes the significance of considering disease subtypes when assessing the impact of intestinal microbiota on the development, diagnosis, and treatment of CKD.

[Introduction to renal pathology]

In recent decades, nephropathology has developed worldwide as a subspeciality of pathology, which requires special methodological and technical equipment to process the material and specific clinical and pathological expertise to interpret the findings. These special requirements mean that nephropathology is not available at all pathology institutes, but is carried out on a large scale in a few highly specialised centres. The history of nephropathology, or in a narrower sense the specialised histopathological examination of kidney biopsies, began in 1958 with the first use or performance of a kidney biopsy [1]. It thus replaced the practice of urinalysis, which had been common since the Middle Ages, as a diagnostic tool for kidney diseases. Specialised techniques such as immunofluorescence or immunohistology but also electron microscopy are required to assess specific renal changes, for which the examination of renal biopsies is one of the few remaining routine applications today. In Germany and German-speaking countries, the discipline developed thanks to the work of outstanding people in the field of pathology who were primarily involved in this discipline and had the necessary technical and human resources in their laboratories to ensure that these biopsies could be analysed.

Clinicopathologic Study of Sickle Cell-associated Kidney Disease: A Nigerian Experience

BACKGROUND

Improvements in sickle cell disease (SCD) care have resulted in the survival of many patients into adulthood, although this is accompanied by the increased incidence of end-organ damage, including chronic kidney disease (CKD).

OBJECTIVES

This study assessed the prevalence, pattern and predictors of renal dysfunction in SCD patients and investigated the associated renal histopathologic changes.

METHODS

We evaluated 105 patients with SCD, for proteinuria, estimated glomerular filtration rate (eGFR), and tubular dysfunction. Renal biopsy was conducted on 22 patients who qualified. Data were analysed using SPSS package version 23.

RESULTS

Thirty-seven (35.2%) of the 105 patients had CKD, as defined by an eGFR of 60 ml/min/1.73 m2 and/or proteinuria. The fractional excretion of potassium (FEK) was elevated in all patients, whereas the fractional excretion of sodium (FENa) was elevated in 98.1%. Glomerular filtration rate was negatively correlated with irreversible percentage sickle cell count (r = -0.616, P = 0.0001), FEK (r = -0.448, P = 0.0001) and FENa (r = -0.336, P = 0.004). Age, irreversible percentage sickle cell count, haemoglobin levels and FENa were the major predictors of CKD. The histological pattern in the 22 patients who had biopsies was consistent with mesangioproliferative glomerulonephritis 11 (50%), minimal change disease 6 (27.3%), focal segmental glomerulosclerosis 3 (13.6%) and interstitial nephritis 2 (9.1%).

CONCLUSIONS

CKD was prevalent in SCD patients, and it was characterised by tubular dysfunction and mesangioproliferative glomerulonephritis. The main predictors of CKD were increased age, severity of vaso-occlusive crisis, worsening anaemia and tubular dysfunction.

Immunofluorescence Use and Techniques in Glomerular Diseases: A Review

Background

Immunofluorescence (IF) studies play an essential role in the evaluation of medical renal biopsies. Particularly, in the study of renal glomerular diseases, where it provides fundamental data for the diagnosis, classification, and etiology of the glomerular pathologies. Diverse techniques may be used to optimize the utilization of IF studies, from variations on the test methodologies to expertise on the interpretation of the results and knowledge of potential pitfalls.

Summary

This manuscript presents a brief review on the history of IF and its utilization in kidney pathology, followed by a description of the IF methods, including the use of IF on paraffin-embedded tissue (paraffin IF), and other novel techniques. Guidelines on how to best report IF findings are reviewed, along with a description of antibodies commonly used in glomerular diseases, highlighting their distribution within the normal kidney and potential pitfalls in interpretation. Finally, the use and interpretation of IF are discussed in more detail in individual entities on a range of glomerular diseases.

Key Messages

IF is crucial for interpretation of renal biopsies and diagnosis of glomerular diseases. Knowledge of IF techniques, alternative procedures, its use and proper interpretation is essential for optimal utilization of IF in renal pathology, and this review proposes to serve as a simplified and practical guide on this topic.

