Steroid-resistant nephrotic syndrome (SRNS) is characterized by edema, nephrotic-range proteinuria, and hyperlipidemia. Mutations in approximately 45 different genes have been discovered as monogenic causes of SRNS1–38 (Supplemental Figure 1A) and our understanding of the pathophysiology of SRNS and podocyte biology in general has been formed by the pathways delineated by discovery of these genes (Supplemental Figure 1A).1,3 The first gene to be found was nephrin (NPHS1), which encodes a major constituent of the slit diaphragm.4 Subsequently, mutations of several proteins associated with the slit diaphragm complex were identified. Linking the slit diaphragm to the actin cytoskeleton to maintain the complex podocyte morphology seems essential because actin-binding and -regulating proteins form the most numerous group among the monogenic causes of SRNS.1,3 More recently, mutations in CoQ10-biosynthesis genes,14–16 nucleoporins,39–41 and the KEOPS complex42 have been discovered as further monogenic causes of SRNS. This opened new avenues toward a better understanding of the complex pathogenesis of SRNS.
A role of endocytosis for podocyte biology has previously been proposed: The slit diaphragm protein nephrin is subject to endocytosis utilizing different branches of the endocytosis pathway.43–48 In mice, phosphoinositide 3-kinases49,50 and effectors of vesicular fission and clathrin uncoating are essential for the glomerular filtration barrier. Knockout of the murine isoforms of dynamin, synaptojanin, or endophilin each resulted in severe proteinuria.51,52 In humans, no direct endosomal regulator has previously been implicated in nephrotic syndrome.
Approval for human subject research was obtained from the University of Michigan and the Boston Children’s Hospital Institutional Review Boards. All participants or their guardians provided written informed consent.
After informed consent, clinical data and blood samples were obtained from individuals with nephrotic syndrome. Clinical data were obtained using an established questionnaire (http://www.renalgenes.org). The diagnosis of NS was made by (pediatric) nephrologists, on the basis of standardized clinical and renal histologic criteria. Renal biopsy samples were evaluated by renal pathologists.
Homozygosity Mapping, Whole-Exome Resequencing, and Mutation Calling
Homozygosity mapping, whole-exome resequencing, and mutation calling were performed as described previously.22
Plasmids, siRNAs, Cell Culture, and Transfection
Human full-length GAPVD1 cDNA was subcloned after PCR from human full-length cDNA (GenBank BC114937; GE Dharmacon). Mouse Gapvd1 was subcloned after PCR from murine full-length cDNA (RefSeq NM_025709) that was a gift from Dr. Alan Saltiel53 (University of California, San Diego). Human ANKFY1 isoform 1 cDNA (GenBank BC152991.1) and human NPHS1 cDNA (GenBank: BC156935.1) were obtained from the Harvard PlasmID Repository. Truncation constructs were generated by PCR. Primers are shown in Supplemental Table 1. ANKFY1 rescue constructs were obtained by introduction of two synonymous mutations within the shRNA target sequences.
The following expression vectors were used: pRK5-N-Myc, pCDNA6.2-N-GFP, pQCXIP mCherry, and pSirenRetroQ. Clones reflecting the mutations identified in individuals with nephrotic syndrome were introduced into the cDNA constructs using Quik change II XL site-directed mutagenesis kit (Agilent Technologies). The following constructs were obtained from addgene: mCherry-Rab5CAQ79L (#35138), mCherry-Rab5DNS34N (#35139), mCh-Rab5 (#49201), pRK5myc Rac1 wt (#37030), and pSpCas9(BB)-2A-GFP (PX458) (#48138).
The GAPVD1- and ANKFY1-specific and control scrambled siRNAs were purchased from GE Dharmacon.
Overexpression experiments were performed in HEK293T cells (ATCC biologic resource center). Immortalized human podocytes were a gift from Dr. Moin Saleem (University of Bristol, Bristol, UK).
HEK cells were maintained in DMEM, supplemented with 10% FBS, 50 IU/ml penicillin, and 50 μg/ml streptomycin. Podocytes were maintained in RPMI 1640 plus GlutaMAX-I (Gibco) supplemented with 10% FBS, 50 IU/ml penicillin/50 μg/ml streptomycin, and insulin-transferrin-selenium-X.
