Matthew Gordon Sampson

Allele-specific expression (ASE), the preferential expression of one gene copy, is a key mechanism of genomic regulation. However, its role in human kidney disease remains poorly understood. In this study, we generated a high-quality, genome-wide ASE map using paired whole-genome sequencing and RNA sequencing from microdissected glomerular and tubulointerstitial compartments of patients with proteinuric kidney disease. We showed that the majority of common ASE events were deterministic and sequence-mediated. We also found that diseased kidneys exhibited significantly more ASE in glomeruli (GLOM) than tubulointerstitium (TUBE) compared to controls. Unexpectedly, higher ASE in GLOM than TUBE was significantly associated with improved kidney disease outcomes in the disease cohort. Differential gene expression analysis suggested that this was the result of an active, protective transcriptional response, including ribosome and adenosine 5′-triphosphate synthesis up-regulation, rather than pathogenic dysregulation. Our work reveals glomerular ASE as a marker of adaptive transcriptional activity in proteinuric kidney disease.

INTRODUCTION RNA editing has been implicated in endogenous double-stranded RNA (dsRNA) sensing and inflammatory disease, but its prevalence, genetic regulation, and consequences in diseased human kidney tissue have not been systematically characterized. Because ADAR enzymes edit multiple neighboring adenosines often in the same transcript, analyzing these sites holistically (as "clusters") may reveal effects missed by single-site analysis. METHODS We profiled both single-site and cluster A-to-I RNA editing in the kidneys of 215 participants from the Nephrotic Syndrome Study Network with focal segmental glomerulosclerosis or minimal change disease who had microdissected glomerular and/or tubulointerstitial RNA-seq and blood genome sequencing. We tested single-site and cluster editing association with estimated glomerular filtration rate, proteinuria, and an interferon stimulated gene expression score. To discover the genetic determinants of editing, we conducted mapping of both single-site, cis-editing QTL and cluster-level editing QTLs (cledQTLs). We then tested cledQTLs for colocalization with kidney eQTLs and kidney-relevant GWAS. RESULTS Greater cluster mean editing in tubulointerstitium was associated with lower interferon-stimulated gene activity (P = 4.81 × 10-9), lower UPCR (P = 0.01) and higher eGFR (P = 8.52 × 10-5). Genetic mapping identified 290 glomerular and 473 tubulointerstitial single-site edQTLs, as well as 21 glomerular and 51 tubulointerstitial cledQTLs. We identified 10 colocalized signals between cledQTL and GWAS and 14 between cledQTL and eQTL. Nine of 51 tubulointerstitial cledQTL clusters were individually associated with eGFR in NEPTUNE. CONCLUSION These results identify A-to-I RNA editing as a measurable and partly genetically regulated molecular phenotype in proteinuric kidney disease and nominate clustered editing of tubulointerstitial transcripts as a putative contributor to attenuated immune activity and higher kidney function. Cluster-level analysis identified additional genetically regulated editing patterns and colocalized signals not detected at individual sites, highlighting the added value of analyzing nearby editing sites as clusters.

Background: Despite the growing role of genetic testing in pediatric kidney disease, translating genomic findings into clinical care remains challenging due to limited kidney genetics expertise and infrastructure. Specialized kidney genetics clinics may optimize both testing strategies and clinical application, though outcomes remain underreported. Methods: We performed a retrospective analysis of the first two years (11/2022 - 11/2024) of the Boston Children’s Hospital kidney genetics clinic, led by two pediatric nephrologists with genetics expertise and a certified genetic counselor. Our referral model, services, outcomes, clinical impacts, and considerations for genetic testing are reviewed. Results: One-hundred and four individuals were referred to our clinic. Indications for referral included pre-test counseling and genetic testing implementation (64/104), counseling or clinical evaluation for externally ordered test results (38/104), and clinical confirmation of research-based results (2/104). Of 64 probands referred for pre-test counseling, we recommended genetic testing for 58% of individuals (37/64) and identified a diagnostic variant in 51% of those tested (19/37). Across all 104 probands, 77 underwent genetic testing, either by our clinic or external providers. The cohort showed substantial genetic heterogeneity; 46 individuals had kidney genetic diagnoses across 28 genes. Forty-seven individuals carried at least one variant of uncertain significance (VUS), seven (15%) of which were considered diagnostic after adjudication. Ten additional candidate variants and incidental findings were detected. Overall, 68% of tested patients had at least one physician-reported clinical impact, including diagnostic certainty (43/77, 56%), change in disease management (49/77, 64%), and family planning implications (20/77, 26%). Conclusions: A specialized pediatric kidney genetics clinic achieves high diagnostic yield and demonstrates measurable clinical impact. By integrating genetic testing, expert variant interpretation, and clinical translation, this multidisciplinary model addresses key barriers in pediatric kidney genetics and supports broader adoption of kidney genetics clinics to optimize genomic evaluation and care for children with kidney disease.

