Kidney International

Introduction: Podocyte injury is central to the pathogenesis of most glomerulonephritides (GN) and causes segmental glomerulosclerotic lesions that predict progression in IgA Nephropathy (IgAN). Recent advances in high-resolution microscopy and AI-assisted image analysis have enabled detailed quantification of podocyte foot process (FP) morphology. However, whether nanoscale podocyte morphometrics can predict disease progression or treatment response in GN has not been investigated. Aim: To evaluate whether nanoscale podocyte morphometric parameters predict clinical characteristics, disease progression, and treatment response in GN, with a focus on IgAN. Method: Podocyte morphometrics were analyzed in kidney biopsies from patients with GN using high-resolution microscopy and the deep learning-based tool Automatic Morphometric Analysis of Podocytes (AMAP). Four morphometric parameters were quantified: slit diaphragm length (SDL), FP area, FP circularity and FP perimeter. These parameters were correlated with clinical characteristics, conventional electron microscopy (EM) findings and longitudinal follow-up data. Results: The study included 37 patients with GN from Danderyd University Hospital (Stockholm, Sweden), with IgAN representing the largest diagnostic subgroup (n = 19). The median follow-up for the cohort was 3.0 years. SDL correlated significantly with urine albumin-to-creatinine ratio (uACR; p = 0.021), whereas conventional EM measurements did not (p = 0.22). Within the IgAN subgroup, lower SDL was associated with a steeper decline in eGFR, higher FP area with increased long-term proteinuria, and higher FP circularity with improvement in uACR during the first year. The association between lower SDL and eGFR decline remained as a trend in IgAN patients not treated with corticosteroids (p = 0.068) but was absent in the treatment group (p = 0.59). Conclusion: In this proof-of-concept study, nanoscale podocyte morphometrics demonstrated greater sensitivity than conventional EM in quantifying podocyte injury and predicting progression in IgAN. These findings suggest that high-resolution morphometrics may improve risk stratification in IgAN but require validation in larger, independent cohorts before clinical implementation.

Background: Single-nephron glomerular filtration rate (GFR) represents a nephron-level functional index that may reveal key pathophysiological mechanisms driving progression in patients with diabetic nephropathy. However, its clinical relevance remains incompletely understood. This cross-sectional study assessed single-nephron estimated GFR (eGFR) across different chronic kidney disease (CKD) stages in patients with advanced diabetic nephropathy. Methods: Nephron number was estimated as the number of nonglobally sclerotic glomeruli per kidney using computed tomography-derived cortical volume combined with biopsy stereology. Single-nephron eGFR was calculated by dividing eGFR by the nephron number of both kidneys. Patients were stratified according to CKD stage at kidney biopsy. Associations between CKD stages and single-nephron eGFR were evaluated using multivariable linear regression models adjusted for age, sex, urinary protein excretion, and eGFR. Results: The study included 105 patients with biopsy-proven diabetic nephropathy and overt proteinuria (median age 59 years, 83% male, HbA1c 6.6%, 57% had nephrotic range proteinuria). The percentage of globally sclerotic glomeruli, mesangial expansion score, and prevalence of nodular lesions increased significantly with advancing CKD stage. Median nephron number declined from 529,178 to 224,458 per kidney, whereas glomerular volume remained constant. Single-nephron eGFR decreased markedly with CKD stage and remained significantly inversely associated with CKD stage after adjustment for clinicopathologic covariates (P for trend <0.001). Conclusion: In overt diabetic nephropathy, single-nephron eGFR decreased with advancing CKD stage, despite relatively preserved glomerular volume. At this stage of disease, structural alterations specific to diabetic nephropathy may impair effective single-nephron filtration capacity.