Plasmids and siRNAs were transfected into HEK293T cells at 37°C or podocytes grown at the permissive temperature of 33°C using Lipofectamine 2000 or Lipofectamine RNAiMax, respectively (Invitrogen). Knockdown in human podocyte cell lines employed pSirenRetroQ with 2–3 independent shRNAs directed against human GAPVD1 or ANKFY1 for retroviral transduction. Puromycin was used to select transduced cells. Knockdown efficiency was confirmed for all experiments, shRNA targets are shown in Supplemental Table 1. For rescue experiments, knockdown podocytes underwent a transient transfection using murine Gapvd1 or human ANKFY1 constructs that are resistant to shRNA.
Immunoblotting, Immunoprecipitation, Pull-Down Assay, and Immunofluorescence Staining
Immunoblotting, immunoprecipitation, and immunofluorescence staining were performed as described previously.39 Briefly, HEK293T cells were lysed and precleared using rec-Protein A-Sepharose 4B Conjugate (Life Technologies) overnight. Then, equal amounts of protein were incubated with EZview Red Anti-c-Myc Affinity Gel (Sigma-Aldrich) or GFP-nAb (Allele Biotechnology). Coimmunoprecipitation (co-IP) experiments were performed in three independent experiments. Immunoblotting was performed using rabbit anti-GAPVD1 (#A302–116; Bethyl Laboratories), mouse anti-ANKFY1 (sc-393353; Santa Cruz Biotechnology), mouse anti–c-Myc (sc-40; Santa Cruz Biotechnology), rabbit anti–c-Myc (sc-789; Santa Cruz Biotechnology), mouse anti-GFP (sc-9996; Santa Cruz Biotechnology), rabbit anti-GFP (sc-8334; Santa Cruz Biotechnology), and rabbit anti-mCherry (ab167452; Abcam).
Immunofluorescence of ANKFY1 was performed with mouse anti-ANKFY1 (sc-393353). Rabbit anti-murine GAPVD1 was a kind gift from Dr. Alan Saltiel.53 Other antibodies used were guinea pig anti-NPHS1 (GP-N2; Progen) and rabbit anti-RAB5 (#ab18211; Abcam). Paraffin-embedded human tissue sections (HP-901; amsbio) were deparaffinized in xylene for 10 minutes, rehydrated, and antigen retrieval was performed by incubating the slides for 40 minutes at 95°C in citrate buffer, pH 6.0.
Fluorescent images were obtained with a Leica SP5X or a Zeiss LSM 880 laser scanning microscope.
RAB5 activity assay was performed using the Rab5 Activation Assay Kit (#83701; NewEast Biosciences) according to the manufacturer’s instructions. Protein concentrations were determined by Lowry’s method and equal amounts of protein were exposed to the RAB5-GTP–specific antibody.
Podocyte Dextran Internalization Assay
Human podocytes were exposed to culture medium containing 500 ng/ml Texas-Red-dextran 10 kD (ThermoFisher) for 30 minutes at 37°C. Afterward, cells were rinsed twice with ice-cold PBS, fixed in 4% paraformaldehyde for 15 minutes in the presence of Hoechst 33342 (1:1000), and mounted in Antifade Diamond (ThermoFisher). Cells were imaged using a Leica SP5X confocal microscope and uptake was quantified using ImageJ software in maximized intensity projections after thresholding.
Podocyte Migration Assay
Real-time migration assay was performed using the IncuCyte videomicroscopy system (Essen Bioscience) in 96-well plates according to the manufacturer’s instructions. Briefly, 24 hours after transfection scratch wounds were made using a 96-pin tool (WoundMaker) as per protocol. Cells were monitored automatically via live cell imaging and time-lapse images. Wound confluency was automatically acquired hourly and recorded by the IncuCyte software (ZOOM). Data processing and analysis for migration assay were performed using the IncuCyte 96-well Kinetic Cell Migration and Invasion Assay software module. Results are presented as time versus wound confluency.
