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Letter
Nature Genetics  34, 455 - 459 (2003)
Published online: 20 July 2003; | doi:10.1038/ng1216

Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis

Heike Olbrich1, 8, Manfred Fliegauf1, 8, Julia Hoefele2, Andreas Kispert3, Edgar Otto2, Andreas Volz1, Matthias T Wolf2, Gürsel Sasmaz1, Ute Trauer4, Richard Reinhardt4, Ralf Sudbrak4, Corinne Antignac5, Norbert Gretz6, Gerd Walz7, Bernhard Schermer7, Thomas Benzing7, Friedhelm Hildebrandt2 & Heymut Omran1

1 Department of Pediatrics and Adolescent Medicine, University Hospital Freiburg, 79106 Freiburg, Germany.

2 Departments of Pediatrics and Human Genetics, University of Michigan, Ann Arbor, Michigan, USA.

3 Institut für Molekularbiologie, Medizinische Hochschule Hannover, Germany.

4 Max-Planck Institute for Molecular Genetics, Berlin, Germany.

5 INSERM U574, Department of Genetics, Necker Hospital, Paris 5 University, Paris, France.

6 Medical Research Center, Klinikum Mannheim, University of Heidelberg, D-68167 Mannheim, Germany.

7 Renal Division and Center for Clinical Research, University Hospital Freiburg, 79106 Freiburg, Germany.

8 These authors contributed equally to this work.

Correspondence should be addressed to Heymut Omran omran@kikli.ukl.uni-freiburg.de
Nephronophthisis (NPHP), a group of autosomal recessive cystic kidney disorders, is the most common genetic cause of progressive renal failure in children and young adults1. NPHP may be associated with Leber congenital amaurosis, tapeto-retinal degeneration, cerebellar ataxia, cone-shaped epiphyses, congenital oculomotor apraxia and hepatic fibrosis2, 3, 4, 5, 6. Loci associated with an infantile type of NPHP on 9q22−q31 (NPHP2), juvenile types of NPHP on chromosomes 2q12−q13 (NPHP1) and 1p36 (NPHP4) and an adolescent type of NPHP on 3q21−q22 (NPHP3) have been mapped7, 8, 9, 10. NPHP1 and NPHP4 have been identified11, 12, 13, and interaction of the respective encoded proteins nephrocystin and nephrocystin-4 has been shown13. Here we report the identification of NPHP3, encoding a novel 1,330-amino acid protein that interacts with nephrocystin. We describe mutations in NPHP3 in families with isolated NPHP and in families with NPHP with associated hepatic fibrosis or tapeto-retinal degeneration. We show that the mouse ortholog Nphp3 is expressed in the node, kidney tubules, retina, respiratory epithelium, liver, biliary tract and neural tissues. In addition, we show that a homozygous missense mutation in Nphp3 is probably responsible for the polycystic kidney disease (pcy) mouse phenotype14. Interventional studies in the pcy mouse have shown beneficial effects by modification of protein intake and administration of methylprednisolone15, 16, 17, suggesting therapeutic strategies for treating individuals with NPHP3.

Using a homozygosity mapping strategy in a Venezuelan kindred with adolescent NPHP (V1), we previously localized NPHP3 to chromosome 3q (ref. 10). Subsequent linkage analysis in a consanguineous German family (F1) showed that a locus associated with NPHP and associated Leber congenital amaurosis called Senior−Løken syndrome (SLSN3) also maps to the NPHP3 region (Fig. 1; ref. 18). We recently excluded KIAA0678, encoding a protein with a DnaJ-like motif, as a candidate for NPHP3 and associated syndromes19. We used haplotype analyses with additional polymorphic markers for the Venezuelan kindred with NPHP (V1) and a Tunisian family with SLSN3 (F353) to further restrict the critical regions of NPHP3 (novel centromeric flank D3S1541) and SLSN3 (novel telomeric flank D3S2322), respectively (data not shown). We focused the gene search on the genomic interval overlapping the NPHP3 and the SLSN3 locus, which spans less than 1 cM and comprises 940 kb (Fig. 1a).

Figure 1. Genomic region and gene structure of NPHP3 and putative protein structure of NPHP3.
Figure 1 thumbnail

(a) The critical regions of SLSN3 and NPHP3 are shown by horizontal bars. Polymorphic microsatellite markers (D3S1541, D3S2322) used to narrow down the critical regions are indicated. (b) NPHP3 consists of 27 exons and one additional exon 3b. Alternative splice variants and transcripts involving exon 3b, 13 and 15 and FLJ12592 are shown. Transcripts that involve NPHP3 and the neighboring gene FLJ12592 (AB082531, AY257867) indicate that both genes may belong to one gene unit. (c) Schematic drawing of the domain structure of the putative NPHP3 protein (nephrocystin-3). CC, coiled coil domain; TTL, tubulin-tyrosine ligase domain; TPR, tetratrico peptide repeat domain.