Glomerular diseases are complex conditions, many of which have a genetic basis. However, although some genetic variants can affect glomerular and thereby kidney function, not all identified variants are pathogenic. The process of evaluating genetic and experimental evidence to determine the validity of gene–disease relationships is known as gene curation, and it is critical for the identification of genes that should be examined in diagnostic tests and used to guide clinical management. Gene curation is a key role of the Clinical Genome Resource (ClinGen) and aims to ensure that the evidence underlying asserted gene–disease relationships across a range of diseases is sufficiently robust through comprehensive review of evidence and standardized evaluation by genetic and disease area-specific experts. The ClinGen Glomerulopathy Gene Curation Expert Panel has evaluated 57 gene–disease relationships from 56 genes that have been putatively linked to glomerular phenotypes. This evaluation identified 34 genes that reached a definitive level of evidence for gene–disease clinical validity. Ten genes had moderate supporting evidence and 11 had limited supporting evidence. A further two genes had insufficient evidence for any clinically valid relationship to disease. This curation establishes a comprehensive framework for the ongoing assessment of gene–disease relationships and provides a valuable reference for diagnostic genetic testing panels that target glomerular disease.

Background APOL1 high-risk variants predispose to chronic kidney disease (CKD) in individuals of African genetic ancestry due to podocyte toxicity. As congenital anomalies of the kidney and urinary tract (CAKUT) have variable outcomes potentially driven by podocyte injury, we hypothesize that the outcome of children with CAKUT is influenced by APOL1 risk genotypes. Methods APOL1 risk status was determined in children and adults with CAKUT from African genetic ancestry using DNA microarrays or exome sequencing. Phenotypic information and CKD outcomes at last follow-up were collected. We computed odds ratios (OR) and hazard ratios between APOL1-high risk (HR) vs. low risk (LR) carriers under different models using logistic regression and Cox proportional hazards. Results Clinical data were available for 195 patients (median age 15.35 years, [IQR 11.01–19.87]), including 20 (10.3%) carrying APOL1-HR. Under a recessive model, APOL1-HR vs. LR showed no differences in proteinuria or hypertension (OR 0.24, 95% CI 0.04–1.30, p = 0.10 and OR 0.99, 95% CI 0.38–2.54, p = 0.98, respectively), nor in CKD stage ≥ G2 risk (OR 0.71, 95% CI 0.29–1.78, p = 0.47). Median time until kidney failure for APOL1 risk groups was 11.59 years [IQR 7.15–21.47] and 14.35 years ([IQR 9.16–17.20]; p = 0.73) for HR and LR, respectively. Additional exploratory analyses showed comparable outcomes between HR and LR variant carriers. Conclusions This pilot study identified no association between APOL1 risk genotypes and kidney outcomes in patients with CAKUT across genetic models. With APOL1-targeted therapies emerging, large-scale prospective studies are needed to identify individuals with CAKUT who may benefit from these treatment strategies. Graphical Abstract A higher resolution version of the Graphical abstract is available as Supplementary information

Allele-specific expression (ASE), the preferential expression of one gene copy, is a key mechanism of genomic regulation. However, its role in human kidney disease remains poorly understood. In this study, we generated a high-quality, genome-wide ASE map using paired whole-genome sequencing and RNA-seq from microdissected glomerular (GLOM) and tubulointerstitial (TUBE) compartments of patients with proteinuric kidney disease. We showed that the majority of common ASE events were deterministic and sequence-mediated. We also found that diseased kidneys exhibited significantly more ASE in GLOM than TUBE, compared to controls. Unexpectedly, higher ASE in GLOM than TUBE was significantly associated with improved kidney disease outcomes in the disease cohort. Differential gene expression analysis suggested this was the result of an active, protective transcriptional response, including ribosome and ATP synthesis upregulation, rather than pathogenic dysregulation. Our work reveals glomerular ASE as a marker of adaptive transcriptional activity in proteinuric kidney disease.

In genetic disease, an accurate expression landscape of disease genes and faithful animal models can facilitate genetic diagnoses and therapeutic advances respectively. Previously, we found that variants in NOS1AP, the gene that encodes nitric oxide synthase 1 adaptor protein, cause monogenic nephrotic syndrome. Here, we determine that an intergenic splice product of NOS1AP/Nos1ap and neighboring C1orf226/Gm7694, which prevents NOS1AP from binding to nitric oxide synthase 1, is the predominant isoform in mammalian kidney transcriptional and proteomic data. Gm7694^−/− mice, whose allele exclusively disrupts the intergenic product, develop nephrotic syndrome phenotypes. In two male human subjects with nephrotic syndrome, we identify causative NOS1AP splice variants, including one predicted to abrogate intergenic splicing but initially misclassified as benign based on the canonical transcript. Finally, by modifying genetic background, we generate a faithful mouse model of NOS1AP-associated monogenic nephrotic syndrome that responds to anti-proteinuric treatment.