Background and hypothesis Autosomal dominant polycystic kidney disease (ADPKD) affects over 12 million people worldwide including an estimated 30,000-70,000 in the United Kingdom (UK). Tolvaptan is the only disease-modifying therapy approved for rapidly progressing disease. Despite national guidance, prescribing rates were hypothesised to vary by kidney centre. Treatment may not always align with guidelines: some patients eligible for tolvaptan may not be initiated, while other patients initiated on tolvaptan may not meet eligibility criteria. This may have important consequences for healthcare costs and health-related quality of life. Methods The National Registry of Rare Kidney Diseases (RaDaR) collects longitudinal data from UK NHS kidney centres. This retrospective cohort study used routinely collected data (2016-2023) to examine tolvaptan prescribing across kidney centres. Kidney centre-level initiation patterns were described, assessed using mixed-effects logistic regression and visualised with funnel plots. Cost-effectiveness analyses combined observed prescribing practices under likely negotiated commercial discounts to estimate costs and quality-adjusted life year (QALY) consequences of prescribing at the national level. Results Our study included 3,609 people with ADPKD from 72 kidney centres. Patients eligible for tolvaptan who were not initiated accounted for 34.8% (292/839). Across centres, five (6.9%) initiated tolvaptan significantly more than expected among eligible participants, while one centre (1.4%) initiated significantly less. Nationally, this could result in up to {pound}53.7 million in lost savings (assuming a 60% medication price reduction) and result in up to 1,245 lost QALYs. Patients initiated on tolvaptan who were not eligible accounted for 26.1% (103/395). Only one centre had significantly fewer eligible patients than expected among initiated patients. Nationally, this could cost up to {pound}15.9 million (assuming a 60% medication price reduction). Conclusions There is evidence of variation in tolvaptan prescribing in the UK. A substantial proportion of patients eligible for tolvaptan were not initiated at the cohort-level, with evidence of variation between centres suggesting differences in treatment decision-making. A substantial proportion of patients initiated on tolvaptan were not eligible at the cohort-level, but there was limited evidence of variation between centres. Together, these findings raise questions regarding the potential consistency of clinical decision-making, equitable access to a sole disease-modifying therapy in a rare disease, alignment with national guidance, and effective use of healthcare resources.

Background: Microvascular dysfunction contributes to chronic kidney disease (CKD), but reproducible clinical measures are limited. Laser Doppler flowmetry (LDF) provides a noninvasive assessment of cutaneous microvascular blood flow and may reflect systemic microvascular health. Its relationship with kidney function and histopathology in CKD remains unclear. Methods: We assessed cutaneous microvascular function in 150 participants with CKD (eGFR <90 mL/min/1.73 m2) using a standardized forearm LDF protocol. Baseline perfusion was recorded at ~30{degrees}C, followed by local heating to 44{degrees}C to induce hyperemia. Percent change in perfusion units (PU) defined microvascular functional reserve. Associations of LDF measures with eGFR and urine protein-to-creatinine ratio (uPCR) were evaluated using multivariable linear regression. K-means clustering identified microvascular phenotypes. In a subset (n=20), associations with glomerulosclerosis (GS) and interstitial fibrosis/tubular atrophy (IFTA) were examined. Results: The mean (SD) age was 64 (14) years, 46% were female. The mean eGFR was 42 (21) mL/min/1.73m2 and median uPCR was 0.21 (interquartile range (IQR) 0.11 to 1.20) mg/mg. Higher baseline PU ({beta} = -12; 95% CI, -24 to -1) and reduced percentage change in PU ({beta} = 7; 95% CI, 2 to 13) were associated with lower eGFR, independent of covariates. Neither measure was associated with uPCR. Clustering identified four phenotypes with graded differences in perfusion and reserve. In biopsy participants, higher baseline PU and lower percent change were associated with greater GS and IFTA severity. Conclusion: CKD is characterized by elevated resting perfusion and impaired microvascular reserve, which are associated with lower eGFR and histopathologic injury.

Although several ancillary tests are available in limited laboratories, diagnosis of microphthalmia (MiT)/TFE family translocation renal cell carcinoma (tRCC) could be challenging due to diverse and overlapping tumor morphology and the lack of reliable biomarkers. GPNMB has been recently identified as a diagnostic marker for various renal neoplasms with FLCN/TSC/mTOR-TFE alterations. However, the sensitivity and specificity of GPNMB immunostain are suboptimal and the result interpretation in ambiguous cases could be difficult. To search additional biomarkers that could improve the screening sensitivity and predict genetic aberrations in FLCN/TSC/mTOR-TFE pathway in renal tumors, we performed bioinformatic analysis of publicly available cancer databases and found GPR143, a transmembrane protein regulated by MiT transcription factors, was highly expressed in a subset of renal cell carcinomas (RCCs). In two the Cancer Genome Atlas (TCGA) kidney cancer cohorts, RCCs with high levels of GPR143 expression were enriched for renal neoplasms with FLCN/TSC/mTOR-TFE alterations. Similar to GPNMB labeling, GPR143 immunostain was positive in the majority of tRCC cases and renal tumors with FLCN/TSC/mTOR alterations, suggesting that GPR143 could function as another surrogate marker for FLCN/TSC/mTOR-TFE alterations in certain renal tumors. Interestingly, despite the concordant GPR143 and GPNMB immunoreactivity in most renal neoplasms with FLCN/TSC/mTOR-TFE alterations, diffuse GPR143 immunostain was observed in some cases with negative or focal GPNMB labeling. Taken together, our results indicate GPR143 could serve as a useful adjunct marker to improve the sensitivity for screening renal tumors with FLCN/TSC/mTOR-TFE alterations.

