Kidney Organoid Modeling of WT1 Mutations Reveals Key Regulatory Paths Underlying Podocyte Development.

Wilms tumor-1(WT1) is a crucial transcription factor that regulates podocyte development. However, the epigenomic mechanism underlying the function of WT1 during podocyte development has yet to be fully elucidated. Here, single-cell chromatin accessibility and gene expression maps of foetal kidneys and kidney organoids are generated. Functional implications of WT1-targeted genes, which are crucial for the development of podocytes and the maintenance of their structure, including BMPER/PAX2/MAGI2 that regulates WNT signaling pathway, MYH9 that maintains actin filament organization and NPHS1 that modulates cell junction assembly are identified. To further illustrate the functional importance of WT1-mediated transcriptional regulation during podocyte development, cultured and implanted patient-derived kidney organoids derived from the Induced Pluripotent Stem Cell (iPSCs) of a patient with a heterozygous missense mutation in WT1 are generated. Results from single-cell RNA sequencing (scRNA-seq) and functional assays confirm that the WT1 mutation leads to delays in podocyte development and causes damage to cell structures, due to its failure to activate the targeting genes MAGI2, MYH9, and NPHS1. Notably, correcting the mutation in the patient iPSCs using CRISPR-Cas9 gene editing rescues the podocyte phenotype. Collectively, this work elucidates the WT1-related epigenomic landscape with respect to human podocyte development and identifies the disease-causing role of a WT1 mutation.

Genetic features and kidney morphological changes in women with X-linked Alport syndrome.

BACKGROUND: X-linked Alport syndrome (XLAS) caused by COL4A5 pathogenic variants usually has heterogeneous phenotypes in female patients. The genetic characteristics and glomerular basement membrane (GBM) morphological changes in women with XLAS need to been further investigated. METHODS: A total of 83 women and 187 men with causative COL4A5 variants were enrolled for comparative analysis. RESULTS: Women were more frequently carrying de novo COL4A5 variants compared with men (47% vs 8%, p=0.001). The clinical manifestations in women were variable, and no genotype-phenotype correlation was observed. Coinherited podocyte-related genes, including TRPC6, TBC1D8B, INF2 and MYH9, were identified in two women and five men, and the modifying effects of coinherited genes contributed to the heterogeneous phenotypes in these patients. X-chromosome inactivation (XCI) analysis of 16 women showed that 25% were skewed XCI. One patient preferentially expressing the mutant COL4A5 gene developed moderate proteinuria, and two patients preferentially expressing the wild-type COL4A5 gene presented with haematuria only. GBM ultrastructural evaluation demonstrated that the degree of GBM lesions was associated with the decline in kidney function for both genders, but more severe GBM changes were found in men compared with women. CONCLUSIONS: The high frequency of de novo variants carried by women indicates that the lack of family history tends to make them susceptible to be underdiagnosed. Coinherited podocyte-related genes are potential contributors to the heterogeneous phenotype of some women. Furthermore, the association between the degree of GBM lesions and decline in kidney function is valuable in evaluating the prognosis for patients with XLAS.

Pathogenic Gene Spectrum and Clinical Implication in Chinese Patients with Lupus Nephritis.

BACKGROUND: Lupus nephritis is a rare immunological disorder. Genetic factors are considered important in its causation. We aim to systematically investigate the rare pathogenic gene variants in patients with lupus nephritis. METHODS: Whole-exome sequencing was used to screen pathogenic gene variants in 1886 probands with lupus nephritis. Variants were interpreted on the basis of known pathogenic variants or the American College of Medical Genetics and Genomics guidelines and studied by functional analysis, including RNA sequencing, quantitative PCR, cytometric bead array, and Western blotting. RESULTS: Mendelian form of lupus nephritis was confirmed in 71 probands, involving 63 variants in 39 pathogenic genes. The detection yield was 4%. The pathogenic genes enriched in nuclear factor kappa-B (NF-κB), type I interferon, phosphatidylinositol-3-kinase/serine/threonine kinase Akt (PI3K/AKT), Ras GTPase/mitogen-activated protein kinase (RAS/MAPK), and Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathways. Clinical manifestation patterns were diverse among different signaling pathways. More than 50% of the pathogenic gene variants were reported to be associated with lupus or lupus nephritis for the first time. The identified pathogenic gene variants of lupus nephritis overlapped with those of autoinflammatory and immunodeficiency diseases. Inflammatory signatures, such as cytokine levels of IL-6, IL-8, IL-1 ß , IFN α , IFN γ , and IP10 in serum and transcriptional levels of interferon-stimulated genes in blood, were significantly higher in patients with pathogenic gene variants compared with controls. The overall survival rate of patients with pathogenic gene variants was lower than those without pathogenic gene variants. CONCLUSIONS: A small fraction of patients with lupus nephritis had identifiable pathogenic gene variants, primarily in NF-κB, type I interferon, PI3K/AKT, JAK/STAT, RAS/MAPK, and complement pathways.

