Exploring the relevance of NUP93 variants in steroid-resistant nephrotic syndrome using next generation sequencing and a fly kidney model

Abstract

Background Variants in genes encoding nuclear pore complex (NPC) proteins are a newly identified cause of paediatric steroid-resistant nephrotic syndrome (SRNS). Recent reports describing NUP93 variants suggest these could be a significant cause of paediatric onset SRNS. We report NUP93 cases in the UK and demonstrate in vivo functional effects of Nup93 depletion in a fly (Drosophila melanogaster) nephrocyte model. Methods Three hundred thirty-seven paediatric SRNS patients from the National cohort of patients with Nephrotic Syndrome (NephroS) were whole exome and/or whole genome sequenced. Patients were screened for over 70 genes known to be associated with Nephrotic Syndrome (NS). D. melanogaster Nup93 knockdown was achieved by RNA interference using nephrocyte-restricted drivers. Results Six novel homozygous and compound heterozygous NUP93 variants were detected in 3 sporadic and 2 familial paediatric onset SRNS characterised histologically by focal segmental glomerulosclerosis (FSGS) and progressing to kidney failure by 12 months from clinical diagnosis. Silencing of the two orthologs of human NUP93 expressed in D. melanogaster, Nup93-1, and Nup93-2 resulted in significant signal reduction of up to 82% in adult pericardial nephrocytes with concomitant disruption of NPC protein expression. Additionally, nephrocyte morphology was highly abnormal in Nup93-1 and Nup93-2 silenced flies surviving to adulthood. Conclusion We expand the spectrum of NUP93 variants detected in paediatric onset SRNS and demonstrate its incidence within a national cohort. Silencing of either D. melanogaster Nup93 ortholog caused a severe nephrocyte phenotype, signaling an important role for the nucleoporin complex in podocyte biology. Graphical Abstract A higher resolution version of the Graphical abstract is available as Supplementary information

Steroid-Resistant Nephrotic Syndrome Caused by NUP93 Pathogenic Variants

“…Our data are consistent with previous reports [ 5 , 6 , 7 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ], highlighting NUP93 variants as a cause of paediatric-onset SRNS. Interestingly, the individual described is heterozygous with two different variants.…”

“…Importantly, NUP93 , expressed in all kidney cell types [ 5 ], is involved in NPC assembly, and its mutations are the direct cause of the complex disruption triggering a distinct renal disease [ 6 ]. To date, 21 different NUP93 mutations are reported in 22 SRNS patients, with the most common variant, c.1772G>T, present in almost half of the described cases [ 7 ].…”

From the sideline: Tissue‐specific nucleoporin function in health and disease, an update

“…Since the first report by Braun et al, numerous mutations in NUP93 (Fig. 3, Table 1) have been identified in patients with SRNS or focal segmental glomeruloscelerosis (FSGS; MIM 603278), a precursor state of SRNS [73][74][75][76][77][78][79][80][81][82]). In SRNS, podocytes, specialised epithelial cells that line the nephrons of the kidney, are mainly affected.…”

JAK-STAT pathway activation compromises nephrocyte function in aDrosophilahigh-fat diet model of chronic kidney disease

“…Both cell types contain highly specialized filtration structures know as slit diaphragms that act in concert with the basement membrane; the fly lacuna channel is similar to the urinary space in the mammalian Bowman’s capsule; and, many key proteins for podocyte function are likewise essential for nephrocyte function (van de Leemput et al, 2022; Wang et al, 2021; Weavers et al, 2009; Zhuang et al, 2009). Indeed, fly in vivo nephrocyte models have been successfully used to study a variety of human kidney diseases, including forms of monogenic nephrotic syndrome and steroid-resistant nephrotic syndrome (SRNS) (Ashraf et al, 2013; Bierzynska et al, 2022; Fu et al, 2017; Gee et al, 2015, 2013; Gonçalves et al, 2018; Hermle et al, 2018, 2017; Milosavljevic et al, 2022; Odenthal et al, 2023; Paul et al, 2023; Zhao et al, 2019; Zhu et al, 2017). The recent study using the HFD Drosophila model recapitulated the ectopic lipid droplets and cellular dysfunction observed in chronic kidney disease and found that the adipose-derived triglyceride lipase protects nephrocyte endocytosis under HFD conditions (Lubojemska et al, 2021).…”