Background: Renal impairment is associated with increased risk of Parkinson's disease (PD) in general populations; however, the renal-PD link within cardiovascular disease (CVD) patients remains unclear through the high comorbidity of renal dysfunction and elevated PD risk among this special population. Objectives: To assess renal function's association, longitudinal trajectories and predictive value for PD specifically within a cardiovascular disease cohort. Methods: Among 29,266 UK Biobank CVD patients, we assessed baseline renal function via creatinine-based (eGFRcr) and cystatin C-based (eGFRcys) estimated glomerular filtration. Multivariable Cox regression analyzed associations with incident PD and all-cause mortality, with wide sensitivity analyses addressing reverse causation/confounding. Nested case-control analysis characterized pre-PD eGFR trajectories over 14 years. We finally evaluated whether renal function improved the PREDICT-PD's predictive ability. Results: Over a median 13.1-year follow-up, 489 incident PD cases and 5,919 deaths occurred. Lower eGFR levels exhibited dose-dependent associations with increased PD risk (eGFRcr: HR=0.87 [0.80~0.95]; eGFRcys: HR=0.90 [0.82~0.99]) and all-cause mortality (eGFRcr: HR=0.77 [0.75~0.79]; eGFRcys: HR=0.64 [0.63~0.66]). Pre-PD eGFR trajectories diverged significantly from controls starting over 14 years before diagnosis. eGFR-defined chronic kidney disease (<60 ml/min/1.73m2) conferred 38~60% higher PD risk and 159~234% elevated mortality risk, and could significantly enhance PREDICT-PD's discrimination, with a 1.18~1.34% increase in prediction accuracy. Conclusions: Impaired renal function is an independent PD and all-cause mortality risk factor of CVD patients, preceded by a slow, progressive eGFR decline starting >14 years before diagnosis. Incorporating renal function substantially improves PD risk prediction in this population.

BackgroundDysregulation of phosphate homeostasis contributes to reduced longevity and vascular complications in chronic kidney disease and aging. This study investigates the role of TMEM174, a proximal tubule-specific protein, in regulating the phosphate co-transporter NPT2A and its subsequent impact on lifespan and vascular health. MethodsTMEM174 knockout (KO) mice (C57BL6/J and DBA/2J) were fed diets with varying phosphate concentrations (0.6% vs. 1.2%). In OKP cells, TIRF and FRET microscopy, alongside immunoprecipitation, were used to identify the TMEM174 protein regions essential for NPT2A binding and endocytosis. ResultsTMEM174 KO mice exhibited significantly shorter lifespans than wild-type controls. High phosphate diets exacerbated vascular calcification, stiffness, and mortality, while low phosphate diets rescued these phenotypes. In vitro, TMEM174 siRNA blocked PTH-induced NPT2A endocytosis, increasing its apical membrane retention. FRET and biochemical assays revealed that the C-terminal region of TMEM174 is essential for its association with NPT2A. While intact TMEM174 and N-terminal mutants (TMEM174{Delta}N) facilitated NPT2A degradation, C-terminal deletions (TMEM174{Delta}C) failed to associate with or degrade NPT2A. ConclusionsTMEM174 is a critical regulator of phosphate homeostasis and longevity. The C-terminal region of TMEM174 is specifically required for NPT2A endocytosis and degradation, identifying it as a potential therapeutic target for managing phosphate-related vascular complications.

Chronic benign proteinuria (PROCHOB), caused by biallelic pathogenic variants in CUBN, presents in childhood as isolated, asymptomatic tubular proteinuria with preserved long-term kidney function. Because its clinical presentation closely mimics early stage glomerular diseases with moderate proteinuria and without increased urinary {beta}2-microglobulin (uBMG) and 1-microglobulin, numerous patients undergo unnecessary kidney biopsies and receive angiotensin-converting enzyme inhibitors or angiotensin II receptor blockers before genetic testing is considered. Using high-throughput aptamer-based urinary proteomics (SomaScan(R)), we identified urinary myoglobin as a disease-specific biomarker for PROCHOB. We developed and confirmed a diagnostic approach in which the urinary myoglobin-to-creatinine (uMB/Cr) ratio robustly distinguishes PROCHOB from other moderate glomerular proteinuric kidney diseases. Although certain cases of Dent disease causing megalin dysfunction exhibit increased urinary myoglobin levels, PROCHOB and Dent disease can be clearly distinguished based on the uBMG-to creatinine ratio. This biomarker reflects impaired proximal tubular protein reabsorption because of cubilin dysfunction and remains normal in healthy individuals or those with typical glomerular diseases with moderate proteinuria. Our findings establish a noninvasive diagnostic tool for PROCHOB that prompts targeted genetic testing for CUBN variants using the uMB/Cr and urinary uBMG-to-creatinine ratios. This strategy has the potential to transform the clinical diagnostic pathway for isolated proteinuria.