Drosophila melanogaster stable RNAi stocks Gapvd1-RNAi 1 (#108453) and Gapvd1-RNAi 2 (#19649) were obtained from the Vienna Drosophila Resource Center. Prospero-GAL454 was used to control expression in garland cell nephrocytes; actin-GAL4 (#3954; Bloomington stock) was used for ubiquitous expression.
Fluorescent tracer uptake in nephrocytes was performed as previously described.55 Briefly, nephrocytes were dissected in PBS and incubated with FITC-albumin (Sigma) for 30 seconds. After a fixation of 5 minutes in 8% paraformaldehyde, cells were rinsed in PBS and exposed to Hoechst 33342 (1:1000) for 20 seconds and mounted in Antifade Diamond. Cells were imaged using a Leica SP5X confocal microscope. Quantitation of fluorescent tracer uptake was performed with ImageJ software. The results are expressed as a ratio to a control experiment with EGFP-RNAi that was done in parallel.
For immunohistochemistry, nephrocytes were dissected, fixed for 15 minutes in PBS containing 4% paraformaldehyde, and stained according to the standard procedure. The following primary antibodies were used: rabbit anti-sns56 (1:500, gift from S. Abmayr) and guinea pig anti-Kirre57 (1:200, gift from S. Abmayr). For imaging, a Leica SP5X confocal microscope was used. Image processing was done by ImageJ and Adobe Photoshop CS4 software.
For transmission electron microscopy (TEM), nephrocytes were dissected and fixed in 4% formaldehyde and 0.5% glutaraldehyde in 0.1 M cacodylate buffer, pH 7.4. TEM was carried out using standard techniques. One complete diameter of six cells from three different animals was analyzed for ectopic slit diaphragms. Areas where the labyrinthine channels are cut obliquely are recognizable by elongated stretches of higher electron density along the cell surface. These areas were excluded from the quantitation.
Quantitative Real-Time PCR
Total RNA was isolated using TRIzol (Invitrogen) and purified with the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. Real-time PCR was performed using Taqman probes (ThermoFisher Scientific). The RPL39 gene was used to normalize expression data.
Paired t test was used to determine the statistical significance between two interventions. ANOVA followed by Dunnett’s correction (unless otherwise indicated) was used for multiple comparisons (GraphPad Prism software). Asterisks indicate significance as follows: *P<0.05, **P<0.01, ***P<0.001. A statistically significant difference was defined as P<0.05. Error bars indicate SD.
Mutations in GAPVD1 and ANKFY1, Two RAB5 Interactors, in Families with Nephrotic Syndrome
To discover novel monogenic causes of SRNS, we performed whole-exome sequencing (WES) in a cohort of 665 patients. We identified two homozygous missense mutations (p.Leu414Val and p.Arg937Gln) of the gene GTPase Activating Protein And VPS9 Domains 1 (GAPVD1) in two individuals (A4619 and B1391) with early-onset nephrotic syndrome (Figure 1A, Supplemental Figures 1, B–D, G–J, and 2, A and B, Table 1). The respective amino acid residues are conserved to C. intestinalis for both mutations (Figure 1, A, C, and D, Table 1) and causative mutations are located within a homozygosity peak (Supplemental Figure 2, A and B). The families were of Mexican and Arabic descent, respectively (Table 1). One patient (A4619) showed the unusual clinical course of congenital nephrotic syndrome with spontaneous remission after 18 months (Table 1), whereas nephrotic syndrome persisted in the other case after 2 years of observation. Spontaneous remission of congenital nephrotic syndrome has previously been described in certain alleles of nephrin (NPHS1).58–63 Neither patient exhibited extrarenal manifestations. The histology in both cases was characterized by mesangial hypercellularity with expansion of the extracellular matrix (Figure 1, F and G, Supplemental Figure 1, G–J). This uncommon histologic pattern is suggestive of glomerular injury and is frequently observed with mutations of nephrin.64,65 TEM revealed foot process effacement (Figure 1, I and J). Renal ultrasound of both cases showed increased echogenicity (Figure 1K, Table 1).