Complete digital pathology transition: A large multi-center experience

INTRODUCTION

Transitioning from glass slide pathology to digital pathology for primary diagnostics requires an appropriate laboratory information system, an image management system, and slide scanners; it also reinforces the need for sophisticated pathology informatics including synoptic reporting. Previous reports have discussed the transition itself and relevant considerations for it, but not the selection criteria and considerations for the infrastructure.

OBJECTIVE

To describe the process used to evaluate slide scanners, image management systems, and synoptic reporting systems for a large multisite institution.

METHODS

Six network hospitals evaluated six slide scanners, three image management systems, and three synoptic reporting systems. Scanners were evaluated based on the quality of image, speed, ease of operation, and special capabilities (including z-stacking, fluorescence and others). Image management and synoptic reporting systems were evaluated for their ease of use and capacity.

RESULTS

Among the scanners evaluated, the Leica GT450 produced the highest quality images, while the 3DHistech Pannoramic provided fluorescence and superior z-stacking. The newest generation of scanners, released relatively recently, performed better than slightly older scanners from major manufacturers Although the Olympus VS200 was not fully vetted due to not meeting all inclusion criteria, it is discussed herein due to its exceptional versatility. For Image Management Software, the authors believe that Sectra is, at the time of writing the best developed option, but this could change in the very near future as other systems improve their capabilities. All synoptic reporting systems performed impressively.

CONCLUSIONS

Specifics regarding quality and abilities of different components will change rapidly with time, but large pathology practices considering such a transition should be aware of the issues discussed and evaluate the most current generation to arrive at appropriate conclusions.

Establishing an effective clinical data collecting tool for optimal evaluation of native and allograft renal biopsies

Introduction

Percutaneous kidney biopsy is the gold standard method to reach a precise diagnosis in most medical kidney diseases, which positively impacts patient care by personalizing the treatment. Accurate diagnosis in the pathology report for medical kidney diseases requires clinicopathological correlation, and clinical data is not always reachable to the nephropathologist. This study aimed to create a standardized, paperless requisition form compatible with medical renal biopsies.

Methods

An initial form was prepared for native and allograft renal biopsies according to the current classification of medical kidney diseases. We invited 33 nephropathologists working in Canadian healthcare institutions to answer survey questions about the need to include a particular aspect of clinical information. According to the responses, we modified the experimental form. Eighty nephrologists were asked to complete a clinical data-collecting form given out as PDF files. The time for completing the form and clinicians' satisfaction were assessed.

Results

The experimental form survey was answered by 20 out of 33 nephropathologists (61%) from 14 Canadian healthcare centers. The agreement rate on the questions was from 38.89% to 100.00% (average 83.33% and 77.14% for the native and the allograft section, respectively). Seventeen out of 80 nephrologists and their assistants (21%) responded by completing 22 PDF forms. The time required to finish a PDF form was 10.4 min on average. Nephrologists considered the form time-consuming and suggested making it more clinically relevant. Only seven nephrologists responded to the satisfaction survey; four (57%) were satisfied.

Conclusions

Medical information is critical in renal pathology diagnoses. A uniform paperless clinical data requisition form was evolved through an agreement by Canadian nephropathologists.

Changes in CT-Based Morphological Features of the Kidney with Declining Glomerular Filtration Rate in Chronic Kidney Disease

Chronic kidney disease (CKD) progression involves morphological changes in the kidney, such as decreased length and thickness, with associated histopathological alterations. However, the relationship between morphological changes in the kidneys and glomerular filtration rate (GFR) has not been quantitatively and comprehensively evaluated. We evaluated the three-dimensional size and shape of the kidney using computed tomography (CT)-derived features in relation to kidney function. We included 257 patients aged ≥18 years who underwent non-contrast abdominal CT at the Inha University Hospital. The features were quantified using predefined algorithms in the pyRadiomics package after kidney segmentation. All features, except for flatness, significantly correlated with estimated GFR (eGFR). The surface-area-to-volume ratio (SVR) showed the strongest negative correlation (r = -0.75, p < 0.0001). Kidney size features, such as volume and diameter, showed moderate to high positive correlations; other morphological features showed low to moderate correlations. The calculated area under the receiver operating characteristic (ROC) curve (AUC) for different features ranged from 0.51 (for elongation) to 0.86 (for SVR) for different eGFR thresholds. Diabetes patients had weaker correlations between the studied features and eGFR and showed less bumpy surfaces in three-dimensional visualization. We identified alterations in the CKD kidney based on various three-dimensional shape and size features, with their potential diagnostic value.