BackgroundPersistent neurohormonal activation is a key driver of maladaptive remodeling and disease progression in heart failure (HF). Sodium-glucose cotransporter 2 inhibitors (SGLT2is) confer robust renoprotective effects in HF; however, the extent to which these benefits involve modulation of renal neurohormonal activity remains unclear. We hypothesized that SGLT2i-mediated renoprotection in HF is associated with attenuation of excessive renal neurohormonal activation. MethodsMale rats with myocardial infarction-induced HF and sham controls were fed standard chow or chow containing empagliflozin (EMPA, 300 mg/kg) for four weeks, followed by assessment of renal inflammatory and neurohormonal markers. Parallel in vitro studies in THP-1 macrophages and HK-2 proximal tubule cells evaluated the direct effects of EMPA on norepinephrine (NE)-dependent tubular inflammatory signaling. ResultsHF rats displayed higher renal cortical renin gene expression and angiotensin II concentrations, which remained unaffected by EMPA. Conversely, EMPA normalized the elevated urinary NE excretion and renal cortical NE content observed in HF rats. Given the inflammatory role of sympathetic hyperactivity, we assessed renal macrophage polarization. EMPA-treated HF rats showed reduced expression of pro-inflammatory markers (Tnf, Ccr2, Nos2, Il-6) and increased expression of markers associated with a reparative macrophage profile (Arg1, Mrc1, CD163), supported by higher CD206 macrophages in kidney sections. While EMPA did not directly alter THP-1 macrophage activation in vitro, it significantly reduced NE-induced SGLT2 expression and interleukin-6 (IL-6) release by HK-2 human proximal tubule epithelial cells. ConclusionThese findings support a model in which SGLT2 inhibitors confer renoprotection in HF by suppressing renal sympathetic hyperactivity, independently of the intrarenal renin-angiotensin system, thereby disrupting a maladaptive renal neuro-epithelial-immune axis and promoting a reparative macrophage phenotype. CLINICAL PERSPECTIVE Whats new?O_LIThis study identifies a renal neuro-epithelial-immune axis underlying empagliflozin-mediated renoprotection in heart failure. C_LIO_LIEmpagliflozin reduces renal cortical and urinary norepinephrine levels in heart failure without altering intrarenal renin-angiotensin system activity, revealing a distinct neurohumoral target of SGLT2 inhibition. C_LIO_LIThis sympatholytic effect is associated with a shift in renal macrophages toward a reparative (M2) phenotype, without changes in total macrophage abundance. C_LIO_LIEmpagliflozin blocks norepinephrine-induced SGLT2 upregulation, limiting proximal tubular glucose reabsorption and IL-6 production, and linking sympathetic signaling to renal inflammation. C_LI What are the clinical implications?O_LIOur findings provide a mechanistic basis for the additive cardiorenal benefits of SGLT2 inhibitors in heart failure, beyond conventional RAS-directed therapies. C_LIO_LITargeting renal sympathetic-driven inflammation may help preserve kidney function and attenuate the progression of cardiorenal syndrome. C_LIO_LISuppression of a renal neuroinflammatory pathway may help explain the early and sustained benefits of SGLT2 inhibitors across heart failure phenotypes, including nondiabetic patients. C_LI

Background: Patients with kidney failure undergoing maintenance hemodialysis suffer high rates of major adverse cardiovascular events(MACE) that are not accurately predicted by traditional cardiovascular risk models. There is an urgent need to identify novel, modifiable cardiovascular risk factors for these patients. Methods: We analyzed associations of 6287 circulating proteins with MACE among 1048 participants undergoing hemodialysis in the Chronic Renal Insufficiency Cohort(CRIC) (14-year follow-up) with validation in the Predictors of Arrhythmic and Cardiovascular Risk in End-Stage Renal Disease study(PACE) (7-year follow-up). In both cohorts, proteins were measured shortly after dialysis initiation and one year later. We compared protein-based risk models derived by elastic net regression to the Pooled Cohort Equations(PCE) optimized for these cohorts(Refit PCE), and to an Expanded Refit PCE that included Troponin T and N-terminal pro-B-type natriuretic peptide. Results: In CRIC, 149 proteins were associated with MACE at false discovery rate<0.05. Among 22 proteins significant at Bonferroni p<8x10-6, proteins that validated in PACE included Sushi von Willebrand factor type A EGF and pentraxin domain-containing protein 1(SVEP1), Complement component C7, R-spondin 4, Tenascin, Fibulin-3 and Fibulin-5. Complement pathways were prominent in network analyses. SVEP1 surpassed other markers by statistical significance, with CRIC HR per log2 1.8 (p=2.1x10-12) and HR per annual doubling 1.6 (p=6.8x10-6). For 2-year MACE, AUC(95%CI) for SVEP1 alone was 0.72(0.59, 0.84) in CRIC, and 0.73(0.63, 0.81) in PACE. SVEP1 surpassed the Expanded Refit PCE in CRIC (0.61 (0.48, 0.73)) (p=0.038). In the pooled CRIC + PACE cohort, SVEP1 AUC(95%CI) (0.79(0.70, 0.88)) surpassed Refit PCE (0.61(0.51, 0.72)) (p=0.004). Conclusions: SVEP1, a 390 kDa protein unlikely to be renally cleared, surpassed over 6000 other proteins and by itself outperformed traditional clinical risk models in predicting MACE in two populations of patients undergoing maintenance hemodialysis. Future studies should provide mechanistic insights behind these findings.