Table 1. -
Mutations in GAPVD1
, in four individuals from three families with SRNS
||Amino Acid Change
||Amino Acid Conserved to Species
||Response to Steroids
||Age of Onset (Proteinuria)
||FSGS (11 yr)
PPH2, PolyPhen-2 prediction score (http://genetics.bwh.harvard.edu/pph2/
); SIFT, Sorting Tolerant From Intolerant prediction score (http://sift.jcvi.org/
); MT, Mutation Taster (http://www.mutationtaster.org/
); ExAC, Exome Aggregation Consortium database (http://exac.broadinstitute.org
); gnomAD, Genome Aggregation Database (http://gnomad.broadinstitute.org
); Hom, homozygous; Tol, tolerated; DC, disease causing; C.i.
, Ciona intestinalis
; F, female; Del, deleteriousness; D.m
., D. melanogaster
; M, male; ND, no data.
aProteinuria spontaneously resolved age 18 mo.
bKidneys enlarged on renal ultrasound.
GAPVD1 has been described as an endosomal regulator that interacts with RAB5.53,66–71 GAPVD1 harbors both a GTPase activating and an inactivating domain, the RasGAP and VPS9 domains, respectively (Figure 1A). An activating role as a guanine nucleotide exchange factor (GEF) for RAB5 has been suggested.66,70
In an unbiased approach by WES, we further identified a homozygous mutation of the gene Ankyrin Repeat And FYVE Domain Containing 1 (ANKFY1) in two siblings of a family with FSGS and proteinuria (Figure 1B, Table 1). Similar to GAPVD1, ANKFY1 interacts with RAB5, serving as a versatile RAB5 effector.72–75 The identified mutation (p.Arg95Leu) is conserved to D. melanogaster and locates within a homozygosity peak that is shared between both siblings (Supplemental Figure 2, C and D). Renal biopsy revealed FSGS (Figure 1H). Renal ultrasound was without pathologic findings (Supplemental Figure 1F).
Sanger sequencing of parental DNA confirmed segregation of the mutations according to the status of affection for the families B1391 and B1027, whereas parental DNA could not be obtained for A4619 (Supplemental Figure 1). WES detected no other likely causative mutations in our patients.
We thus identify mutations of GAPVD1 as a novel monogenic cause of early-onset nephrotic syndrome, and ANKFY1 most likely shares this role. Interestingly, both encoded proteins play a regulatory role for RAB5.
GAPVD1 and ANKFY1 Are Interaction Partners and Colocalize in HEK293T Cells
All genes that may cause monogenic SRNS in humans are expressed in podocytes.3 Immunoblotting revealed expression of GAPVD1 and ANKFY1 in immortalized podocytes (Figure 2, A and B) and also in HEK293T cells (Figure 2, C and D).
Next, we explored the subcellular localization of GAPVD1. Overexpression constructs of GAPVD1, including constructs representing the patient mutations, predominantly localized to the cytosol (Figure 2E, Supplemental Figure 3, A–C). Truncations of GAPVD1 lacking the RasGAP domain localized to (RAB5-positive) vesicles (Supplemental Figure 3, D–F), although deleting the VPS9 domain had no overt effect (Supplemental Figure 3G). Eight different antibodies detected overexpressed GAPVD1 in podocytes using immunofluorescence but never the endogenous protein (data not shown).
We analyzed the subcellular localization of ANKFY1 in podocytes using a conditional CRISPR/Cas approach.76 ANKFY1 was observed in intracellular vesicles that were absent from the gRNA/GFP-expressing cells (Figure 2, F and F’). Applying Airyscan technology for enhanced resolution in human tissue sections, we confirmed a vesicular staining pattern of ANKFY1 in podocytes that was absent in the control (Figure 2, G–H’’). GFP-tagged overexpression constructs of ANKFY1 localized to vesicles in cultured human podocytes that in turn fully colocalized with mCherry-RAB5 (Supplemental Figure 4, A–B’’), whereas endogenous RAB5 and ANKFY1 showed partial colocalization (Supplemental Figure 4, C–C’’). The deletion of the FYVE domain of ANKFY1 abrogated vesicular localization of overexpressed ANKFY1 (Supplemental Figure 4, D and E), whereas the patient mutation ANKFY1-R95L showed no overt mislocalization (Supplemental Figure 4F). We conclude that the SRNS-causing mutation does not alter endosomal localization of ANKFY1.