Full FigureFull Figure and legend (35K)
Mutational screening in four families with NPHP10, 18, 20 identified a homozygous obligatory splice acceptor site mutation in family F624 (Supplementary Fig. 1 online) in a new gene, designated NPHP3. Extending our sequence analysis, we found mutations in NPHP3 in nine unrelated families with NPHP (Table 1). In three families, we detected mutations on both alleles explaining the recessive phenotype in these families (Supplementary Fig. 1 online). We found that affected individuals in the Venezuelan kindred (V1), which previously enabled localization of the NPHP3 locus, were homozygous with respect to a deletion of 3 bp. In a family with NPHP and hepatic fibrosis (F23), we detected two heterozygous mutations that segregated with disease status in the family. A nonsense mutation was present on one allele. The mutation on the other allele resulted in a substitution of an evolutionary conserved amino acid residue (S360T). In six families, we observed different missense mutations on only one allele, leaving the mutation on the second allele unidentified. Most detected mutations affected amino acids that are evolutionarily conserved (Supplementary Fig. 2 online). Single-nucleotide polymorphism analysis did not indicate parental non-contribution suggestive of heterozygous deletions. Thus, unidentified mutations may reside in the non-coding regulatory region and in introns. We did not detect mutations in NPHP3 in two families with SLSN3 (F1 and F353). This raises the possibility that another gene located near NPHP3 is responsible for the association of NPHP and Leber congenital amaurosis.

Table 1. Clinical and genetic information in patients with NPHP3 mutations
Table 1 thumbnail

Full TableFull Table
The NPHP3 genomic region comprises 27 exons and spans 40.5 kb (Fig. 1a). The longest transcript of NPHP3 contains an open reading frame of 3,990 nucleotides encoding a protein with 1,330 amino acids (Supplementary Fig. 2 online). An additional exon 3b predicts premature termination of translation. Other in-frame splice variants involve exons 13 and 15 (Fig. 1b). The EST clone AB082531, which contains almost the entire coding region except the stop codon of NPHP3, continues with the cDNA sequence corresponding to exon 2 of the neighboring gene FLJ12592 (Fig. 1b). We confirmed the existence of such in-frame transcripts by PCR amplification on kidney and testis cDNA libraries, which indicates that both genes may belong to one gene unit. Sequence analysis of FLJ12592 in families with NPHP identified no mutations.

Renal pathology in adolescent NPHP is characterized by alterations of tubular basement membranes, tubular atrophy and dilatation, sclerosing tubulointerstitial nephropathy and renal cyst development predominantly at the cortico-medullary junction10. This phenotype resembles that observed in the recessive pcy mouse mutant21. We recently showed homology between the pcy locus on mouse chromosome 9 and the human NPHP3 locus21. Therefore, we considered the mouse ortholog of NPHP3 (Nphp3) a strong candidate to harbor the pcy mutation.

We obtained a full-length cDNA for Nphp3 with an open reading frame of 3,972 nucleotides encoding a protein with 1,324 amino acids. Human NPHP3 and mouse Nphp3 show 88% sequence identity (92% similarity), which indicates a high degree of evolutionary conservation (Supplementary Fig. 2 online). Nphp3 sequence analysis in pcy mice identified one homozygous mutation (Supplementary Fig. 1 online), which was absent in 22 different mouse strains including the diabetic KK strain, in which the spontaneous pcy mutation initially arose14. This mutation predicts the exchange of a conserved amino acid (I614S). By analogy to human NPHP3 mutations, which mostly consist of missense mutations involving conserved amino acids, the identified mutation in the pcy mouse probably causes the cystic kidney disease (pcy) phenotype (Supplementary Fig. 2 online). The finding that mutations of NPHP3 orthologs underlie both human NPHP and the mouse pcy phenotype might have clinical implications, because interventional studies in pcy mice have indicated a slowing of disease progress by diet modification, including protein restriction and soy protein application15, 16, and administration of methylprednisolone17.

