Kidney International Reports

BackgroundHeterozygous ALG8 variants have previously been associated with polycystic liver disease (PLD) with or without kidney cysts. A clear-cut relationship between application of PKD diagnostic criteria and kidney manifestations of ALG8 variants remains to be described. We therefore sought to determine whether ALG8 protein-truncating variant (PTV) heterozygotes are at increased risk of polycystic kidney disease (PKD). MethodsWe identified participants heterozygous for pathogenic (P) and likely pathogenic (LP) ALG8 (NM_024079.5) PTVs described in ClinVar from the Geisinger-Regeneron DiscovEHR MyCode study, an unselected health system-based cohort linked to electronic health records. ALG8 PTV heterozygotes were matched 1:1 to non-heterozygote family members by age at time of imaging (within 10 years) and sex. Phenotypes were assessed by International Classification of Disease (ICD) codes, chart review, and imaging, which was reviewed by a blinded radiologist. Imaging diagnosis of PKD was defined as [≥]4 kidney cysts on an abdominal ultrasound or computed tomography. Secondary outcomes included bilateral renal cysts, and [≥]1 liver cyst. ResultsOut of 174,418 participants in MyCode,103 participants (mean age 56.7 years) were heterozygous for an ALG8 P/LP variant: p.Arg364Ter (n=86), p.Arg41Ter (n=7), p.Arg179Ter (n=9), and c.368+2T>G (n=2). None of the ALG8 P/LP variant heterozygotes had an ICD diagnosis of PKD or PLD. Out of 51 participants [≥]40 years of age with available imaging, 51% had [≥]4 renal cysts and 14% had [≥]1 liver cyst. After matching 23 ALG8 P/LP variant heterozygotes with 23 related non-heterozygotes by age and imaging modality, ALG8 P/LP heterozygotes had higher prevalence of 4+ kidney cysts (48% versus 9% in non-heterozygotes; p=0.007) and bilateral kidney cysts (61% vs. 17%; p=0.006). ConclusionsOur study demonstrates that patients heterozygous for ALG8 P/LP variants are at increased risk of PKD on imaging but not by ICD diagnosis codes. Additional studies are needed to determine whether ALG8 P/LP heterozygotes are at increased risk of kidney failure.

BackgroundChronic kidney disease (CKD) affects over 10% of the global population. A genetic diagnosis can be identified in about 30% of pediatric and 10-30% of adults, informing treatment, prognosis, and family-based risk assessment. However, access to renal genetics services remains limited across many healthcare systems. ObjectivesTo characterize the clinical and genetic landscape of CKD in patients referred for genetic evaluation within a Canadian single-centre nephrology-genetics program, and to evaluate the diagnostic yield and clinical utility of an integrated renal genetics clinic. MethodsWe conducted a retrospective study of 206 probands referred for suspected hereditary kidney disease to the McGill University Health Centre Renal Genetics Clinic between 2019 and 2024. Genetic testing was performed in accredited laboratories, predominantly through comprehensive multi-gene panels or phenotype-directed exome sequencing. All reported variants were classified according to the ACMG/AMP criteria, and variants of uncertain significance were reevaluated post hoc using standardized quantitative and evidence-tier frameworks to determine whether they trended toward "likely pathogenic" ("hot") or "likely benign" ("cold"), without implying formal reclassification. ResultsA molecular diagnosis was established in 34.5% of probands (71/206), implicating pathogenic or likely pathogenic variants across 35 genes representing diverse monogenic kidney disease etiologies. The highest diagnostic yields were observed in cystic nephropathy (51.9%), tubulopathy (38.5%), and glomerulopathy (35.6%). Genetic results affected clinical management in 23.9% of diagnosed cases, leading to changes in treatment for 16.9%, modification of transplant management in 5.6%, informed living donor risk assessment in 14.1%, and facilitated cascade testing in 66.2% of families. CKD of unknown etiology comprised 28% of the cohort, with a genetic diagnosis reached in 25.9% of these cases. Variants of uncertain significance (VUS) were reported in 39.3% of probands, with higher overall variant burden and lower diagnostic yields among individuals of non-European ancestry. Post hoc internal reassessment stratified 67.7% of VUS as mid or lower confidence ("cold") and 32.2% as higher confidence ("hot") or likely pathogenic. ConclusionsIn a diverse urban population, integration of a dedicated renal genetics service within nephrology care achieved high diagnostic yield, substantially influenced management, and facilitated family risk assessment. Structured referral pathways and multidisciplinary variant interpretation optimize the clinical utility of genetic testing in CKD.