Studying HEK293T cells, we noted that overexpressed GFP-ANKFY1 and mCherry-GAPVD1 colocalize completely (Figure 2, I and J), whereas Mock-mCherry (Figure 2, K and L) showed partial colocalization. In cultured podocytes, tagged overexpression constructs of both proteins partially colocalized (Supplemental Figure 4, G–G’’). The extent of colocalization of GAPVD1 and ANKFY1 thus appears cell-type dependent.
We hypothesized that GAPVD1 and ANKFY1 proteins interact. Using co-IP, we demonstrated interaction between GFP-GAPVD1 and Myc-ANKFY1 (Figure 2M). Reciprocally, GFP-ANKFY1 precipitates Myc-GAPVD1 (Supplemental Figure 5A). Introducing the mutations of GAPVD1 that caused nephrotic syndrome reduced binding of GAPVD1 to ANKFY1 (Figure 2N, quantitation Figure 2O). These mutations thus weaken the interaction of GAPVD1 with ANKFY1.
GAPVD1 Interacts with Nephrin
Nephrin is subject to endocytosis51 and IQGAP1, another RasGAP domain protein, interacts with nephrin.77 We therefore hypothesized that GAPVD1 might interact with nephrin. Performing co-IP experiments in HEK293T cells, we found that Myc-nephrin precipitated with GFP-GAPVD1 (Figure 3A). The reverse experiment confirmed this finding (Supplemental Figure 5B).
Analyzing the GAPVD1 patient mutations R937Q and L414V, we observed a significantly reduced binding to Myc-nephrin for cDNA constructs reflecting these mutations (Figure 3B, quantitation Figure 3C). The mutations of GAPVD1 that cause nephrotic syndrome thus affect the interaction with nephrin.
To map the interacting domains on GAPVD1, we performed truncation mapping by co-IP and found that the RasGAP domain of GAPVD1 (aa 1–458) and the VPS9 domain of GAPVD1 (aa 1355–1460) were precipitated by full-length nephrin, whereas the large interjacent domain of GAPVD1 (aa 458–1355) was not (Figure 3, D and F). Each of the functional domains of GAPVD1 seem to be sufficient for interaction with nephrin (Figure 3, D and F).
We similarly employed truncation mapping for nephrin. The N-terminal half of the cytosolic domain (intracellular domain, ICD) of nephrin (nephrin aa 1084–1160) was precipitated by Myc-GAPVD1, whereas Mock-GFP or the C-terminal half of the ICD (aa 1160–1241) were not (Figure 3, E and G). Consequently, we found that a nephrin lacking the last 82 aa (R1160Stop) shows robust interaction with GAPVD1 (Supplemental Figure 5C). We conclude that a domain of 76 residues located at the N-terminal half of the ICD of nephrin (aa 1084–1160) is sufficient for GAPVD1 interaction.
GAPVD1 and Nephrin Partially Colocalize in Newborn Rat Glomeruli
To analyze the localization of GAPVD1 in vivo together with nephrin, we stained newborn rat kidney sections using antibodies directed against nephrin and murine Gapvd1.53 The control staining (Figure 3, H–I’’) resulted in virtual absence of a fluorescent signal, whereas the antibody recorded at identical confocal settings revealed expression of GAPVD1 in podocytes and mesangial cells. Interestingly, GAPVD1 and nephrin partially colocalize in podocytes, further supporting a functional connection between these proteins.
