Histological diagnosis from kidney transplant biopsy can contribute to prediction of graft survival

Aim

The primary aim of this study was to in depth examine if the histological findings in a transplanted kidney biopsy can predict the prognosis for the graft and the patient. The secondary aim was to extend knowledge of the impact of time elapsed on biopsy findings.

Methods

Data from 1462 patients were merged from a kidney transplantation registry and a biopsy registry during 1 January 2007 and 30 September 2017. Kaplan–Meier analysis and multivariate Cox‐regression analysis were performed and hazard ratios (HR) with 95% confidence intervals (CI) were presented.

Results

Compared to normal biopsy findings, graft survival after biopsy (gsaBiopsy) was shorter for patients with glomerular diseases (HR 8.2, CI:3.2–21.1), rejections (HR 4.2, CI:1.7–10.3), chronic changes including IFTA (HR 3.2, CI:1.3–8.0), acute tubular injuries (HR 3.0, CI:1.2–7.8), and borderline changes (HR 2.9, CI:1.1–7.6). Sub‐analysis of rejections showed shorter gsaBiopsy for chronic TCMR (HR 4.7, CI:1.9–11.3), active ABMR (HR 3.6, CI:1.7–7.7) and chronic ABMR (HR 3.5, CI:2.0–6.0). Patients with TCMR Banff grade II (HR 0.35, CI:0.20–0.63) and grade I (HR 0.52, CI:0.29–0.93) had a better gsaBiopsy compared to all other types of rejections.

Conclusion

Shorter gsaBiopsy was noted in kidneys with glomerular diseases, rejections, acute tubular injuries and borderline changes. TCMR Banff rejections grade I and II were associated with a better prognosis.

This Swedish single centre study showed that the impact on allograft survival is dependent on the nature of the biopsy findings, with histological findings of glomerular disease, severe rejections and chronic changes being associated with more rapid allograft loss.

Predictors of hematoma as a complication in pediatric kidney biopsies

BACKGROUND

Kidney biopsies are crucial in the diagnosis of kidney diseases but they carry the risk of various complications, most commonly hematoma. Here we tried to identify the predictors of hematomas as a complication of kidney biopsies and we constructed an algorithm to stratify the risk.

METHODS

The present report retrospectively reviewed 118 pediatric percutaneous kidney biopsies of native kidneys in 102 children (59 females) with the median age of 9 years (range: 1-19 years) at Kumamoto University Hospital between August 2008 and October 2019. We defined hematoma size using the hematoma index: the short axis of the hematoma/major axis of the kidney on ultrasonography. The inclusion criteria for a hematoma as a complication of a kidney biopsy were hematoma index ≥0.1 and the presence of concomitant, post-kidney biopsy fever or flank pain.

RESULTS

Eight patients presented with a hematoma as a complication. All had hematoma index ≥0.1 and age ≥6 years. On univariate logistic analysis, these patients had a larger hemoglobin (Hgb) decrease on post-biopsy day 1, which was unrelated to a Hgb decrease 2 h after the biopsy, than the patients with no hematoma. All eight patients with a hematoma presented with a fever or flank pain on post-biopsy days 5 to 7, underscoring the need to observe patients with decreased Hgb carefully for about 1 week after a biopsy.

CONCLUSION

Predictors of hematoma as a complication in children after a kidney biopsy were hematoma index ≥0.1, age >6 years, and Hgb decrease ≥15% on post-biopsy day 1.

Detection and localization of calcium oxalate in kidney using synchrotron deep ultraviolet fluorescence microscopy

Renal oxalosis is a rare cause of renal failure whose diagnosis can be challenging. Synchrotron deep ultraviolet (UV) fluorescence was assayed to improve oxalosis detection on kidney biopsies spatial resolution and sensitivity compared with the Fourier transform infrared microspectroscopy gold standard. The fluorescence spectrum of synthetic mono-, di- and tri-hydrated calcium oxalate was investigated using a microspectrometer coupled to the synchrotron UV beamline DISCO, Synchrotron SOLEIL, France. The obtained spectra were used to detect oxalocalcic crystals in a case control study of 42 human kidney biopsies including 19 renal oxalosis due to primary (PHO, n = 11) and secondary hyperoxaluria (SHO, n = 8), seven samples from PHO patients who received combined kidney and liver transplants, and 16 controls. For all oxalocalcic hydrates samples, a fluorescence signal is detected at 420 nm. These spectra were used to identify standard oxalocalcic crystals in patients with PHO or SHO. They also revealed micrometric crystallites as well as non-aggregated oxalate accumulation in tubular cells. A nine-points histological score was established for the diagnosis of renal oxalosis with 100% specificity (76-100) and a 73% sensitivity (43-90). Oxalate tubular accumulation and higher histological score were correlated to lower estimated glomerular filtration rate and higher urinary oxalate over creatinine ratio.

Assessment of a computerized quantitative quality control tool for whole slide images of kidney biopsies

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.

Clinicopathological features of fast eGFR decliners among patients with diabetic nephropathy

INTRODUCTION

The speed of declining kidney function differs among patients with diabetic nephropathy. This study was undertaken to clarify clinical and pathological features that affect the speed of declining kidney function in patients with diabetic nephropathy.

RESEARCH DESIGN AND METHODS

This study was design as multicenter retrospective study. The subjects (377 patients with diabetic nephropathy diagnosed by kidney biopsy at 13 centers in Japan) were classified into three groups based on the estimated glomerular filtration rate (eGFR) declining speed. The eGFR increasing group, the control group, and the eGFR declining group were divided at 0 and 5 mL/min/1.73 m²/year, respectively. Characteristics of clinicopathological findings of declining kidney function were evaluated.