Acute kidney injury (AKI) is a serious and common clinical syndrome that currently has no effective treatment. Emerging evidence links coagulation pathways to kidney injury, particularly through coagulation proteases. Protease-activated receptors (PARs) are a family of G-protein coupled receptors (GPCRs) that are activated by proteolytic cleavage of their N termini, exposing a tethered ligand that initiates receptor signaling. PARs have been shown to play a major role in inflammation, vascular regulation, and tissue injury. PARs play key roles in inflammation, vascular regulation, and tissue injury. Previous work from the Hamm laboratory demonstrated that PAR4 contributes to AKI progression, as PAR4 knockout mice were protected in both unilateral ureteral obstruction and ischemia-reperfusion-based models of kidney disease. In this study, we investigated the potential of a PAR4 antagonist, VU6073819, at mitigating AKI progression in an ischemia-reperfusion injury (IRI) mouse model. PAR4 antagonism not only alleviated kidney injury and inflammatory response, but it significantly improved the survival. These findings identify PAR4 as a promising therapeutic target for AKI.

Middle Eastern and North African populations remain underrepresented in genomic databases, comprising less than 1% of genome-wide association study participants despite representing approximately 6% of the global population. Here we present the Egypt Genome Project (EGP1K), in which we performed whole-genome sequencing on 1,024 unrelated Egyptian individuals originating from 21 of Egypts 27 governorates, recruited through eight clinical and research centers across Upper and Lower Egypt. We identified over 51.3 million variants, of which 17.1 million (33.4%) were absent from dbSNP. Allele frequency comparisons across 6.5 million shared variants showed the strongest concordance with Middle Eastern populations ({tau} = 0.977). Principal component analysis and ADMIXTURE modeling at K = 7 revealed that Egyptians share a dominant ancestry component (71.8%) with Middle Eastern populations and carry a smaller Egyptian-enriched component (18.5%) that distinguishes them from neighboring groups. Runs of homozygosity varied substantially across subregions, with Upper Egypt showing the highest burden, paralleling elevated consanguinity rates. Carrier frequency analysis identified MEFV (Familial Mediterranean Fever) at 9.1% as the most prevalent pathogenic carrier state; when adjusted for the national consanguinity rate, MEFV carrier status alone projects approximately 6,600 affected births per year. HLA class I typing identified allele frequencies placing Egyptians within the Levantine-Eastern Mediterranean cluster, providing baseline immunogenetic data currently absent from international databases. Analysis of polygenic risk score distributions revealed substantial differences in threshold-based risk stratification between Egyptians and European reference populations. When the Europeanderived 90th percentile threshold was applied, 83.3% of Egyptians were assigned to high-risk strata for stroke, 76.4% for chronic kidney disease, and 72.8% for gout, compared to the intended 10% high-risk proportion. These distributional shifts were observed across several cardiometabolic traits (Cohens d = 1.55-1.61), while other traits showed closer cross-population concordance, indicating that the degree of threshold miscalibration varies by trait. Together, these findings establish EGP1K as a genomic reference for Egypt and indicate that European-derived risk stratification thresholds may not be directly transferable to the Egyptian population, supporting the need for population-specific calibration of polygenic risk scores.