Chronic kidney disease (CKD) is a complex condition with diverse underlying causes that lead to a progressive decline in kidney function. Genome-wide association studies (GWASs) have identified numerous genetic loci associated with CKD, yet much of the genetic basis remains unexplained. Part of the reason is that most GWASs have only assessed kidney function via single biomarkers such as estimated glomerular filtration rate (eGFR). This study employs a novel multi-phenotype approach, combinatorial Principal Component Analysis (cPCA), to better understand the genetic architecture of CKD. Utilizing a discovery cohort of white British individuals from the UK Biobank (n=337,112), we analyzed 21 CKD-related phenotypes using cPCA to generate over 2 million composite phenotypes (CPs). More than 46,000 CPs demonstrated superior performance in classifying clinical CKD compared to any single biomarker, and those CPs were most frequently comprised of eGFR, cystatin C, HbA1c, microalbuminuria, albumin, and LDL. GWASs of the top 1,000 CPs revealed seven novel genetic loci, with CST3 and SH2B3 successfully replicated in an independent Irish cohort (n=11,106). Notably, the index SNP of the SH2B3 gene, which encodes a regulator in immune responses and cytokine signaling, is a loss-of-function variant with a combined beta of -0.046 and a p-value of 3.1E-56. These results highlight the effectiveness of a multi-phenotype approach in GWASs and implicate a novel functional variant in SH2B3 in CKD phenotypes. TRANSLATIONAL STATEMENTThe application of combinatorial Principal Component Analysis (cPCA) in our study has identified SH2B3 as a novel genetic locus associated with chronic kidney disease (CKD). This discovery advances our understanding of CKDs genetic architecture beyond single biomarker analyses, potentially leading to more precise diagnostic tools and personalized treatment strategies. Future research should focus on validating these findings in diverse populations and integrating cPCA-derived biomarkers into clinical practice to enhance CKD prediction and management, ultimately improving patient outcomes.

BackgroundProgression into more severe stages of chronic kidney disease (CKD) based on estimated glomerular filtration rate (eGFR) and albuminuria are associated with increased risk of end-stage renal failure, cardiovascular diseases, and mortality. Vesicles in the urine are cell-derived particles containing constituents of the cells of origin. Little is known about the prognostic capacity of urinary vesicles for CKD progression. PurposeTo evaluate the association between components of urinary vesicles and incident CKD. MethodsIn the AugUR study, a prospective population-based cohort study in individuals aged 70-95 years at baseline, we isolated and characterized urinary vesicles from 580 participants at two timepoints. In cross-sectional data, influences of age, sex and established kidney biomarkers on vesicular albumin and podocalyxin were characterised. Longitudinal data were used to test associations of vesicular albumin and podocalyxin with incident eGFR-based CKD and albuminuria. ResultsCross-sectionally, urinary vesicle albumin and urinary vesicle-bound podocalyxin were moderately correlated with each other and with urinary albumin and alpha1-microglobulin, but not with eGFR. Vesicular albumin concentrations were influenced by sex, whereas age showed an effect on podocalyxin. After adjusting for age and sex, higher vesicular albumin was associated with higher urinary albumin and lower eGFR. Higher vesicular podocalyxin concentrations were associated with higher urinary albumin but not with eGFR. Both markers showed identical associations with urinary alpha1-microglobulin. In longitudinal analyses, baseline vesicular albumin showed association with incident CKD based on eGFR. This association was no longer present after adjustment for baseline eGFR. In contrast, higher baseline podocalyxin concentrations were predictive for decreased risk of incident albuminuria after adjustment for baseline free urinary albumin. Baseline-adjusted change in urinary vesicle albumin and urinary vesicle-bound podocalyxin were both associated with incident albuminuria, independent of free urinary albumin and other kidney biomarkers. Here, increase in follow-up versus baseline values were associated with higher risk for incident albuminuria, with higher effect sizes for vesicular albumin. ConclusionThis study indicates that higher vesicular podocalyxin at baseline might be a potential predictor for lower risk for albuminuria over three years in an old-aged cohort. In contrast, longitudinal increase in urinary vesicle biomarkers, especially vesicular albumin, might be diagnostic markers for incident albuminuria in the elderly. KEY MessagesWhat is known O_LIAccording to a previous study in animals, accumulation of albumin in the subpodocyte space leads to subsequent endocytosis by the podocytes. C_LIO_LIPodocyte-produced vesicles contain potential biomarkers of the deterioration of kidney function in humans. C_LI What is new O_LIBiomarkers from urinary vesicles can be quantified from biobanked human samples. C_LIO_LIHigher vesicular podocalyxin at baseline might be a potential predictor for lower risk for albuminuria over three years in an old-aged cohort. C_LIO_LIChanges in urinary vesicle biomarkers over time, especially vesicular albumin, are associated with incident albuminuria independent of eGFR and free urinary albumin. C_LI

BackgroundRenal intratubular casts are frequently observed in the distal nephron segments of the kidney and have long been regarded as a sign of renal disease. However, the composition and pathological significance of intratubular casts have remained understudied. MethodsWe leveraged Hematoxylin and Eosin (H&E) staining to identify intratubular casts along with concurrent Co-detection by indexing (CODEX) multiplexed spatial protein imaging on human kidney biopsy sections from the Kidney Precision Medicine Project (KPMP). We also conducted immunoblotting of Prominin-1 (PROM1) in urine and assessed its levels from publicly available urinary proteomics datasets of the KPMP consortium. ResultsWe analyzed 424 intratubular casts across 33 individuals with kidney disease or healthy controls. We identified PROM1 and IGFBP7 as major constituents of casts (positive staining in 90.1% and 35.6%, respectively). Staining for UMOD, an established cast component, was present in 86.1%. These components exhibited distinct alterations depending on the disease state. Intratubular casts were predominantly detected in the distal nephron segments, and their presence was associated with a marked loss of NCC and AQP2 expression in the cast-containing tubular epithelium, suggesting underlying injury. The loss of these membrane transporters correlated with protein components within casts, and the presence of intra-cast PROM1 showed the strongest association, with an odds ratio of 30.8 (95% confidence interval: 13.4-71.0). Urinary PROM1 secretion was confirmed by immunoblotting and was increased in patients with acute kidney injury (AKI) compared to healthy controls (p = 0.01). ConclusionsWe identified PROM1, a dedifferentiation and injury marker expressed in epithelial cells, as a novel major constituent of intratubular casts. Our studies suggest that protein composition signature within casts varies with disease state and is associated with tubular injury in distal nephron segments. Our study also suggests that urinary PROM1 may serve as a biomarker for AKI. Key Points{checkmark} Utilized CODEX multiplex protein imaging to elucidate the intratubular cast components and the associated tubular alterations. {checkmark}Identified PROM1, a dedifferentiation marker, as a major constituent of intratubular casts. {checkmark}Protein components within casts were altered by disease state and were associated with the injury of the surrounding tubular epithelium.