Mutations of GAPVD1 that Cause Nephrotic Syndrome Increase Binding to Active RAB5
RAB5 exists in a GTP-bound active state and a GDP-bound inactive state (Figure 4A). As is characteristic for a GEF, GAPVD1 was shown to specifically bind to inactive RAB5.53,66,70 To test if the GAPVD1 mutations alter the RAB5 interaction, we performed co-IP using constitutively active and dominant negative cDNA constructs of RAB5. These RAB5 derivatives with substitution of a single amino acid are locked in the active and inactive state, respectively (Figure 4B). We quantified the relative density of the respective RAB5 constructs that precipitated with GAPVD1. The low active/inactive RAB5 ratio of wild-type GAPVD1 confirms the published findings (Figure 4C, quantitation in Figure 4D). Evaluating the mutants R937Q and L414V in this fashion, we observed a significantly higher ratio indicating an increased binding of mutant GAPVD1 to active RAB5. The mutations that cause nephrotic syndrome thus impair the specificity of GAPVD1 for inactive RAB5. Further, we observed strongly reduced binding of the mutant ANKFY1-R95L to active RAB5 (Figure 4E, quantitation Figure 4F). The patient mutations of both genes thus alter RAB5-binding.
To analyze the functional consequence of the altered RAB5 interaction of the GAPVD1 mutations, we used a RAB5 activity assay that employs a RAB5-GTP–specific antibody. We observed an increase of active RAB5 compared with wild-type GAPVD1 for mutation R937Q but not L414V (Supplemental Figure 6A, quantitation Supplemental Figure 6B). In this assay, we observed a relative increase of mutant GAPVD1 precipitating with active RAB5 (Supplemental Figure 6A). This suggests increased binding to endogenous RAB5-GTP.
RAB5 is an essential regulator of endocytosis. To evaluate endocytic activity in podocytes, we applied Texas-Red-dextran (10 kD). The extent of tracer endocytosis reflects fluid-phase endocytosis. We observed reduced tracer uptake upon CRISPR/Cas-mediated loss of function of GAPVD1 (Figure 4, G–I). GAPVD1 thus appears to promote endocytic activity. Surprisingly, overexpression of GAPVD1 did not result in increased RAB5 activity or increased uptake of dextran (Supplemental Figure 6, A–E).
Analysis of Podocyte Migration Rate Indicates Functional Significance of the Patient Mutations of GAPVD1 and ANKFY1
The evaluation of podocyte migration rate is an established functional assay in podocyte cell lines and has been extensively used to characterize the deleteriousness of monogenic mutations in SRNS genes.2,7,14,22,24,32,38 To analyze the role of GAPVD1, we generated stable shRNA-expressing human podocyte lines and measured the podocyte migration rate using the IncuCyte videomicroscopy system. Two independent shRNAs caused a reduced podocyte migration rate (Supplemental Figure 7, A–G). Transient expression of a murine wild-type Gapvd1 cDNA construct rescued the reduced migration rate, whereas constructs corresponding to the patient mutations resulted in a partial rescue. This indicates a hypomorphic function of these alleles regarding podocyte migration rate (Figure 5, A–E, quantitation in Figure 5F). Knockdown and expression of the rescue constructs was confirmed by immunoblotting (Supplemental Figure 7, A and B).
To analyze a role of ANKFY1 for podocyte migration, we generated shRNA directed against human ANKFY1 and confirmed efficient silencing (Supplemental Figure 8A). Upon knockdown of ANKFY1, we observed a significantly reduced podocyte migration rate for three independent shRNAs (Supplemental Figure 8, C–G). ANKFY1, similar to GAPVD1, is thus required for podocyte migration. Transient expression of shRNA-resistant ANFKY1 completely rescued the reduced migration, whereas introducing the mutation R95L into the rescue construct abrogated the ability to rescue. This indicates a pronounced functional effect of this mutation (Figure 5, G–J, quantitation Figure 5K). The expression of the rescue constructs was verified by immunoblotting (Supplemental Figure 8B).
Silencing the Drosophila Ortholog of GAPVD1 Impairs Nephrocytes and Results in Mislocalization of Fly Nephrin
To further validate a causative role of GAPVD1 for hereditary nephrotic syndrome, we employed the Drosophila model. Garland cell nephrocytes are podocyte-like cells that are an established model for glomerular disease,54,78 including monogenic SRNS.55 In nephrocytes, the ortholog of nephrin forms autocellular slit diaphragms across membrane invaginations called labyrinthine channels.54,55,78
By sequence analysis, we identified the uncharacterized Drosophila gene CG1657 as the ortholog of human GAPVD1 (Figure 6A). This gene encodes a protein of 1712 aa that contains both a RasGAP and a VPS9 functional domain. We introduce the term Gapvd1 for the Drosophila ortholog CG1657.