Background: Chronic kidney disease (CKD) affects approximately 850 million individuals worldwide and remains a leading cause of morbidity, premature mortality, and escalating healthcare costs. Despite the availability of clinical biomarkers, CKD progression to end stage renal disease (ESRD) is frequently identified late, limiting opportunities for preventive intervention. Conventional predictive models have relied predominantly on static cross sectional laboratory values, failing to capture the temporal dynamics of disease trajectory that longitudinal claims data can provide. Objective: This study proposes a novel hybrid machine learning framework: XGBoost LSTM Attention (XLA), that integrates gradient boosted feature selection with long short-term memory (LSTM) networks and a temporal attention mechanism to improve early prediction of CKD progression from Stage 3 to Stages 4/5 or ESRD using longitudinal claims based features. Methods: We conducted two complementary analyses. Primary analysis: a cross sectional validation using real NHANES 2015 to 2018 data (n=701 CKD Stage 3 adults) predicting significant proteinuria (UACR greater than or equal to 30 mg/g) from clinical features excluding UACR. Supplementary analysis: an NHANES-calibrated longitudinal cohort (n=8,412) with simulated quarterly measurements demonstrated XLA performance under real world longitudinal data conditions. All models were evaluated using 5-fold stratified cross-validation. Results: In the primary NHANES cross sectional analysis, the XLA framework achieved AUC ROC of 0.684 (95% CI: 0.641 to 0.727), with all models performing comparably (AUC 0.684 to 0.710), confirming that cross sectional clinical features alone provide limited signal for proteinuria prediction and underscoring the necessity of UACR measurement. In the longitudinal supplementary analysis, XLA achieved AUC ROC of 0.994 versus 0.939 for the best cross-sectional baseline (+5.5%), demonstrating that temporal trajectory features particularly eGFR slope and RAAS adherence trends: confer substantial incremental predictive value when longitudinal data are available. Conclusion: The XLA framework demonstrates meaningful advantages over traditional approaches when applied to longitudinal claims data. Cross sectional findings highlight the irreplaceable role of direct UACR measurement in CKD risk stratification. Together, these results provide actionable evidence for both the limitations of static prediction and the promise of trajectory based approaches in value based care programs managing large CKD populations. Keywords: chronic kidney disease, CKD progression, machine learning, XGBoost, LSTM, temporal attention, claims data, NHANES, proteinuria, healthcare informatics, value based care.

Background: Kidney transplantation is the preferred treatment strategy for end-stage kidney disease. Deceased donor kidneys usually undergo cold storage until kidney transplantation, leading to cold ischemia injury that may contribute to poor graft outcomes. However, the molecular characterization of potential mechanisms of cold ischemia injury remains incomplete. Results: To bridge this knowledge gap, we leveraged the 10x Visium spatial transcriptomic technology to perform full transcriptome profiling of murine kidneys subject to varying durations of cold ischemia typical in a deceased donor kidney transplant setting. We developed a computational workflow to identify and compare spatiotemporal transcriptomic changes that accompany the injury pathophysiology in a tissue compartment-specific manner. We identified proportional enrichment of oxidative phosphorylation (OXPHOS) genes with increasing duration of cold ischemia injury within the oxygen-lean inner medulla region, suggestive of atypical metabolic presentation. This was distinct in cold ischemia injury tissue compared to warm ischemia-reperfusion kidney injury tissue. Spatiotemporal trends were validated by qPCR and immunofluorescence in a larger cohort of mice. We provide an interactive online browser at https://jef.works/CellCarto-ColdIschemia/ to facilitate exploration of our results by the broader scientific and clinical community. Conclusions: Altogether, our spatiotemporal transcriptomic analysis identified coordinated molecular changes within metabolic pathways such as OXPHOS deep within the cold ischemic kidney, highlighting the need for increased attention to the inner medulla and potential opportunities for new insights beyond those available from superficial biopsy-focused tissue examinations.

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract that encompasses ulcerative colitis and Crohns disease. Here we identify the cystine/glutamate antiporter xCT as being markedly upregulated in the inflamed intestinal epithelium of patients with IBD. To clarify its functional contribution to disease pathogenesis, we performed genetic loss-of-function study and found that inhibition of xCT confers robust protection against dextran sulfate sodium (DSS)-induced colitis in mice. Intestinal epithelial cell (IEC)-specific deletion of xCT markedly attenuated colitis severity, demonstrating that epithelial xCT upregulation acts as a disease-exacerbating factor in IBD. Mechanistically, xCT deficiency preserved intracellular glutamate levels and protein polyglutamylation, thereby maintaining epithelial barrier integrity and protecting IECs from inflammatory injury. Consistently, pharmacological inhibition of glutamine synthetase, which increases intracellular glutamate, exerted a potent anti-inflammatory effect on the DSS-induced colitis. These findings identify intracellular glutamate retention in IECs as a previously unrecognized mechanism of epithelial protection and highlight both inhibition of xCT-dependent glutamate efflux and suppression of glutamine synthetase as potential therapeutic strategies for IBD.