Northern-blot analysis showed moderate expression of two primary transcripts of approx6.5 kb and approx8.0 kb in all studied tissues (Fig. 2a). The 6.5-kb transcript matches the size of the complete NPHP3 cDNA. The 8.0-kb transcript could represent an incompletely spliced transcript containing intron 3, as present in EST clone AL832877 (Fig. 1). Analysis of the same northern blot with a FLJ12592 probe showed only smaller transcripts (data not shown), indicating that transcripts comprising both NPHP3 and FLJ12592 are only rarely generated. NPHP3 expression resembles that of NPHP1 and NPHP4, genes known to be mutated in NPHP and tapeto-retinal degeneration11, 12, 13. To characterize expression on a cellular level, we carried out in situ hybridization analysis of mouse Nphp3 (Fig. 2). In gastrulation-stage embryos, expression was confined to the node between 7.5 and 8.25 days post coitum (d.p.c.). In sections of 14.5 and 16.5 d.p.c. embryos, strong expression was found in neural tissue (brain and ganglions). Other weaker expression domains included kidney tubules, retina, respiratory epithelium, biliary tract and liver (Fig. 2 and data not shown). In the adult kidney, we observed weak but specific expression in distal tubules located at the cortico-medullary border, which corresponds to the site of cyst formation in adolescent NPHP. Expression in retina and liver is in agreement with associated tapeto-retinal degeneration or hepatic fibrosis in individuals with mutations in NPHP3 (Table 1).

Figure 2. Expression analysis of human NPHP3 and its mouse ortholog Nphp3.
Figure 2 thumbnail

(a) Adult tissue northern blot of NPHP3. Heart, placenta, lung and skeletal muscle show a predominant expression of a transcript of approx6.5 kb; in brain, a transcript of approx8.0 kb is more abundant. In liver, kidney and pancreas, both forms are equally expressed. RNA size markers are indicated. (b) Whole-mount in situ hybridization analysis of Nphp3 in early gastrulation−stage mouse embryos. Nphp3 expression is restricted to the node (arrow) in a 7.75 d.p.c. embryo. (c) Expression in developing kidney tubules (lower arrow) and spinal ganglia (upper arrows) in a 16.5 d.p.c. embryo. (d) Expression in the adult kidney is predominantly located in tubular structures at the cortico-medullary border (between arrows). Expression in retina (e), respiratory epithelium (f), and biliary tract (arrow) and liver (g) of a 16.5 d.p.c. embryo is shown.



Full FigureFull Figure and legend (36K)
The similar phenotype of adolescent and juvenile NPHP suggests that the products of the NPHP genes may function in a common pathway. We therefore examined whether NPHP3 (nephrocystin-3) interacts with NPHP1 (nephrocystin). We coexpressed different truncations of nephrocystin-3 with nephrocystin in HEK 293T cells. Epitope-tagged nephrocystin coprecipitated with nephrocystin-3 but not with control proteins (Fig. 3). Truncations of nephrocystin-3 indicated that the interaction can be mapped to amino acids 517−841.

Figure 3. Interaction of NPHP3 and NPHP1.
Figure 3 thumbnail

Myc-tagged nephrocystin (NPHP1) was coexpressed with different N-terminally FLAG-tagged nephrocystin-3 truncations (FLAG−NPHP3) or FLAG-tagged TRAF2 protein (FLAG−TRAF2) as a negative control. (a) After immunoprecipitation with antibody to FLAG, coprecipitating nephrocystin was detected with nephrocystin-specific antiserum. (b) Expression of proteins in cellular lysates was confirmed by immunoblotting with nephrocystin. (c) As control, FLAG-specific antibodies detected precipitated NPHP3 truncations. Numbers indicate amino acid positions of nephrocystin-3. The additional band of approx60 kDa visible in all lanes represents the heavy chain.



Full FigureFull Figure and legend (64K)
TgN737Rpw encodes a ciliary intraflagellar transport protein22 and has an expression pattern similar to that of Nphp3, including nodal expression23. The hypomorphic mutation TgN737Rpworpk causes cystic kidney disease, tapeto-retinal degeneration, skeletal deformity and biliary duct hyperplasia in mice24. Loss-of-function mutations of the cystic kidney disease genes TgN737Rpw and Pkd2 result in embryonic lethality and randomization of left/right body asymmetry23, 25. Furthermore, the respective gene products have been sublocalized to renal monocilia26. We did not detect loss-of-function mutations on both alleles of NPHP3 in individuals with NPHP3 or in pcy mice, suggesting that recessive loss-of-function mutations might be embryonic lethal. This could also explain the absence of situs inversus in individuals with NPHP3 and pcy mice.