To analyze conservation of a functional role of the ortholog of GAPVD1 in this Drosophila model, we expressed two independent RNAis directed against Gapvd1 in nephrocytes. Using the established read-out of FITC-albumin endocytosis,55 we observed significantly reduced nephrocyte function for both Gapvd1-RNAi lines (Figure 6, B and C). Knockdown efficiency was confirmed by quantitative PCR (Supplemental Figure 9D). Staining the slit diaphragm proteins Sns (ortholog of nephrin) and Kirre (ortholog of NEPH1), we found both slit diaphragm proteins to adhere to the nephrocyte surface in a fine, well defined line under control conditions (Figure 6, D–D’’). Silencing of Gapvd1 resulted in the appearance of subcortical vesicles/puncta and the line of slit diaphragm proteins appeared distorted, including protrusions from the surface toward the interior of the cell (Figure 6, E–E’’). To visualize the slit diaphragms directly, we performed TEM. In control nephrocytes, slit diaphragms were formed at regular intervals along the surface but never ectopically. Labyrinthine channels were narrow and limited to the cortical area of the cell (Figure 6F). Upon knockdown of Gapvd1, the slit diaphragms on the surface were formed properly but ectopic slit diaphragms appeared in addition (Figure 6, G and H). On average, about one ectopic slit diaphragm per micrometer surface area was formed upon Gapvd1-silencing, whereas ectopic slit diaphragms were absent in control nephrocytes (Figure 6I). The mislocalized slit diaphragms correspond to the protrusions of slit diaphragm proteins that were observed by immunofluorescence. We did not detect a transcriptional upregulation of the ortholog of nephrin upon Gapvd1 silencing (Supplemental Figure 9D), suggesting that the excess of nephrin reflects reduced protein degradation.
TEM further revealed that the labyrinthine channels became strongly dilated and protruded deeper into the cell (Figure 6, G and H). These enlarged channels impressed as cortical areas of reduced electro-density in lower magnifications that were absent from control cells (Figure 6, J and K). Because the channel formation is dependent on the slit diaphragm proteins, the enlarged channels are potentially caused by the ectopic formation of slit diaphragms.
We performed immunostaining of Sns/Kirre and TEM upon expression of a second, independent RNAi line and observed a similar phenotype to the first Gapvd1-RNAi (Supplemental Figure 9, A–C). Taken together, these findings imply that loss of Gapvd1 impairs the function of the podocyte-like nephrocytes and results in altered trafficking of the ortholog of nephrin.
Here, we describe the discovery of recessive mutations in GAPVD1 and likely also ANKFY1 as novel monogenic causes of hereditary nephrotic syndrome in humans. Interestingly, we found that both proteins are interaction partners that are expressed in podocytes. We demonstrate that GAPVD1 interacts with nephrin and both proteins partially colocalize in rat glomeruli. Overexpressing GAPVD1 that reflects mutations from patients with nephrotic syndrome resulted in reduced ANKFY1 and nephrin affinity, whereas the mutations conversely increased binding to GTP-bound RAB5. GAPVD1 and ANKFY1 were required for podocyte migration and this assay indicated functional significance for the mutations of both genes. Finally, silencing the ortholog of GAPVD1 in Drosophila nephrocytes impaired tracer uptake in these podocyte-like cells and resulted in mislocalization of fly nephrin.