Clinical Implications of a New DDX58 Pathogenic Variant That Causes Lupus Nephritis due to RIG-I Hyperactivation.

BACKGROUND: Lupus nephritis (LN) is one of the most severe complications of systemic lupus erythematosus, with heterogeneous phenotypes and different responses to therapy. Identifying genetic causes of LN can facilitate more individual treatment strategies. METHODS: We performed whole-exome sequencing in a cohort of Chinese patients with LN and identified variants of a disease-causing gene. Extensive biochemical, immunologic, and functional analyses assessed the effect of the variant on type I IFN signaling. We further investigated the effectiveness of targeted therapy using single-cell RNA sequencing. RESULTS: We identified a novel DDX58 pathogenic variant, R109C, in five unrelated families with LN. The DDX58 R109C variant is a gain-of-function mutation, elevating type I IFN signaling due to reduced autoinhibition, which leads to RIG-I hyperactivation, increased RIG-I K63 ubiquitination, and MAVS aggregation. Transcriptome analysis revealed an increased IFN signature in patient monocytes. Initiation of JAK inhibitor therapy (baricitinib 2 mg/d) effectively suppressed the IFN signal in one patient. CONCLUSIONS: A novel DDX58 R109C variant that can cause LN connects IFNopathy and LN, suggesting targeted therapy on the basis of pathogenicity. PODCAST: This article contains a podcast at.

Dissecting the genotype-phenotype correlation of COL4A5 gene mutation and its response to renin-angiotensin-aldosterone system blockers in Chinese male patients with Alport syndrome.

BACKGROUND: Alport syndrome (AS) is an inherited type IV collagen-related disorder with an irreversible tendency to progress to end-stage renal disease (ESRD). X-linked AS (XLAS) is caused by mutations in the COL4A5 gene. The aim of this study was to investigate the effects of underlying mutations on clinical manifestations and the response to therapy in XLAS. METHODS: We conducted a retrospective cohort study of 187 Chinese male patients with XLAS confirmed by pathological examination and genetic analysis. The Kaplan-Meier method and Cox proportional hazards model were used to assess the age and risk of progression to ESRD under different genotypes and treatment conditions. RESULTS: A strong relationship between transcript type and renal outcome was observed, with the median age of ESRD onset being 22 years for truncating mutations and 39 years for non-truncating mutations. The response of affected patients to renin-angiotensin-aldosterone system (RAAS) blockers was genotype-associated. This therapy delayed the onset of ESRD by 16 years in patients with non-truncating mutations and 3 years in patients with truncating mutations. The efficacy of RAAS blockers functioned in a time-dependent manner, with a 7% reduction in the risk of progression to ESRD per each 6-month increase in treatment duration [hazard ratio 0.93 (95% confidence interval 0.89-0.96); P < 0.001]. CONCLUSIONS: Clinical features and response to RAAS blockers were observed to be strongly correlated with the genotypes of male XLAS patients. Genotyping of COL4A5 gene mutations is essential and is a useful tool to assess the prognosis of AS patients.

Establishment of the induced pluripotent stem cell line (NCKDi005-A) from a male patient with Alport syndrome carrying a homozygous frameshift mutation in the COL4A4 gene.