BackgroundCongenital anomalies of the kidney and urinary tract (CAKUT) are the predominant cause for chronic kidney disease below 30 years of age. Many monogenic forms have been discovered mainly due to comprehensive genetic testing like exome sequencing (ES). However, disease-causing variants in known disease-associated genes still only explain a proportion of cases. Aim of this study was to unravel the underlying molecular mechanism of syndromic CAKUT in two multiplex families with presumed autosomal recessive inheritance. Methods and ResultsES in the index individuals revealed two different rare homozygous variants in FOXD2, a transcription factor not previously implicated in CAKUT in humans: a frameshift in family 1 and a missense variant in family 2 with family segregation patterns consistent with autosomal-recessive inheritance. CRISPR/Cas9-derived Foxd2 knock-out (KO) mice presented with bilateral dilated renal pelvis accompanied by renal papilla atrophy while extrarenal features included mandibular, ophthalmologic, and behavioral anomalies, recapitulating the phenotype of humans with FOXD2 dysfunction. To study the pathomechanism of FOXD2-dysfunction-mediated developmental renal defects, in a complementary approach, we generated CRISPR/Cas9-mediated KO of Foxd2 in ureteric-bud-induced mouse metanephric mesenchyme cells. Transcriptomic analyses revealed enrichment of numerous differentially expressed genes important in renal/urogenital development, including Pax2 and Wnt4 as well as gene expression changes indicating a cell identity shift towards a stromal cell identity. Histology of Foxd2 KO mouse kidneys confirmed increased fibrosis. Further, GWAS data (genome-wide association studies) suggests that FOXD2 could play a role for maintenance of podocyte integrity during adulthood. ConclusionsIn summary, our data implicate that FOXD2 dysfunction is a very rare cause of autosomal recessive syndromic CAKUT and suggest disturbances of the PAX2-WNT4 cell signaling axis contribute to this phenotype.

IntroductionCongenital anomalies of the kidneys and urinary tract (CAKUT) are the commonest cause of kidney failure in children and young adults. Over 50 monogenic causes have been identified, however less than 20% of patients have a genetic diagnosis identified using targeted or whole exome sequencing. We sought to characterise the genomic architecture of CAKUT using whole genome sequencing (WGS). MethodsUsing WGS from 1,052 unrelated individuals with CAKUT recruited to the UKs 100,000 Genomes Project, we determined diagnostic yield and looked for gene-based enrichment of rare variants exome-wide. We performed sequencing based genome-wide association studies (seqGWAS) and used these results to estimate the heritability explained by common variants. ResultsThe overall diagnostic yield was 4.9% with family history (P=0.02; OR 2.2; 95% CI 1.1-4.4), consanguinity (P=0.01; OR 3.0; 95%CI 1.2-6.9) and extra-renal features (P=1.1x10-4; OR 3.1; 95% CI 1.7-5.7) independently predicting a monogenic diagnosis. Diagnostic yield was highest in cystic kidney dysplasia (11.1%) and kidney agenesis/hypodysplasia (7.4%). Exome-wide rare variant and genome-wide common variant (minor allele frequency [MAF] [&ge;] 0.5%) association testing in a subset of 813 patients and 25,205 ancestry-matched controls identified significant association at 6q16.3 (rs117473527; P=4.83x10-8; OR 3.13; 95% CI 2.08-4.72; MAF 0.01) which requires replication. Common variants were estimated to explain up to 23% of the phenotypic variance observed in CAKUT in those with European ancestry suggesting that larger studies are needed to recover some of this missing heritability. A genomic risk score for posterior urethral valves was also validated in an independent European cohort of 77 cases and 2,746 controls (P<0.001). ConclusionsOnly a minority of patients in this large, unselected cohort received a monogenic diagnosis, with common variants estimated to account for a substantial proportion of phenotypic heritability. This suggests that non-Mendelian genomic factors may be important for the pathogenesis of CAKUT. Lay SummaryThis study shows that single-gene causes of isolated and non-familial CAKUT are rare, and that genomic testing should be targeted towards those with kidney cysts and/or small kidneys that have not formed properly in the womb. Individuals with a close relative with CAKUT and those with involvement of other organ systems were more likely to receive a genetic diagnosis. These data support a possible polygenic basis for CAKUT, where many common DNA changes cumulatively affect risk, particularly in posterior urethral valves, the most common cause of kidney failure in boys. Larger collaborative genomic studies are needed to increase our ability to identify these DNA changes and the mechanisms and pathways important for kidney and urinary tract development.