To obtain further insights into the potential role of nephrocystin-3, we used computer programs to predict functional domains (Fig. 1c). An N-terminal coiled coil region also present in NPHP1 (ref. 11) and a C-terminal tetratrico peptide repeat domain also found in Tg737 (ref. 22) might function in protein-protein interactions. But these regions do not map to the site of interaction between nephrocystin and nephrocystin-3. Notably, a tubulin-tyrosine ligase domain27, which might carry out posttranslational modification of alpha-tubulin by C-terminal tyrosination involved in microtubule organization and function, is predicted at the site of interaction. Microtubule regulation mediated by nephrocystin-3 might have a role in renal monocilia or in cell-cell and cell-matrix signaling, as was shown for the docking complex protein nephrocystin, which also interacts with nephrocystin-4, p130Cas, tensin and focal adhesion kinase-2 (refs. 13,28,29). Recently, it was shown that polycystin-1 and polycystin-2 mediate mechanosensation in the primary cilium of kidney cells. Dysfunction of these proteins causes autosomal dominant polycystic kidney disease probably due to the inability to sense mechanical cues that normally regulate tissue morphogenesis30. Our findings suggest that the NPHP genes (NPHP1, NPHP3, NPHP4) involved in the pathogenesis of recessive cystic kidney disease also belong to a common pathway in the primary cilium of kidney cells.

The identification of the gene underlying adolescent NPHP will advance our understanding of cystic kidney disease, tapeto-retinal degeneration and hepatic fibrosis. The search for therapeutic strategies for individuals affected with these disorders will benefit from the discovery that the pcy mouse represents a model of human NPHP3.

Methods
Affected individuals and families.
We obtained signed informed consent from affected individuals and family members using protocols approved by the Institutional Ethics Review Board at the University of Freiburg and collaborating institutions. We collected blood samples from members of 118 families diagnosed for NPHP as defined by reported criteria1. Twenty-three of these families had several affected individuals or parental consanguinity. Some individuals showed additional extrarenal disease manifestations (see Table 1). We excluded homozygous deletions of NPHP1 and mutations in NPHP4 in studied individuals as described previously11, 12.

Haplotype analysis.
We restricted the genetic region of interest defined by recombination events of the Venezuelan kindred with isolated NPHP (V1) and the Tunisian family characterized by NPHP and Leber congenital amaurosis (F353) using additional polymorphic markers18.

Detection of mutations in NPHP3.
We studied genes and presumptive transcribed regions residing in the genomic interval between D3S1541 and D3S2322. To obtain the complete sequence information of the region of interest, we sequenced BAC clone AL592209. We did mutational screening by direct sequencing of PCR amplification products of genomic fragments from affected individuals of four families with NPHP and haplotype analyses compatible with homozygosity by descent at the NPHP3 locus (F1, F353, F624, V1). For these affected individuals, we excluded mutations in FLJ23251 (12 exons), PSMC2 (1 exon), CCRL1 (1 exon) and presumptive transcribed regions based on expressed-sequence tag (EST) clones AA018697 (1 exon), AA018713 (1 exon), AW894396 (1 exon), BC043583 (12 exons), BF680077 (1 exon), BF813194 (1 exon), BF960925 (1 exon), BF988958 (1 exon), BI870420 (3 exons), BM557429 (4 exons), BQ232818 (1 exon), nf22a06 (2 exons) and ZW70g02 (4 exons).

Mutational screening of exons of FLJ35693 identified a homozygous mutation of a splice acceptor site in family F624 suggesting that FLJ35693 is NPHP3. After identifying the entire coding region, we examined all 28 exons including alternative exon 3b of NPHP3 in a total of 118 individuals with NPHP. We verified all detected mutations bi-directionally. Primer sequences are available on request. We used direct sequencing, single-strand conformational polymorphism analysis, denaturing high-performance liquid chromatography or allele-specific digests for segregation analyses and screening for mutations. We excluded all detected mutations in a minimum of 200 control chromosomes. After identification of in-frame transcripts between NPHP3 and FLJ12592 by PCR amplification on kidney and testis cDNA libraries, we sequenced all 20 exons of FLJ12592 for families F1 and F353 and the six families in whom we found mutations in NPHP3 on only one of the two alleles.

Isolation of human NPHP3 and mouse Nphp3.
To obtain the complete cDNA sequence of NPHP3 we carried out RACE experiments and PCR amplification of overlapping fragments using kidney and testis cDNA libraries (Marathon-Ready, Clontech) as templates. We designed primers based on EST sequences, including FLJ35693, available from databases. Sequencing of amplification products and EST clones confirmed the complete cDNA sequence and indicated splice variants. The genomic organization of NPHP3 was elucidated by comparing cDNA and genomic sequences (AC055732).