Alport syndrome is an inherited chronic kidney disease with genetic heterogeneity. There are three modes of inheritance: X-linked dominant inheritance, autosomal recessive inheritance, and autosomal dominant inheritance. Autosomal recessive inheritance accounts for about 14%-15% of all cases of Alport syndrome and is caused by the COL4A3 or COL4A4 gene mutation. In this study, the peripheral blood mononuclear cells (PBMCs) of a patient with a novel COL4A4 homozygous mutation were reprogrammed into an induced pluripotent stem cell (iPSC) line. The iPSC line can provide a cell model for studying the pathogenesis of the disease and drug screening.

Next-Generation Sequencing-Based Genetic Diagnostic Strategies of Inherited Kidney Diseases.

BACKGROUND: At least 10% of adults and most of the children who receive renal replacement therapy have inherited kidney diseases. These disorders substantially decrease their life quality and have a large effect on the health-care system. Multisystem complications, with typical challenges for rare disorders, including variable phenotypes and fragmented clinical and biological data, make genetic diagnosis of inherited kidney disorders difficult. In current clinical practice, genetic diagnosis is important for clinical management, estimating disease development, and applying personal treatment for patients. SUMMARY: Inherited kidney diseases comprise hundreds of different disorders. Here, we have summarized various monogenic kidney disorders. These disorders are caused by mutations in genes coding for a wide range of proteins including receptors, channels/transporters, enzymes, transcription factors, and structural components that might also have a role in extrarenal organs (bone, eyes, brain, skin, ear, etc.). With the development of next-generation sequencing technologies, genetic testing and analysis become more accessible, promoting our understanding of the pathophysiologic mechanisms of inherited kidney diseases. However, challenges exist in interpreting the significance of genetic variants and translating them to guide clinical managements. Alport syndrome is chosen as an example to introduce the practical application of genetic testing and diagnosis on inherited kidney diseases, considering its clinical features, genetic backgrounds, and genetic testing for making a genetic diagnosis. KEY MESSAGES: Recent advances in genomics have highlighted the complexity of Mendelian disorders, which is due to allelic heterogeneity (distinct mutations in the same gene produce distinct phenotypes), locus heterogeneity (mutations in distinct genes result in similar phenotypes), reduced penetrance, variable expressivity, modifier genes, and/or environmental factors. Implementation of precision medicine in clinical nephrology can improve the clinical diagnostic rate and treatment efficiency of kidney diseases, which requires a good understanding of genetics for nephrologists.

Generation of the induced pluripotent stem cell line (NCKDi004-A) from a 17-year-old patient with Alport syndrome carrying a homozygous mutation in COL4A3 gene.

Alport syndrome is the second most common genetic renal disease which caused by mutations in COL4A3/COL4A4/COL4A5, according to different modes of inheritance. Recently, we identified a novel homozygous mutation in COL4A3 gene in a patient with Alport syndrome. The Peripheral Blood Mononuclear Cells (PBMCs) of the patient were obtained and a line of induced pluripotent stem cells (iPSCs) was successfully generated. The iPSC line will be useful for further study of the pathogenesis and drug screening for Alport syndrome.

Generation of the induced pluripotent stem cell line (NCKDi002-A) from a 22-year-old patient with Focal Segmental Glomerular Sclerosis carrying a heterozygous mutation in WT1 gene.

Focal Segmental Glomerular Sclerosis (FSGS) is a glomerular disease which can be classified into primary, secondary, genetic, and unknown forms. WT1 mutation has been shown to be associated with this disorder. Recently, we identified a mutation in the Zinc finger C2H2 domain of WT1 gene in a patient with FSGS who also carried a family history of end-stage renal disease (ESRD). The Peripheral Blood Mononuclear Cells (PBMCs) of the patient were obtained and a line of induced pluripotent stem cells (iPSCs) was successfully generated. The iPSC line will be useful for further study of the pathogenesis and drug screening for FSGS.

Generation of induced pluripotent stem cell line (NCKDi001-A) from a 19-year-old patient with a novel COL4A5 gene mutation in Alport syndrome.

The clinical manifestations of Alport syndrome may vary depending on the involved organs such as the kidneys, cochlea and eyes. The pathogenic genes involved are those encoding different chains of type IV collagen. We collected PBMCs of a patient with a novel COL4A5 gene mutation(c.2687G > C). Subsequently, we used the electroporation system to transfer the reprogramming plasmids expressing OCT3/4, SOX2, KLF4, LIN28 and L-MYC into the PBMCs. We simultaneously carried out the tests on the iPSCs including Sanger sequencing for confirming the mutation site, immunofluorescence assay and flow cytometry for pluripotency markers as well as teratoma experiment for validating the pluripotency.