BackgroundWithin the kidney, (pro) renin receptor (PRR) is abundantly expressed in the collecting duct (CD) and modulate physiological and pathophysiological processes. We have recently reported that activation of CD PRR mediates obstructive renal fibrosis in a mouse model of unilateral ureteral obstruction (UUO). The current study addresses the underlying mechanisms by examining the profibrotic pathway mediated by soluble PRR (sPRR)-dependent alternative macrophage activation. MethodsWe performed UUO or sham surgery on mice with CD-specific deletion of PRR (CD PRR KO) and floxed controls. After 7 days, we assessed fibrosis-related parameters, inflammatory cytokines, M1/M2 macrophage markers, other gene expression markers of kidney injury, and the concentration of plasma sPRR. We also administered vehicle or site-1 protease (S1P) inhibitor PF-429242 (PF) to C57BL/6 mice with UUO to determine the role of sPRR. Experiments were performed in vitro to examine the mechanism of sPRR-His-mediated macrophage M2 polarization and activation of potential target genes in bone-marrow-derived macrophages (BMDMs). ResultsCompared with the floxed control, CD PRR KO decreased macrophage accumulation, M2 polarization, and Yap/Taz expression while improving renal fibrosis and suppressing plasma sPRR levels following UUO. In BMDMs, sPRR-His treatment promoted macrophage M2 polarization, fibrosis, and Yap/Taz expression, which was dependent on angiotensin type 1 receptor (AT1R). ConclusionCD PRR-derived sPRR acts via ATR to promote macrophage M2 polarization and stimulates the AT1R/Yap/Taz axis, which leads to renal fibrosis during UUO.

Background: We aimed to identify data-driven FEV1 trajectory phenotypes post-chronic lung allograft dysfunction (CLAD), relate these phenotypes to patient factors and future graft loss, and develop a classification approach for prospective patients. Methods: We studied adult first lung recipients with probable CLAD from two prospective multicenter cohorts: CTOT-20 (n=206) and LTOG (n=1418). FEV1 trajectories over the first nine months post-CLAD were characterized using joint latent class mixed models, jointly modelling time-to-graft loss to account for informative censoring. Models were fit independently in both cohorts and also only among LTOG bilateral recipients. A classification and regression tree (CART) model was derived in LTOG bilateral recipients and applied to CTOT-20 bilateral recipients. Findings: Four distinct early FEV1 trajectory classes were identified in CTOT-20, with large differences in nine month graft loss (72.3%, 31.1%, 2.2%, 0%). In LTOG, similar trajectory patterns were reproduced, with an additional class demonstrating early post-CLAD FEV1 improvement. Among bilateral recipients, trajectory classes showed a clear risk gradient, including a high-risk class with 100% graft loss and a low-risk class with no early graft loss. A CART model incorporating clinical and spirometric variables demonstrated good discrimination in LTOG bilateral recipients (multiclass AUC 0.85) and consistent class assignment and trajectory patterns when applied to CTOT-20. Interpretation: We identified reproducible, clinically meaningful early post-CLAD FEV1 trajectory phenotypes with differential graft loss risk. These phenotypes and a pragmatic classification tool may support risk stratification, trial enrichment, and improved prognostication for patients and clinicians.

BackgroundKidney cell lines are widely used to model kidney physiology and disease; however, their gene expression profiles may differ from primary cells due to immortalization, culture conditions, or experimental treatments. Determining whether a cell line resembles its native cell type is critical for interpreting in vitro findings. We developed a transcriptome-based approach that matches bulk RNA-seq data from kidney cell lines, primary cells, or tissues to reference cell types derived from single-cell RNA-seq (scRNA-seq) datasets. MethodsReference transcriptomic profiles were generated from two human and two murine kidney scRNA-seq datasets by pseudobulk aggregation. Bulk RNA-seq data from microdissected kidney tissue, non-kidney negative controls, and kidney cell lines were matched to these references using three statistical similarity measures (Spearman correlation, Euclidean distance, Poisson distance) and three machine learning classifiers (Random Forest, XGBoost, TabPFN). Each was assessed with global gene expression, curated kidney marker gene lists, and the most variable genes. Matching accuracy was evaluated through a three-step validation strategy: within-dataset matching, cross-reference comparison, and validation against primary kidney tissue and negative controls. ResultsGene expression rank-based Spearman correlation and TabPFN, a foundation model for tabular data, emerged as the most accurate and specific approaches, particularly with curated kidney marker gene lists. Both methods correctly identified microdissected kidney tubule segments and were robust against non-kidney negative controls. Applied to commonly used kidney cell lines, OK cells retained proximal tubule identity, particularly under shear stress, while other proximal tubule lines (HK-2, HKC-8, HKC-11) showed inconsistent matching. Collecting duct-derived mIMCD-3 maintained stable similarity across passages, culture conditions, and genetic modifications. ConclusionWe provide two complementary implementations: CellMatchR, an accessible web-based tool using Spearman correlation for routine use, and comprehensive scripts for TabPFN-based matching (link will be added after peer reviewed publication). Together, these resources enable researchers to make informed decisions about kidney cell culture model selection, interpretation, and stability. Translational StatementKidney cell lines are fundamental tools in nephrology research, yet their transcriptomic similarity to native cell types is rarely validated systematically. We demonstrate that combining bulk RNA-seq data with single-cell reference datasets enables robust assessment of cell line identity using gene expression-rank-based correlation and machine learning approaches. By providing a comprehensive evaluation of matching methods, curated kidney marker gene lists, and reference datasets, our study serves as both a practical resource and a methodological framework for the kidney research community, facilitating informed selection of cell culture models, quality control of experimental conditions, developing new experimental cell culture models, and more reliable translation of in vitro findings to kidney physiology and disease.