RESULTS

The mean observation period of this study was 6.9 years. The control group, the eGFR increasing group, and the eGFR declining group included 81, 66, and 230 patients, respectively. The incidences of composite kidney events represented by 100 persons/year were 25.8 in the eGFR declining group and 2.0 in the eGFR increasing group. After adjustment for age, sex, systolic blood pressure, hemoglobin, and urinary albumin levels, three clinicopathological findings (urinary albumin levels, presence of nodular lesion, and mesangiolysis) were risk factors for inclusion in the eGFR declining group (the ORs were 1.49, 2.18, and 2.08, respectively). In contrast, the presence of subendothelial space widening and polar vasculosis were characteristic findings for inclusion in the eGFR increasing group (the ORs were 0.53 and 0.41, respectively).

CONCLUSIONS

As well as urinary albumin elevation, nodular lesion and mesangiolysis were characteristic pathological features of patients with fast declining kidney function.

Genetic Analyses in Dent Disease and Characterization of CLCN5 Mutations in Kidney Biopsies

Dent disease (DD), an X-linked renal tubulopathy, is mainly caused by loss-of-function mutations in CLCN5 (DD1) and OCRL genes. CLCN5 encodes the ClC-5 antiporter that in proximal tubules (PT) participates in the receptor-mediated endocytosis of low molecular weight proteins. Few studies have analyzed the PT expression of ClC-5 and of megalin and cubilin receptors in DD1 kidney biopsies. About 25% of DD cases lack mutations in either CLCN5 or OCRL genes (DD3), and no other disease genes have been discovered so far. Sanger sequencing was used for CLCN5 gene analysis in 158 unrelated males clinically suspected of having DD. The tubular expression of ClC-5, megalin, and cubilin was assessed by immunolabeling in 10 DD1 kidney biopsies. Whole exome sequencing (WES) was performed in eight DD3 patients. Twenty-three novel CLCN5 mutations were identified. ClC-5, megalin, and cubilin were significantly lower in DD1 than in control biopsies. The tubular expression of ClC-5 when detected was irrespective of the type of mutation. In four DD3 patients, WES revealed 12 potentially pathogenic variants in three novel genes (SLC17A1, SLC9A3, and PDZK1), and in three genes known to be associated with monogenic forms of renal proximal tubulopathies (SLC3A, LRP2, and CUBN). The supposed third Dent disease-causing gene was not discovered.

Nephron ultrastructural alterations induced by zinc oxide nanoparticles: an electron microscopic study

Due to their unique properties, zinc oxide nanoparticles (ZnO NPs) are invested in many industries, commercial products, and nanomedicine with potential risk for human health and the environment. The present study aims to focus on alterations that might be induced by ZnO NPs in the nephron ultrastructure. Male Wister Albino rats were subjected to ZnO NPs at a daily dose of 2 mg/kg for 21 days. Kidney biopsies were processed to transmission electron microscopy (TEM) and ultrastructural pathology examinations. Exposure to ZnO NPs‐induced ultrastructural alterations in the proximal convoluted tubules (PCTs) and to lesser extent in the distal ones (DCTs), while the loops of Henle were almost not affected. The glomeruli demonstrated dilatation, partial mesangial cells loss, matrix ballooning, slits filtration widening, and basement membrane thickening. Moreover, PCT revealed cytoplasmic necrosis, vacuolation, erosion, and disorganisation of the apical microvilli together with mitochondrial swelling and cristae destruction. The nuclei of the renal cells exhibited nuclear deformity, heterochromatin accumulation, and apoptotic activities. The findings indicate that ZnO nanomaterial have the potential to affect the nephron ultrastructure suggesting alteration in the kidney functions. More work is needed for better understanding the toxicity and pathogenesis of ZnO oxide nanomaterial.

RNA extraction for RNA sequencing of archival renal tissues

BACKGROUND

Next generation sequencing (NGS) and especially ribonucleic acid (RNA) sequencing is a powerful tool to acquire insights into molecular disease mechanisms. Therefore, it is of interest to optimize methods for RNA extraction from archival, formalin fixed and paraffin embedded (FFPE) tissues. This is challenging due to RNA degradation and chemical modifications. The aim of this study was to find the most appropriate method to extract RNA from FFPE renal tissue to enable NGS.

METHOD

We evaluated seven commercially available RNA extraction kits: High Pure FFPE RNA Isolation (Roche), ExpressArt Clear FFPE RNAready (Amsbio), miRNeasy FFPE, RNeasy FFPE (Qiagen), PureLink FFPE Total RNA (Invitrogen), RecoverAll Total Nucleic Acid Isolation (Ambion) and Absolutely RNA FFPE Kit (Agilent). RNA was obtained from tissue blocks of two healthy, male Wistar rats and from normal renal tissue of patients undergoing nephrectomy. Yield and quality of RNA extracted from rat whole kidney sections, human kidney core biopsies and laser capture microdissected (LCM) glomerular cross-sections were assessed: Analyses of RNA quantity were performed using NanoDrop and Qubit. RNA quality is reflected by DV200 values (% of RNA fragments >200 nucleotides) utilizing the Agilent 2100 BioAnalyzer. RNA of human LCM samples was subsequently sequenced using the Illumina TruSeq(®) RNA Access Library Preparation Kit.

CONCLUSION

Total RNA can be extracted from archival renal biopsies in sufficient quality and quantity from one human kidney biopsy section and from around 100 LCM glomerular cross-sections to enable successful RNA library preparation and sequencing using commercially available RNA extraction kits.