Nocardiosis in patients with nephrotic syndrome: a retrospective analysis of 11 cases and a literature review.

OBJECTIVES: We evaluated the clinical manifestations and outcomes of nocardiosis, a rare opportunistic infection that occurs in patients with nephrotic syndrome. METHODS: The records of NS patients with nocardiosis in a single hospital during 2000-2019 were retrieved and studied in detail. RESULTS: Eleven patients were included. The mean time to develop nocardiosis after glucocorticoid therapy was 11.5 ± 14.8 months. Most patients had fever, elevated white blood cell counts and C-reactive protein, whereas procalcitonin levels were normal or slightly elevated in 91% (10/11) patients, except one patient suffered from septic shock. Nine patients were tested for CD4+ T-cell counts; of these, four patients had counts < 200 cells/µL. The most common site of nocardiosis involvement was lung (100%), followed by subcutaneous tissue (72.7%). Radiological findings for lungs in seven cases were characterized by isolated or scattered nodules and masses, usually located subpleural or close to the hilum. Positive smears of Nocardia were detected in 100% of samples of subcutaneous abscess and pleural fluid. Nine patients received oral trimethoprim-sulfamethoxazole, four of which received combined carbapenem, and the remaining two patients received carbapenem monotherapy. The long-term prognosis was excellent, with a treatment success rate of 100% in all patients. CONCLUSIONS: NS patients can develop immunodeficiency after treatment with glucocorticoid and immunosuppressants. In cases where patients develop systemic multiple abscesses, or lung images reveal isolated or scattered nodules and masses that are subpleural or close to the hilum, nocardial infection should be considered. Early diagnosis and specific treatment may improve patient outcomes.

A Novel COL4A5 Splicing Mutation Causes Skipping of Exon 14 in a Chinese Family with Alport Syndrome.

BACKGROUND: Alport syndrome (AS) is an inherited progressive renal disease caused by mutations in COL4A3, COL4A4, and COL4A5. Although mutation screening in the genes responsible for AS is typically performed, only a small proportion of patients receive genetic testing in China, and the functional consequences of multiple splicing variants in AS patients have not been investigated. METHODS: A family with X-linked AS was diagnosed based on family history and pathological findings from a kidney biopsy. Targeted next-generation sequencing was used to identify the causative mutation, and a minigene assay was performed to test the influence of the mutation on splicing. RESULTS: A c.834+2T>G in COL4A5 was identified and shown to co-segregate with AS in the family. The variant is located in the canonical splicing site and is predicted to induce aberrant splicing. Minigene assay using HEK 293T cells indicated the skipping of exon 14 in -COL4A5. CONCLUSIONS: The novel COL4A5 splicing mutation identified in the current study broadened the genetic spectrum of X-linked AS and further deepened our insight of the disease's molecular mechanism.

Autosomal Dominant Tubulointerstitial Kidney Disease Due to UMOD Mutation: A Two-Case Report and Literature Review.

Autosomal dominant tubulointerstitial kidney disease due to UMOD (encoding uromodulin) mutation (ADTKD-UMOD) is a rare hereditary disease. In the present study, we reported 2 ADTKD cases with confirmed UMOD mutations (Arg185His, Trp258Gly) by gene testing. They were young men and presented with hyperuricemia and renal dysfunction with no hematuria or proteinuria. Renal histology showed chronic tubulointerstitial nephropathy with fibrillar inclusions in the cells of distal tubules. Electron microscopy illustrated extensive bundled and cystic endoplasmic reticulum. Immunohistological analysis confirmed intracytoplasmic aggregates of uromodulin in the distal tubules. Since ADTKD-UMOD is an underdiagnosed disease, electron microscopy and immunohistochemical staining for uromodulin are helpful in the diagnosis of ADTKD-UMOD and genetic analysis is the gold standard.

A Case of Switch from C3 Glomerulonephritis to Proliferative Glomerulonephritis with Monoclonal IgG Deposits.