Boundary-aware glomerulus segmentation: Toward one-to-many stain generalization

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.

Natural Language Processing in Diagnostic Texts from Nephropathology

Introduction: This study investigates whether it is possible to predict a final diagnosis based on a written nephropathological description—as a surrogate for image analysis—using various NLP methods. Methods: For this work, 1107 unlabelled nephropathological reports were included. (i) First, after separating each report into its microscopic description and diagnosis section, the diagnosis sections were clustered unsupervised to less than 20 diagnostic groups using different clustering techniques. (ii) Second, different text classification methods were used to predict the diagnostic group based on the microscopic description section. Results: The best clustering results (i) could be achieved with HDBSCAN, using BoW-based feature extraction methods. Based on keywords, these clusters can be mapped to certain diagnostic groups. A transformer encoder-based approach as well as an SVM worked best regarding diagnosis prediction based on the histomorphological description (ii). Certain diagnosis groups reached F1-scores of up to 0.892 while others achieved weak classification metrics. Conclusion: While textual morphological description alone enables retrieving the correct diagnosis for some entities, it does not work sufficiently for other entities. This is in accordance with a previous image analysis study on glomerular change patterns, where some diagnoses are associated with one pattern, but for others, there exists a complex pattern combination.

Relationship between glomerular number in fresh kidney biopsy samples and light microscopy samples

BACKGROUND

On-site evaluation of fresh kidney biopsy (FKB) samples at the time of biopsy is useful to verify that adequate specimens are acquired. However, some cases present poor correlation between glomerular number in FKB samples and light microscopy (LM) samples. We examined the usefulness of such on-site evaluation.

METHODS

We conducted a retrospective cross-sectional observational study (n = 129) to assess the correlation between glomerular number in FKB samples and LM samples and the associated factors hindering the evaluation.

RESULTS

There was a significant positive correlation between glomerular number in FKB samples and LM samples. The median ratio of glomerular number (LM samples/FKB samples) was 0.74. According to this ratio, cases were divided into three groups: reasonable estimation (65 cases), underestimation (32 cases), and overestimation (32 cases). Comparing the reasonable and underestimation groups, significant differences were detected in the extent of interstitial fibrosis and tubular atrophy (IFTA) and interstitial inflammation. Logistic regression analysis demonstrated that IFTA and interstitial inflammation were significantly associated with the underestimation. Moreover, the cortex length of FKB samples correlated with glomerular number in LM samples regardless of tubulointerstitial lesions.

CONCLUSIONS

Glomerular number determined during on-site evaluation can be a reference for the actual number of glomeruli in LM samples. Since tubulointerstitial lesions make it difficult to recognize glomeruli in FKB samples, the possibility of underestimation for cases with possibly severe tubulointerstitial lesions should be considered. In such cases, evaluation of cortex length of FKB samples may substitute for evaluating glomeruli on-site.

Systematic reporting of medical kidney biopsies

The medical kidney biopsy has an important added value in patient care in nephrology. In order to facilitate communication between the pathologist and the nephrologist and optimize patient care, both the content and form of the medical kidney biopsy report matter. With some exceptions, current guidelines in nephropathology focus on content rather than form and, not surprisingly, medical kidney biopsy reports mostly consist of unformatted and often lengthy free text. In contrast, in oncology, a more systematic reporting called synoptic reporting has become the dominant method. Synoptic formats enable complete, concise and clear reports that comply with agreed upon standards. In this review we discuss the possibilities of systematic reporting in nephropathology (including synoptic reporting). Furthermore, we explore applications of electronic formats with structured data and usage of international terminologies or coding systems. The benefits include the timely collection of high-quality data for benchmarking between centres as well as for epidemiologic and other research studies. Based on these developments, a scenario for future medical kidney biopsy reporting is drafted.

AI applications in renal pathology

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.