Diabetic kidney disease is a growing health burden that lacks specific early non-invasive diagnostic procedures. To approach a solution for this clinical need, we sequenced microRNAs of urinary extracellular vesicles and performed biomarker discovery by small RNA sequencing in a type 1 diabetes cohort including males with and without albuminuria. The results were replicated by sequencing or qPCR in two independent cohorts and four previously published datasets including type 1 and 2 diabetes as well as both sexes. Non-diabetic and prostate cancer cohorts were used as additional controls and miRNAs changed due to preanalytical urine collection variables were excluded. Using these data, we additionally validated previously identified reference candidate miRNAs. Correlations with clinical parameters, receiver operating characteristic analysis, targeted mRNAs and pathways including integrated single cell data, and targeted circulating proteins from type 1 and 2 diabetes cohorts were analyzed. We pinpointed 6 stable microRNAs, 11 differentially expressed microRNAs, 9 target proteins and 16 DKD-associated pathways in individuals with diabetic kidney disease. Replication showed that the differentially expressed miRNAs in DKD were partly shared between diabetes subtypes and sexes with overall strongest evidence for miR-192-5p, miR-146a-5p, miR-486-5p, and miR-574-5p. Combination of these miRNAs with clinical variables showed potential to classify individuals with the fastest kidney function decline (sensitivity 0.75-1.00 and specificity 0.83-1.00) even in the normoalbuminuria group, thus holding the potential as early diagnostic markers. Altogether, the candidate microRNAs show specificity for diabetic kidney disease, identify declining kidney function, and target key kidney cell types, mRNAs, proteins, and pathogenic mechanisms. Lay summaryDiabetic kidney disease (DKD) damages the kidneys severely. DKD progression differs between diabetes subtypes and sexes and currently the diagnosis comes too late when the kidney is already damaged. Thus, clinical care needs better and earlier diagnostic markers. Here we studied the microRNAs in urinary extracellular vesicles, small particles secreted actively by the kidney cells. We found 11 candidate microRNA markers for DKD. The discovery was made in males with type 1 diabetes, but some of the microRNAs were confirmed across type 1 and 2 diabetes, as well as female or combined sex populations. Altogether we studied over 250 samples. Analysis of miRNAs regulatory pathways and correlations with clinical measurements in individuals with DKD suggest that some miRNAs may hold the potential as early diagnostic markers. Our findings could thus impact clinical practice by providing early and specific DKD diagnostic tools allowing effective care at an early DKD stage.

BackgroundClassification of nephrotic syndrome relies on clinical presentation and descriptive patterns of injury on kidney biopsies. This approach does not reflect underlying disease biology, limiting the ability to predict progression or treatment response. MethodsSystems biology approaches were used to categorize patients with minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) based on kidney biopsy tissue transcriptomics across three cohorts and assessed association with clinical outcomes. Patient-level tissue pathway activation scores were generated using differential gene expression. Then, functional enrichment and non-invasive urine biomarker candidates were identified. Biomarkers were validated in kidney organoid models and single nucleus RNA-seq (snRNAseq) from kidney biopsies. ResultsTranscriptome-based categorization identified three subgroups of patients with shared molecular signatures across independent North American, European and African cohorts. One subgroup demonstrated worse longterm outcomes (HR 5.2, p = 0.001) which persisted after adjusting for diagnosis and clinical measures (HR 3.8, p = 0.035) at time of biopsy. This subgroups molecular profile was largely (48%) driven by tissue necrosis factor (TNF) activation and could be predicted based on levels of TNF pathway urinary biomarkers TIMP-1 and MCP-1 and clinical features (correlation 0.63, p <0.001 for predicted vs observed score). Kidney organoids confirmed TNF-dependent increase in transcript and protein levels of these markers in kidney cells, as did snRNAseq from NEPTUNE biopsy samples. ConclusionsMolecular profiling identified a patient subgroup within nephrotic syndrome with poor outcome and kidney TNF pathway activation. Clinical trials using non-invasive biomarkers of pathway activation to target therapies are currently being evaluated. Significance StatementMechanistic, targeted therapies are urgently needed for patients with nephrotic syndrome. The inability to target an individuals specific disease mechanism using currently used diagnostic parameters leads to potential treatment failure and toxicity risk. Patients with focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD) were grouped by kidney tissue transcriptional profiles and a subgroup associated with poor outcomes defined. The segregation of the poor outcome group was driven by tumor necrosis factor (TNF) pathway activation and could be identified by urine biomarkers, MCP1 and TIMP1. Based on these findings, clinical trials utilizing non-invasive biomarkers of pathway activation to target therapies, improve response rates and facilitate personalized treatment in nephrotic syndrome have been initiated.