Monoclonal immunoglobulins have been implicated in the development of C3 glomerulonephritis (C3GN) and Proliferative glomerulonephritis with monoclonal IgG deposits (PGNMID). We report a 58-year-old female who showed a switch from C3GN to PGNMID. She presented with mild proteinuria and normal renal function for the first time. Her renal biopsy showed a severe mesangial proliferation with isolated C3 deposits, thus being diagnosed as C3GN. Two years later, her condition became serious. Repeat renal biopsy showed a membranoproliferative glomerulonephritis with deposition of the κ light chain of IgG3 in the glomeruli. She was diagnosed with proliferative glomerulonephritis with monoclonal IgG deposits (IgG3-κ). This case demonstrates that there are several types of monoclonal gammopathy (MGP)-associated glomerulonephritis, and they can switch among each other in some patients.

The COL4A3 and COL4A4 Digenic Mutations in cis Result in Benign Familial Hematuria in a Large Chinese Family.

Mutations in the COL4A5 gene result in X-linked Alport syndrome, homozygous or compound heterozygous mutations in COL4A3 or COL4A4 are responsible for autosomal recessive Alport syndrome, and heterozygous mutations in COL4A3 or COL4A4 cause autosomal dominant Alport syndrome or benign familial hematuria. Recently, the existence of a digenic inheritance in Alport syndrome has been demonstrated. We here report heterozygous COL4A3 and COL4A4 digenic mutations in cis responsible for benign familial hematuria. Using bioinformatics analyses and pedigree verification, we showed that COL4A4 c.1471C>T and COL4A3 c.3418 + 1G>T variants in cis are pathogenic and co-segregate with the benign familial hematuria. This result suggests that COL4A3 and COL4A4 digenic mutations in cis mimicking an autosomal dominant inheritance should be considered as a novel inheritance pattern of benign familial hematuria, although the disease-causing mechanism remains unknown.

Three Novel Heterozygous COL4A4 Mutations Result in Three Different Collagen Type IV Kidney Disease Phenotypes.

Thin basement membrane nephropathy (TBMN), autosomal dominant Alport syndrome (ADAS), and focal segmental glomerulosclerosis (FSGS) are kidney diseases that differ in clinical diagnosis, treatment, and prognosis. Nevertheless, they may result from the same causative genes. Here, we report 3 COL4A4 heterozygous mutations (p.Gly208Arg, p.Ser513Glufs*2, and p.Met1617Cysfs*39) that lead to 3 different collagen type IV kidney disease phenotypes, manifesting as TBMN, ADAS, and FSGS. Using bioinformatics analyses and pedigree verification, we show that these novel variants are pathogenetic and cosegregate with TBMN, ADAS, and FSGS. Furthermore, we found that the collagen type IV-associated kidney disease phenotypes are heterogeneous, with overlapping pathology and genetic mutations. We propose that COL4A4-associated TBMN, ADAS, and FSGS should be considered as collagen type IV kidney disease subtypes that represent different phases of disease progression.

Novel mutations in COL4A3, COL4A4, and COL4A5 in Chinese patients with Alport Syndrome.

Alport syndrome (AS) is a clinically and genetically heterogeneous, progressive nephropathy caused by mutations in COL4A3, COL4A4, and COL4A5, which encode type IV collagen. The large sizes of these genes and the absence of mutation hot spots have complicated mutational analysis by routine polymerase chain reaction (PCR)-based approaches. Here, in order to design a rapid and effective method for the genetic diagnosis of AS, we developed a strategy by utilizing targeted capture associated with next-generation sequencing (NGS) to analyze COL4A3, COL4A4, and COL4A5 simultaneously in 20 AS patients. All the coding exons and flanking sequences of COL4A3, COL4A4, and COL4A5 from the probands were captured followed by HiSeq 2500 sequencing. Candidate mutations were validated by classic Sanger sequencing and quantitative (q)PCR. Sixteen patients (16/20, 75%) showed X-linked inheritance, and four patients (4/20, 20%) showed autosomal recessive inheritance. None of the individuals had autosomal-dominant AS. Fifteen novel mutations, 6 known mutations, and 2 novel fragment deletions were detected by targeted capture and NGS. Of these novel mutations, 12, 3, and 2 mutations were detected in COL4A5, COL4A4, and COL4A3, respectively. A comparison of the clinical manifestations caused by different types of mutations in COL4A5 suggested that nonsense mutations and glycine substitution by an acidic amino acid are more severe than the other missense mutations. Pathogenic mutations were detected in 20 patients. These novel mutations can expand the genotypic spectrum of AS. Our results demonstrated that targeted capture and NGS technology are effective in the genetic diagnosis of AS.