Our findings implicate RAB5 regulation in human hereditary nephrotic syndrome. The interaction of GAPVD1 and nephrin suggests that endocytic trafficking of nephrin may play a role in an RAB5-mediated pathogenesis. Consistent with such a role, the mutations that we discovered in our patients affected RAB5 binding and the interaction with nephrin. This is supported by our findings in Drosophila nephrocytes, where slit diaphragms are mislocalized. This may be caused by a lack of endocytic removal of ectopic fly nephrin and/or impaired degradation. Ectopic slit diaphragms have been reported in pericardial nephrocytes upon silencing of RAB7, which blocks endo-lysosomal function further downstream.79 From these findings we derived a hypothetic working model (shown in Supplemental Figure 10). In line with previous reports,43–48,51,80,81 our data thus underscore the importance of the endocytic pathway for nephrin trafficking. This pathway may further be involved in the delivery of nephrin to the slit diaphragm and/or slit diaphragm maintenance by endocytic turnover. Similar to dynamin, endophilin, and synaptojanin,52GAPVD1 has been implicated in clathrin uncoating71 but a connection with these proteins currently remains unclear. Actin regulation and endocytosis are intertwined, and RAB5 also promotes activation of RAC1.82 As suggested by the effect on podocyte migration rate, actin dysregulation thus may contribute to the roles of GAPVD1 and ANKFY1 in nephrotic syndrome.
Endocytosis is a fundamental cellular process. Although it may seem surprising that recessive mutations in a RAB5 regulator such as GAPVD1 manifest exclusively as nephrotic syndrome, the functional redundancy with RAB5-GEFs like RIN1, ALS2, and RABGEF1 may compensate for most cellular functions. Similarly, a complete GAPVD1 knock out was found to be viable in Caenorhabditis elegans.70
GAPVD1 and ANKFY1 appear to be rare causes of nephrotic syndrome. This is consistent with a number of recently discovered novel monogenic causes1,19,22,24,32 that are similarly uncommon. Nevertheless, the identification of monogenic causes, including the less frequent ones, has shaped our understanding of podocyte biology.3 In conclusion, our findings implicate two RAB5-interacting proteins in hereditary nephrotic syndrome and suggest RAB5 regulation as a novel pathogenetic mechanism.
Human GAPVD1 full-length protein is GenBank accession number NM_015635.3.
Human ANKFY1 full-length is GenBank accession number NM_001257999.2.
F.H. is a cofounder of Goldfinch-Bio and receives royalties from Claritas. The remaining authors declare that they have no competing financial interests.
We are grateful to the families and study individuals for their contribution. We thank the Yale Center for Mendelian Genomics and the Broad Center for Mendelian Genomics for whole-exome sequencing analysis. F.H. is the William E. Harmon Professor. We thank R. Nitschke, Life Imaging Centre, University of Freiburg, for help with confocal microscopy.
This research was supported by grants from the National Institutes of Health to F.H. (DK076683), H.L.R., and D.M. (UM1 HG008900), and to the Yale Center for Mendelian Genomics (U54HG006504); by the Deutsche Forschungsgemeinschaft (DFG) to T.H. (HE 7456/1-1), A.T.v.d.V. (VE916/1-1), and T.J.-S. (Jo 1324/1-1); by the Iinuma-Tsuchiya Foundation for Overseas Research to M.N.; and by the German National Academy of Sciences Leopoldina to E.W. (LPDS-2015-07). The Broad Center for Mendelian Genomics was funded by the National Human Genome Research Institute, the National Eye Institute, and the National Heart, Lung, and Blood Institute.
T.H., R.S., S.S., D.S., D.A.B., J.K.W., A.D., A.T.v.d.V., E.W., M.N., T.J.-S., A.J.M., J.R., S.A., R.P.L., S.M., K.L., M.L., D.M., and H.L.R. generated total genome linkage analysis, performed exome capture and massively parallel sequencing, and performed whole-exome evaluation and mutation analysis. R.S. and T.H. performed cDNA cloning, protein purification, tracer endocytosis and immunofluorescence, and subcellular localization studies in cell lines by confocal microscopy. R.S., E.W., and A.T.v.d.V. performed migration assays in immortalized human podocytes. T.H. and R.S. performed coimmunoprecipitation and the experiments in Drosophila. V.T., J.D.H., A.B., S.E.D., J.A.K., V.T., and F.H. recruited patients and gathered detailed clinical information for the study. L.S.F. and S.M.J. analyzed renal histology and electron microscopy and provided images. F.H. conceived of and directed the study. T.H. wrote the manuscript with help from F.H. The manuscript was critically reviewed by all of the authors.
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