IntroductionThere remains considerable debate as to the cause of the epidemic of Mesoamerican Nephropathy (MeN). We have previously reported early loss of estimated glomerular filtration rate (eGFR) as a surrogate for disease onset in a population-representative cohort study of young-adults at risk of disease from Northwest Nicaragua. Using a nested case-control approach we analysed urine and serum proteins surrounding this timepoint with the aim of gaining insight into the primary disease aetiology. MethodsWe conducted label-free ultra high-performance liquid chromatography mass-spectrometry based proteomics using urine samples collected at the study visit before, and at, first observed eGFR loss amongst cases and compared results to matched controls. We then performed direct protein measurements in a discovery cohort followed by quantification of serum total immunoglobulin E (stIgE) at multiple timepoints in a replication cohort. ResultsProteomic analysis demonstrated no differences in the levels of any single protein between cases and controls (n=25 each), at either timepoint, after correction for multiple comparisons. However, functional enrichment analysis demonstrated upregulation of adaptive immune pathways amongst cases. Direct measurements in the discovery cohort using high-sensitivity PCR-based immunoassay (n=21 controls, 19 cases) demonstrated higher stIgE in cases at the study visit immediately prior to first observed eGFR loss (mean difference 810kU/L, 95% confidence interval (CI): 162-1457kU/L). In the replication cohort (n=22 cases, 21 controls) an stIgE level >500kU/L measured by electrochemiluminescence in study samples from any timepoint in the 3 years prior to the first observed loss of eGFR was independently associated with case status when compared to samples from controls at matched visits (adjusted Odds Ratio: 8.1, 95% CI: 1.4-47.8). DiscussionA high level of stIgE precedes loss of eGFR in those at risk of MeN. Understanding what leads to this rise is likely to be key to understanding the cause of the MeN epidemic. Lay SummaryMesoamerican nephropathy describes an epidemic-level chronic kidney disease impacting rural working age adults in Central America. Although a number of exposures, including occupational heat exposure, have been proposed the cause of the epidemic, there remains much debate as to the primary aetiology of the disease. In this study we interrogated urine and blood samples from individuals from affected communities at risk of disease both before and after they develop kidney dysfunction. Using two different approaches, analysis of both urine and blood samples provide evidence of upregulation of immunoglobulin-E (IgE) related pathways in the 2-3 years before individuals develop evidence of kidney disease. Infections (particularly those involving parasites) and allergic reactions, but not heat exposure, have been reported to increase IgE levels. Going forwards, understanding the cause of this increase in IgE in individuals at risk of disease is likely to provide insight into the cause of Mesoamerican Nephropathy epidemics.

Sparsentan, a dual endothelin receptor A inhibitor and angiotensin blocker, reduced proteinuria in patients with focal segmental glomerulosclerosis (FSGS) in Phase II and Phase III studies. However, the estimated glomerular filtration rate (eGFR) endpoint was not achieved, partially attributed to disease heterogeneity among participants. Sparsentan reversed the molecular fingerprint in kidneys of an adriamycin-challenged rat model of chronic kidney disease, consistent with the phenotypic data. Transcriptomic profiles from this model were used to identify differentially expressed genes, 388 of which had reversed directionality, and networks responsive to sparsentan. These included disease networks relevant to FSGS, including suppression of cytokine signaling, immune and inflammatory pathways as well as inhibition of networks downstream of endothelin and angiotensin activation. Human orthologs of genes upregulated and reversed by sparsentan in the rat model were elevated in glomerular (p<0.001) and tubulointerstitial (p<0.0001) profiles of participants with FSGS in the Nephrotic Syndrome Study Network (NEPTUNE) compared to healthy living donors, pointing to a likely anti- inflammatory action of sparsentan on kidneys. The gene signature in both compartments was negatively correlated with eGFR (p<0.005) and positively correlated with UPCR (p<0.005) and the response profile was elevated in a molecular subgroup of patients with greater disease severity. Several urine proteins were associated with the sparsentan response score highlighting opportunities for the development of non-invasive surrogates of sparsentan response to enable a precision medicine approach for treatment with dual endothelin angiotensin receptor antagonists. Translational StatementCross-species mapping of sparsentan response in rat and human studies identified similar networks which were elevated in a subset of people with more severe focal segmental glomerulosclerosis (FSGS) providing the basis for implementing precision medicine in for sparsentan treatment.

Previous cross-sectional transcriptomic studies on diabetic kidney disease (DKD) kidney tissue have shown correlations between gene expression and both disease status and kidney function at time of biopsy, but longitudinal data is scarce. We utilized clinical follow-up data up to five years post-biopsy, linking the transcriptomes of diagnostic kidney biopsies to progression rates and outcomes in 19 DKD patients. Patients were stratified into "rapid progressors" and "non-rapid progressors" based on clinical parameters (eGFR slope, CKD stage advancement, degree of albuminuria, composite of kidney failure or 40% eGFR decline). Differential expression and pathway enrichment analyses were performed to identify dysregulated genes and pathways associated with rapid progression. We identified 265 genes in glomeruli and tubulointerstitium that were significantly modulated in rapid vs non-rapid DKD progression. Rapid progression-associated genes showed enrichment for well-established (extracellular matrix organization, inflammation) as well as novel pathways in the context of DKD (circadian rhythm, cytoskeleton reorganization, NOTCH signaling). This study illuminates kidney gene expression patterns that may be predictive of rapid progression in DKD and are distinct from those associated with cross-sectional kidney function.