Risk Factors for Renal Survival in Chinese Patients with Myeloperoxidase-ANCA-Associated GN.

BACKGROUND AND OBJECTIVES: Our study explored the association of histopathologic classification of ANCA-associated GN with renal survival in Chinese patients with myeloperoxidase-ANCA-associated GN. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Two hundred fifteen patients with biopsy-proven myeloperoxidase-ANCA-associated GN were included from January of 1996 to December of 2014. The biopsies included focal (n=27), mixed (n=82), crescentic (n=47), and sclerotic (n=59) classes. The long-term renal outcome and risk factors of myeloperoxidase-ANCA-associated GN for different histopathologic classes were retrospectively analyzed. RESULTS: During a median follow-up time of 22 (9-51) months, 88 (40.9%) patients reached ESRD. The 5-year renal survival (overall 58.7%) was highest in the focal class (100.0%) and lowest in the sclerotic class (20.7%), with no difference between the mixed (58.9%) and crescentic (67.4%) classes. Patients in the mixed (hazard ratio, 0.34; 95% confidence interval, 0.20 to 0.57; P<0.001) and crescentic (hazard ratio, 0.31; 95% confidence interval, 0.16 to 0.59; P<0.001) classes were at lower risk for ESRD compared with patients in the sclerotic class, as were patients who received glucocorticoids plus mycophenolate mofetil (hazard ratio, 0.32; 95% confidence interval, 0.18 to 0.60; P<0.001) compared with those receiving glucocorticoids alone. In addition, patients with a serum creatinine level ≥4 mg/dl (hazard ratio, 2.93; 95% confidence interval, 1.77 to 4.85; P<0.001) or hypoalbuminemia (hazard ratio, 2.11; 95% confidence interval, 1.32 to 3.34; P=0.002) were at higher risk for ESRD. A serum creatinine level ≥4 mg/dl and a percentage of global sclerotic glomeruli ≥60% were the two independent risk factors for ESRD in the sclerotic class. CONCLUSIONS: The histopathologic classification of ANCA-associated GN in combination with serum creatinine and serum albumin levels and treatment regimen is associated with renal outcome in myeloperoxidase-ANCA-associated GN. The evaluation of serum creatinine level and percentage of global sclerotic glomeruli provides additional information on the risk of renal survival in the sclerotic class of myeloperoxidase-ANCA-associated GN.

Long-term outcome of mycophenolate mofetil treatment for patients with microscopic polyangiitis: an observational study in Chinese patients.

This study aimed to retrospectively analyze the long-term outcome of mycophenolate mofetil (MMF) therapy for microscopic polyangiitis (MPA) with mild to moderate renal involvement in Chinese patients. Thirty-four MPA patients (24 females, 10 males, aged 44.7 ± 17 years, BVAS score 13.8 ± 3.2, SCr 2.2 ± 1.1 mg/dl) with SCr < 5 mg/dl and who received glucocorticoids plus MMF therapy for inducing and maintaining remission were included in this study. The remission and relapse rates, patient and renal survival rates and adverse events were retrospectively analyzed. We found that 31 (91.2 %) of 34 patients achieved remission and were continuously treated with glucocorticoids plus MMF for maintaining remission. The median duration of MMF treatment was 24 months (IQR 15-53 months) and follow-up time was 86 months (IQR 29-124 months). During the follow-up, 7 (22.6 %) patients relapsed, one patient died, and one patient progressed into end-stage renal disease. The 5-year patient and renal survival rates were 92.8 and 95.2 %, respectively. 11 (32.4 %) patients suffered 16 adverse events, 13 of which were pulmonary infection. In conclusion, glucocorticoids plus MMF regimen as induction and maintenance therapy could achieve high remission rate and good long-term renal survival in MPA patients with mild to moderate renal involvement. Prospective controlled trials with a large sample size are needed to confirm the efficacy of MMF in this population.