Interpreting the pathogenic significance of missense variants in human disease gene candidates remains a major challenge in precision medicine. Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic cause of kidney failure and caused by mutations in the PKD1 or PKD2 genes that encode polycystin-1 and polycystin-2. Here, we establish C. elegans as a platform for the functional classification of PC2 variants by characterizing PKD-2C180S, the C. elegans ortholog of the likely pathogenic human variant PC2C331S. Using CRISPR/Cas9 endogenous genome editing combined with dual-color fluorescent reporters and super-resolution imaging, we show that PKD-2C180S severely reduces protein stability, abolishes ciliary and extracellular vesicle (EV) localization, and eliminates sensory function comparable to a pkd-2 null allele. In heterozygous animals, PKD-2C180S is recessive and exerts no dominant-negative effect on wild-type PKD-2 trafficking, protein levels, or function, establishing that PKD-2 is haplosufficient in this model. PKD-2C180S also abolishes ciliary and EV localization of the PC1 homolog LOV-1 and reduces LOV-1 cell body levels comparable to pkd-2 null animals, consistent with PC2 functioning as a molecular chaperone for PC1 stability and trafficking. Genetic epistasis experiments show that PKD-2C180S protein levels are unaffected in lov-1 mutants, indicating that the PKD-2C180S mutation acts prior to complex assembly. Quantitative analysis reveals that LOV-1*PKD-2 complexes are more stable at the ciliary membrane and more efficiently packaged into EVs than PKD-2 lacking LOV-1. Together, this work demonstrates that PC2C331S may act recessively via loss of polycystin complex function and establishes a C. elegans pipeline for the mechanistic classification of ADPKD-associated variants.

BackgroundAutosomal dominant polycystic kidney disease (ADPKD) is a common inherited disorder marked by numerous renal cysts that impair kidney function, with about half of affected individuals progressing to kidney failure by midlife. Patients exhibit reduced circulating apelin, a ligand of the apelin receptor, known to regulate cardiovascular function including hypertension. We tested whether diminished apelin signaling contributes to cystogenesis and if exogenous apelin receptor activation can improve disease outcomes. MethodsPlasma samples from age- and sex-matched healthy controls and ADPKD participants were analyzed for circulating apelin peptides. To assess direct cystic effects, primary ADPKD renal epithelial cells were grown as 3D collagen-embedded cysts and treated with apelin agonists. Male and female Pkd1RC/RC; Pkd2+/- (PKD) mice were treated for 27 days with apelin agonists, vehicle, or the standard of care drug, Mozavaptan. Kidney and heart weight ratios, BUN, renal cAMP, and kidney transcriptional profiles were evaluated. ResultsCirculating apelin peptides were significantly reduced in ADPKD patients despite normal kidney function (eGFR, BUN, and creatinine). In vitro, both apelin and the small molecule apelin receptor agonist Azelaprag inhibited cyst growth. Apelin and Mozavaptan reduced kidney weight, cystic index, blood urea nitrogen and renal cAMP in PKD mice, whereas Azelaprag did not. Apelin downregulated expression of genes associated with cyst progression, including Lcn2 (Ngal), Postn, and Havcr1 (Kim-1). Mozavaptan, but not apelin, induced diuresis and reduced urinary concentration. ConclusionApelin receptor activation by exogenous apelin inhibited cAMP synthesis and cyst growth and improved kidney function in an orthologous mouse model of ADPKD. We propose that the apelin receptor may be a potential therapeutic target in ADPKD.