BackgroundChronic kidney disease (CKD) is a genetically complex disease determined by an interplay of monogenic, polygenic, and environmental risks. Most forms of monogenic kidney diseases have incomplete penetrance and variable expressivity. It is presently unknown if some of the variability in penetrance can be attributed to polygenic factors. MethodsUsing the UK Biobank (N=469,835 participants) and the All of Us (N=98,622 participants) datasets, we examined two most common forms of monogenic kidney disorders, autosomal dominant polycystic kidney disease (ADPKD) caused by deleterious variants in the PKD1 or PKD2 genes, and COL4A-associated nephropathy (COL4A-AN caused by deleterious variants in COL4A3, COL4A4, or COL4A5 genes). We used the eMERGE-III electronic CKD phenotype to define cases (estimated glomerular filtration rate (eGFR) <60 mL/min/1.73m2 or kidney failure) and controls (eGFR >90 mL/min/1.73m2 in the absence of kidney disease diagnoses). The effects of the genome-wide polygenic score (GPS) for CKD were tested in monogenic variant carriers and non-carriers using logistic regression controlling for age, sex, diabetes, and genetic ancestry. ResultsAs expected, the carriers of known pathogenic and rare predicted loss-of-function variants in PKD1 or PKD2 had a high risk of CKD (ORmeta=17.1, 95% CI: 11.1-26.4, P=1.8E-37). The GPS was comparably predictive of CKD in both ADPKD variant carriers (ORmeta=2.28 per SD, 95%CI: 1.55-3.37, P=2.6E-05) and non-carriers (ORmeta=1.72 per SD, 95% CI=1.69-1.76, P< E-300) independent of age, sex, diabetes, and genetic ancestry. Compared to the middle tertile of the GPS distribution for non-carriers, ADPKD variant carriers in the top tertile had a 54-fold increased risk of CKD, while ADPKD variant carriers in the bottom tertile had only a 3-fold increased risk of CKD. Similarly, the GPS was predictive of CKD in both COL4-AN variant carriers (ORmeta=1.78, 95% CI=1.22-2.58, P=2.38E-03) and non-carriers (OR =1.70, 95%CI: 1.68-1.73 P<E-300). The carriers in the top tertile of the GPS had a 2.5-fold higher risk of CKD while the risk for carriers in the bottom tertile was similar to the middle tertile of non-carriers. ConclusionsVariable penetrance of kidney disease in ADPKD and COL4-AN is partially explained by differences in polygenic risk profiles. Accounting for polygenic factors has the potential to improve risk stratification in monogenic kidney disease and may have implications for genetic counseling.

BackgroundUnexplained kidney failure (uKF) affects 15% of individuals requiring kidney replacement therapy. Absence of a diagnosis creates uncertainty around recurrence after transplantation, familial risk, and participation in therapeutic trials. Whole genome sequencing (WGS) was used to identify genetic variants contributing to uKF. Methods218 patients who presented with uKF < 50 years old were recruited to the UKs 100,000 Genomes Project. Candidate variants in 183 genes were reviewed for pathogenicity by a multidisciplinary team. Gene-based association testing, structural variant analyses, and assessment of high-risk APOL1 genotypes were performed. Polygenic risk scores (PRS) were calculated for chronic kidney disease (CKD), and various glomerulonephritides. HLA associations in those with APOL1 high-risk genotype were also investigated. ResultsA positive genetic diagnosis was made in 17% (38/218) of patients. The median age of uKF onset was 36 years. Fewer genetic diagnoses were found in those aged [&ge;] 36 years compared to younger individuals, both with (11% vs. 35%, P=0.03) and without (5% vs. 19%, P=0.05) a family history. Three patients [&ge;] 36 years without a family history had pathogenic variants in type IV collagen genes. High-risk APOL1 genotypes were enriched in patients with recent African ancestry (52% vs 8.4%, P=5.97x10-8). Dividing the uKF cohort by subsequent identification of monogenic diagnosis, High-risk APOL1 genotype, or neither, we found that the SSNS PRS was higher in those with High-risk APOL1 (P=0.048), driven by differences at HLA-DQB1*03:19 (P=0.001). ConclusionsThese findings estimate the likelihood of a genetic diagnosis using WGS in uKF patients, showing fewer diagnoses in older patients without a family history. APOL1 contributes significantly to uKF in those with recent African ancestry, potentially interacting with HLA-DQB1. The lack of PRS signal for CKD suggests distinct biology between uKF and more common causes of CKD.

IntroductionGenomic testing is reshaping nephrology practice, yet the structure, outcomes, and implementation of kidney genetics services remain poorly characterized. MethodsWe conducted a two-part scoping study comprising (i) a literature review (JBI methodology, PRISMA-ScR compliant; OSF registration doi.org/10.17605/OSF.IO/N32VA) of English-language publications (2000-2025) describing kidney genetics services and outcomes, and (ii) an international stakeholder consultation of clinic leads to capture real-world service and implementation experiences. ResultsSixty studies were included, predominantly from North America (n=23), followed by United Kingdom/Ireland (n=5), Europe (n=17), Australia/New Zealand (n=10), and Asia (n=5). Among the 25 studies describing clinic models, four types were identified: multidisciplinary integrated (n=12), nephrologist-led (n=9), mainstreaming (n=2), and traditional genetics referral (n=2). Clinic structure varied by region. Outcome reporting focused on diagnostic yield (92%), with limited data on timeliness (16%), patient-reported outcomes (12%), or implementation outcomes (4%). Test penetration was high across regions and models, while diagnostic yield varied. Nephrologist-led clinics demonstrated comparable performance to multidisciplinary models when adequately supported. International stakeholder consultation data (n=48) revealed diversification of clinic models across regions. In Australia/New Zealand, multidisciplinary clinics predominated, supported by public funding and in-house or hybrid laboratory. United Kingdom/Ireland clinics used public funding and a national laboratory. North American clinics show greater heterogeneity, with higher prevalence of nephrologist-led models, reliance on commercial laboratories, and mixed or private funding. Asian clinics reported nephrologist-led models, with resource constraints, and hybrid testing and funding arrangements. Comprehensive sequencing with virtual panels predominated in Australia/New Zealand, United Kingdom, and Europe; phenotype-driven panels {+/-} reflex testing were more common in North America. ConclusionsKidney genetics care is expanding but remains unevenly implemented. Nephrologist-led and multidisciplinary models can be effective with appropriate support. Patient selection may influence diagnostic yield more than testing modality. Standardized outcome reporting and theory-driven implementation evaluation are essential for delivering equitable, sustainable genomic services. Lay SummaryThis study examined how kidney genetics services are delivered across the globe. We reviewed 60 studies (2000-2025) and consulted 48 clinic leaders globally. Four service models were identified--multidisciplinary integrated, nephrologist-led, mainstreaming, and traditional genetics referral--and mapped variation in care teams, test strategies, test laboratories, and funding. Most studies reported diagnostic yield, but few assessed patient experience or how well services were implemented. European programs showed the highest performance, attributed to clear referral criteria, deep phenotyping, detailed family histories, multidisciplinary review, and strong public funding. Clinics led by nephrologists performed comparably to multidisciplinary teams when adequately supported. Across all settings, patient selection was more important than the specific type of genetic test used in determining diagnostic success. Kidney genetics services are expanding but remain uneven. This study highlights the need for context-specific, theory-informed, and determinants-targeted strategies to support scalable, equitable, and sustainable genomic care worldwide.