PathoSpotter-K: A computational tool for the automatic identification of glomerular lesions in histological images of kidneys

PathoSpotter is a computational system designed to assist pathologists in teaching about and researching kidney diseases. PathoSpotter-K is the version that was developed to detect nephrological lesions in digital images of kidneys. Here, we present the results obtained using the first version of PathoSpotter-K, which uses classical image processing and pattern recognition methods to detect proliferative glomerular lesions with an accuracy of 88.3 ± 3.6%. Such performance is only achieved by similar systems if they use images of cell in contexts that are much less complex than the glomerular structure. The results indicate that the approach can be applied to the development of systems designed to train pathology students and to assist pathologists in determining large-scale clinicopathological correlations in morphological research.

Current status of pediatric renal transplant pathology

Histopathology is still an indispensable tool for the diagnosis of kidney transplant dysfunction in adult and pediatric patients. This review presents consolidated knowledge, recent developments and future prospects on the biopsy procedure, the diagnostic work-up, classification schemes, the histopathology of rejection, including antibody-mediated forms, ABO-incompatible transplants, protocol biopsies, recurrent and de novo disease, post-transplant lymphoproliferative disorder, infectious complications and drug-induced toxicity. It is acknowledged that frequently the correct diagnosis can only be reached in consensus with clinical, serological, immunogenetical, bacteriological and virological findings. This review shall enhance the understanding of the pediatric nephrologist for the thought processes of nephropathologists with the aim to facilitate teamwork between these specialist groups for the benefit of the patient.

Mayo Clinic/Renal Pathology Society Consensus Report on Pathologic Classification, Diagnosis, and Reporting of GN

Renal pathologists and nephrologists met on February 20, 2015 to establish an etiology/pathogenesis-based system for classification and diagnosis of GN, with a major aim of standardizing the kidney biopsy report of GN. On the basis of etiology/pathogenesis, GN is classified into the following five pathogenic types, each with specific disease entities: immune-complex GN, pauci-immune GN, antiglomerular basement membrane GN, monoclonal Ig GN, and C3 glomerulopathy. The pathogenesis-based classification forms the basis of the kidney biopsy report. To standardize the report, the diagnosis consists of a primary diagnosis and a secondary diagnosis. The primary diagnosis should include the disease entity/pathogenic type (if disease entity is not known) followed in order by pattern of injury (mixed patterns may be present); score/grade/class for disease entities, such as IgA nephropathy, lupus nephritis, and ANCA GN; and additional features as detailed herein. A pattern diagnosis as the sole primary diagnosis is not recommended. Secondary diagnoses should be reported separately and include coexisting lesions that do not form the primary diagnosis. Guidelines for the report format, light microscopy, immunofluorescence microscopy, electron microscopy, and ancillary studies are also provided. In summary, this consensus report emphasizes a pathogenesis-based classification of GN and provides guidelines for the standardized reporting of GN.

Mayo Clinic/Renal Pathology Society Consensus Report on Pathologic Classification, Diagnosis, and Reporting of GN

Renal pathologists and nephrologists met on February 20, 2015 to establish an etiology/pathogenesis-based system for classification and diagnosis of GN, with a major aim of standardizing the kidney biopsy report of GN. On the basis of etiology/pathogenesis, GN is classified into the following five pathogenic types, each with specific disease entities: immune-complex GN, pauci-immune GN, antiglomerular basement membrane GN, monoclonal Ig GN, and C3 glomerulopathy. The pathogenesis-based classification forms the basis of the kidney biopsy report. To standardize the report, the diagnosis consists of a primary diagnosis and a secondary diagnosis. The primary diagnosis should include the disease entity/pathogenic type (if disease entity is not known) followed in order by pattern of injury (mixed patterns may be present); score/grade/class for disease entities, such as IgA nephropathy, lupus nephritis, and ANCA GN; and additional features as detailed herein. A pattern diagnosis as the sole primary diagnosis is not recommended. Secondary diagnoses should be reported separately and include coexisting lesions that do not form the primary diagnosis. Guidelines for the report format, light microscopy, immunofluorescence microscopy, electron microscopy, and ancillary studies are also provided. In summary, this consensus report emphasizes a pathogenesis-based classification of GN and provides guidelines for the standardized reporting of GN.