Using BLAST analysis, we found all 27 putative Nphp3 exons located on the mouse genomic draft sequence (NW_000356). Using this sequence information, we identified a full-length cDNA for Nphp3 by RACE experiments and PCR amplification of overlapping fragments using kidney and testis cDNA libraries (Marathon-Ready, Clontech) as templates.

Detection of the pcy mutation.
Animal studies were approved by the local government. We sequenced all 27 exons of Nphp3 in pcy mice. Histopathology of the pcy mice showed the typical cystic kidney changes (Supplementary Fig. 1 online). As a control, we directly sequenced all sequence variants detected in several mouse strains (BALB/cJ, CALB/Rk, CASA/Rk, CAST/Ei, CZECHII/Ei, CD1, DBA/2J, FVB/NJ, KK/Upj-Ay/J, LEWES/Ei, Mus caroli, Mus pahari, PANCEVO/Ei, PERA/Ei, PERC/Ei, PWK/Ph, SF/CamEi, SKIVE/Ei, SPRET/Ei, TIRANO/Ei, WSB/Ei and ZALENDE/Ei), including the diabetic KK mouse strain in which the spontaneous pcy mutation initially arose14. We excluded mutations in all 20 exons of the mouse ortholog of FLJ12592 by direct sequencing of pcy genomic DNA.

Northern-blot analysis.
We determined expression and transcript size of NPHP3 by northern-blot analysis. A NotI−SalI fragment of approx3 kb isolated from EST clone BQ424818 was radiolabeled with alpha32P-dCTP and hybridized to a human adult tissue blot (Clontech) according to standard methods. The same blot was also probed with a FLJ12592 cDNA fragment (EST clone BQ925721).

In situ hybridization analysis.
We carried out in situ hybridization analysis of whole mouse embryos (7.5 d.p.c. to 11.5 d.p.c.) and embryonic (14.5 d.p.c. and 16.5 d.p.c.) and adult kidney sections using a digoxigenin-labeled antisense riboprobe derived from the 3' untranslated region of Nphp3 cDNA (protocols available on request).

Coimmunoprecipitation.
We carried out co-immunoprecipitation experiments as described28. Briefly, we transiently transfected HEK 293T cells with the indicated plasmids by the calcium phosphate method. After incubation for 24 h, we washed the cells twice and lysed them in a 1% Triton X-100 lysis buffer. After centrifugation (at 15,000g for 15 min at 4 °C), we incubated cell lysates containing equal amounts of total protein at 4 °C with anti-FLAG (M2) agarose beads for approximately 2 h. The beads were washed extensively with lysis buffer and bound proteins were resolved by 10% SDS−PAGE and visualized with enhanced chemiluminescence after incubation of the blots with the respective antibodies. We repeated the experiments four times with identical results.

URLs.
We used the BLAST tools (http://www.ncbi.nlm.nih.gov/blast/) to establish the genomic organization of NPHP3 and Nphp3 and the Ensembl website (http://www.ensembl.org) to obtain exon and intron borders. To predict the structure of NPHP3, we used the programs SMART (http://smart.embl-heidelberg.de/) and PSORT (http://psort.nibb.ac.jp/). We constructed the multiple-protein alignment with ClustalW (http://www.ebi.ac.uk/clustalw/) and predicted functional domains with the Scansite program (http://scansite.mit.edu/).

GenBank accession numbers.
Full-length human NPHP3 cDNA sequence, AY257864; full-length mouse Nphp3 cDNA sequence, AY259499; partial NPHP3 cDNA sequences, AY257865, AY257866, AY257867; partial Nphp3 cDNA sequence, AY259500.

 Top
Received 25 March 2003; Accepted 19 June 2003; Published online: 20 July 2003.

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 Top
Acknowledgments
We thank the affected individuals and their families for their participation in this study, R. Melkaoui and M. Petry for technical assistance and B. Kränzlin for microscopic photographs. This work was supported by the Italian Association for Leber's Congenital Amaurosis and by grants from the German Research Foundation (H.O. and A.K.), Zentrum für klinische Forschung Freiburg (H.O.) and the F.G. L. Huetwell fund (F.H.).

Competing interests statement:  The authors declare that they have no competing financial interests.

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ISSN: 1061-4036
EISSN: 1546-1718
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