Polycystic kidney disease (PKD) is an important cause of end stage renal disease, but treatment options are limited. While later stages of the disease have been extensively studied, mechanisms driving the initial conversion of renal tubules into cysts are not understood. To identify factors that promote the initiation of cysts we deleted polycystin-2 (Pkd2) in mice and surveyed transcriptional changes before and immediately after cysts developed. We identified 74 genes which we term cyst initiation candidates (CICs). To identify conserved changes with relevance to human disease we compared these murine CICs to single cell transcriptomic data derived from patients with PKD and from healthy controls. Tumor-associated calcium signal transducer 2 (Tacstd2) stood out as an epithelial-expressed gene whose levels were elevated prior to cystic transformation and further increased with disease progression. Human tissue biopsies and organoids show that TACSTD2 protein is low in normal kidney cells but is elevated in cyst lining cells. While TACSTD2 has not been studied in PKD, it has been studied in cancer where it is highly expressed in solid tumors while showing minimal expression in normal tissue. This property is being exploited by antibody drug conjugates that target TACSTD2 for the delivery of cytotoxic drugs. Our finding that Tacstd2 is highly expressed in cysts, but not normal tissue, suggests that it should be explored as a candidate for drug development in PKD. More immediately, our work suggests that PKD patients undergoing TACSTD2 treatment for cancer should be monitored for kidney effects. One Sentence SummaryThe oncogene, tumor-associated calcium signal transducer 2 (Tacstd2) mRNA increased in abundance shortly after Pkd2 loss and may be a driver of cyst initiation in polycystic kidney disease.

Poor outcomes in proteinuric kidney diseases are challenging to successfully manage therapeutically due to the heterogeneity of underlying disease pathogenesis and associated risk for progression. The role of cytoskeleton-associated proteins, including the scaffolding protein Anillin (ANLN), are of specific interest in kidney disease given the importance of actin dynamics in the kidneys specialized epithelial cell types. In this study, we identify the prevalence of genetic variants in ANLN, the gene encoding ANLN, in a cohort of deeply phenotyped individuals with non-diabetic proteinuric kidney disease. Thirty-one individuals (of 864 genotyped) harbor heterozygously expressed variants in ANLN; 7 unrelated individuals shared the same variant (I1109V) in the C-terminal pleckstrin homology (PH) domain, a region necessary for interaction with the plasma membrane. Kidney organoids generated from I1109V induced pluripotent stem cells from 1 of these individuals showed increased epithelial cell mitogen-activated protein kinase 8 network activity and apoptosis, which was enhanced by tumor necrosis factor alpha (TNF-) and phenocopied by actin polymerization inhibition. TNF--treated I1109V organoids also exhibited tubular lumen expansion. Knockdown and re-expression of the analogous ANLN variant in Xenopus laevis embryonic epithelia resulted in defects in cell-cell junction dynamics including wavy cell membranes exhibiting increased transverse movements as well as abnormal junctional F-actin remodeling in response to mechanical stress and leaky barrier function. Taken together, these results indicate that enhanced tubular epithelial cell death, perturbed cell-cell contacts and barrier function defects are associated with a novel ANLN variant discovered in individuals with non-diabetic proteinuric kidney disease. ONE SENTENCE SUMMARYEnhanced tubular epithelial cell death and perturbed cell-cell junction integrity and barrier function are associated with a novel Anillin coding variant discovered in a cohort of individuals with proteinuric kidney disease.

Rare kidney diseases are not well characterised, despite making a significant contribution to the burden of kidney disease globally. The National Registry of Rare Kidney Diseases (RaDaR) collects longitudinal disease and treatment-related data from people living with rare kidney diseases across the UK, and is the largest rare kidney disease registry in the world. We present the clinical demographics and renal function of 25,880 prevalent patients and evaluate for any potential recruitment bias to RaDaR. RaDaR has automatic linkage with the UK Renal Registry (UKRR, with which all UK patients receiving Kidney Replacement Therapy (KRT) are registered). To assess for recruitment bias to RaDaR, ethnicity and socioeconomic status of 1) prevalent RaDaR patients receiving KRT were compared with patients with eligible rare disease diagnoses receiving KRT in the UKRR 2) patients recruited to RaDaR and all eligible unrecruited patients at two renal centres were compared 3) the age-stratified ethnicity distribution of RaDaR patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD) was compared to the English Census. We found evidence of some disparities in ethnicity and social deprivation in recruitment to RaDaR, however these were not consistent across all comparisons. Predominant rare kidney diseases in adults were ADPKD (29.2%), Vasculitis (15.8%) and IgA nephropathy (15.7%), compared to Idiopathic nephrotic syndrome (43.6%), Vasculitis (10.8%) and Alport Syndrome (5.9%) in children. Compared with either adults recruited to RaDaR or the English population, children recruited to RaDaR were more likely to be of Asian ethnicity and live in more socially deprived areas. Lay SummaryRare kidney diseases make a significant contribution to the number of people living with kidney disease globally: >25% of adults and >50% of children with kidney failure have a rare disease. However, there is a lack of high-quality published data on how these conditions present, and in which patient groups. Patients often face delays in diagnosis and lack of reliable information on their condition once diagnosed. The UK National Registry of Rare Kidney Diseases (RaDaR) was formed in 2010 to address this knowledge gap. It collects long-term data for UK patients with rare kidney conditions, and is the largest rare kidney disease registry in the world. Here, we present information about 25,880 adults and children recruited to RaDaR, including ethnicity, socioeconomic status, and kidney function, and investigate whether there is any bias in recruitment to RaDaR. To our knowledge, this is the largest epidemiological description of rare kidney diseases worldwide.

Shroom Family Member 3 (SHROOM3) encodes an actin-binding protein that impacts kidney development. Genome-wide association studies (GWAS) identified CKD-associated common variants around SHROOM3 and Shroom3 knock-out mice develop glomerular abnormalities. We sought to evaluate the impact of genetically predicted SHROOM3 expression on kidney traits and the circulating proteome, and validate findings in a mouse model. Genetic instruments for SHROOM3 expression in distinct kidney compartments (glomerular n=240, tubulointerstitial n=311) were constructed using single cell sequencing data from NephQTL2. Using two-sample Mendelian randomization, we evaluated the effects of glomerular and tubulointerstitial SHROOM3 expression on kidney traits and the concentration of 1,463 plasma proteins in the UK Biobank and CKDGen Consortium. Genetically predicted tubulointerstitial SHROOM3 expression colocalized with the genetic signals for eGFR and albuminuria. A 34% reduction in genetically predicted tubulointerstitial SHROOM3 expression was associated with a 0.3% increase in cross-sectional eGFR (P = 6.8x10-4), a 1.5% increase in albuminuria (P = 0.01), and a 2.2% reduction in plasma COL18A1 concentration (P = 1.2x10-5). In contrast, genetically predicted glomerular SHROOM3 expression showed neither colocalization nor significant Mendelian randomization results. Using immunofluorescence, heterozygous Shroom3 knockout mice had a concordant reduction of Col18a1 in their kidneys, primarily around the tubules. Thus, reduced tubulointerstitial SHROOM3 expression, but not glomerular, is associated with increased cross-sectional eGFR, increased uACR, and reduced plasma COL18A1 and Shroom3 knockout leads to reduced kidney Col18a1, agnostically linking SHROOM3 and COL18A1 in CKD pathogenesis. Lay SummaryThe SHROOM3 gene is consistently linked to kidney disease, but we have yet to fully understand why. We looked at how genetic changes affecting SHROOM3 impact different regions of the kidney. We found that less SHROOM3 in kidney tubules led to increased kidney filtration, but also increased leakage of protein into the urine. After looking at over 1000 proteins, we identified a new link between SHROOM3 and a collagen protein called COL18A1. We then confirmed the link between SHROOM3 and COL18A1 by imaging the kidneys of mice designed to have less SHROOM3. Our results suggest an interaction of SHROOM3 and COL18A1 leads to increased pressure on the kidney filtration system.

Urinary proteins are valuable biomarkers for physiological processes and early detection and monitoring of systemic and kidney diseases. However, comprehensive quantification and characterization of the urine proteome using high-throughput platforms remains limited. Using an affinity-based assay for large-scale proteomics, the Olink Explore 3072 platform, we quantified 2,868 proteins in urine samples from 1,268 participants of the German Chronic Kidney Disease (GCKD) study. Protein detectability in urine, defined as the percentage of samples with measurements above the limit of detection, showed a bimodal distribution: 659 (23%) proteins had high (>80%) and 1,336 proteins (47%) had low (<20%) detectability. Over 95% of highly detectable proteins were confirmed as present in urine by mass spectrometry. They were enriched for extracellular, exosomal, and cell-surface localization, and showed tissue-specific expression in hepatocytes, immune cells, and proximal tubule cells. Significant associations of protein levels with sex (921 proteins), BMI (367 proteins) and age (157 proteins) showed plausible relationships such as prostate-specific antigen and male sex. Unsupervised correlation analysis of protein levels detected multiple biologically meaningful protein clusters, reflecting shared cellular compartments (e.g., lysosomal origin), tissue of origin (e.g., liver), and molecular interactions (e.g., receptor-ligand or chaperone-transporter complexes). In conclusion, the Olink Explore 3072 platform is well-suited for large-scale urine proteomics and identifies biologically plausible representations of ongoing processes in health and disease. Our comprehensive characterization provides a valuable resource for biomarker discovery and future targeted studies of urine proteins. Translational StatementUrinary proteins reflect kidney-specific and systemic processes, with the potential to serve as disease biomarkers. We demonstrate that the Olink Proximity Extension Assay enables high-throughput urine proteome screening with sufficient specificity to identify biologically plausible protein signatures and demographic associations. By providing comprehensive data on protein detectability, variability, and clinical associations, our study serves as a reference resource for designing targeted proteomic investigations, facilitating the development of urine-based biomarker panels for different purposes, potentially including early detection of impaired kidney function, monitoring kidney disease progression, and predicting treatment response.