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A Gene Mutated in Nephronophthisis and Retinitis Pigmentosa Encodes a Novel Protein, Nephroretinin, Conserved in Evolution
Abstract
Nephronophthisis (NPHP) comprises a group of autosomal recessive cystic kidney diseases, which constitute the most frequent genetic cause for end-stage renal failure in children and young adults. The most prominent histologic feature of NPHP consists of development of renal fibrosis, which, in chronic renal failure of any origin, represents the pathogenic event correlated most strongly to loss of renal function. Four gene loci for NPHP have been mapped to chromosomes 2q13 (NPHP1), 9q22 (NPHP2), 3q22 (NPHP3), and 1p36 (NPHP4). At all four loci, linkage has also been demonstrated in families with the association of NPHP and retinitis pigmentosa, known as "Senior-Løken syndrome" (SLS). Identification of the gene for NPHP type 1 had revealed nephrocystin as a novel docking protein, providing new insights into mechanisms of cell-cell and cell-matrix signaling. We here report identification of the gene (NPHP4) causing NPHP type 4, by use of high-resolution haplotype analysis and by demonstration of nine likely loss-of-function mutations in six affected families. NPHP4 encodes a novel protein, nephroretinin, that is conserved in evolution--for example, in the nematode Caenorhabditis elegans. In addition, we demonstrate two loss-of-function mutations of NPHP4 in patients from two families with SLS. Thus, we have identified a novel gene with critical roles in renal tissue architecture and ophthalmic function.
... Meckel-Gruber syndrome MKS1 [143], MKS3 (TMEM67) [144], CEP290 [137], RPGRIP1L [136], CC2D2A [145], and TMEM216 [142] Senior-Løken syndrome CEP290 (also known as NPHP6 and MKS4) [140], NPHP1 [146], NPHP3 [147], NPHP4 [148], and NPHP5 (also known as IQCB1) [149]. Type 1 orofacial syndrome OFD1 [150] Leber's congenital amaurosis GUCY2D [151], RPE65 [152], SPATA7 [153], AIPL1 [154], LCA5 [155], RPGRIPL1 [156], CRX [157], CRB1 [158], IMPD1 [159], RD3 [160], CEP290 [140], NPHP5 [149], and RDH12 [161]. ...
... Meckel-Gruber syndrome MKS1 [143], MKS3 (TMEM67) [144], CEP290 [137], RPGRIP1L [136], CC2D2A [145], and TMEM216 [142] Senior-Løken syndrome CEP290 (also known as NPHP6 and MKS4) [140], NPHP1 [146], NPHP3 [147], NPHP4 [148], and NPHP5 (also known as IQCB1) [149]. Type 1 orofacial syndrome OFD1 [150] Leber's congenital amaurosis GUCY2D [151], RPE65 [152], SPATA7 [153], AIPL1 [154], LCA5 [155], RPGRIPL1 [156], CRX [157], CRB1 [158], IMPD1 [159], RD3 [160], CEP290 [140], NPHP5 [149], and RDH12 [161]. ...
Over the years, several studies have shown that kinase-regulated signaling pathways are involved in the development of rare genetic diseases. The study of the mechanisms underlying the onset of these diseases has opened a possible way for the development of targeted therapies using particular kinase inhibitors. Some of these are currently used to treat other diseases, such as cancer. This review aims to describe the possibilities of using kinase inhibitors in genetic pathologies such as tuberous sclerosis, RASopathies, and ciliopathies, describing the various pathways involved and the possible targets already identified or currently under study.
... This was named nephrocystin 1 (NPHP1). Over the next decade, similar approaches allowed the identification of the next eight genes [47][48][49][50][51][52][53]. The advent of NGShas allowed more rapid identification of genes with causal roles in NPHP; the count currently stands at 26 [3,54,55]. ...
... Homozygosity mapping and genome-wide linkage analysis led to the identification of mutations in NPHP4 (1p36.31) in NPHP patients lacking mutations in NPHP1, 2 and 3 genes [85]. Individuals with NPHP4 mutation frequently present with a retinal phenotype [52,85,86]. The protein encoded nephrocystin-4 localises to primary cilia, basal body, and the cortical actin cytoskeleton in polarized cells [86]. ...
The exponential rise in our understanding of the aetiology and pathophysiology of genetic cystic kidney diseases can be attributed to the identification of cystogenic genes over the last three decades. The foundation of this was laid by positional cloning strategies which gradually shifted towards next-generation sequencing (NGS) based screenings. This shift has enabled the discovery of novel cystogenic genes at an accelerated pace unlike ever before and, most notably, the past decade has seen the largest increase in identification of the genes which cause nephronophthisis (NPHP). NPHP is a monogenic autosomal recessive cystic kidney disease caused by mutations in a diverse clade of over 26 identified genes and is the most common genetic cause of renal failure in children. NPHP gene types present with some common pathophysiological features alongside a diverse range of extra-renal phenotypes associated with specific syndromic presentations. This review provides a timely update on our knowledge of this disease, including epidemiology, pathophysiology, anatomical and molecular features. We delve into the diversity of the NPHP causing genes and discuss known molecular mechanisms and biochemical pathways that may have possible points of intersection with polycystic kidney disease (the most studied renal cystic pathology). We delineate the pathologies arising from extra-renal complications and co-morbidities and their impact on quality of life. Finally, we discuss the current diagnostic and therapeutic modalities available for disease management, outlining possible avenues of research to improve the prognosis for NPHP patients.
... 11 These children presented predominately with a restricted renal phenotype of a urinary concentration defect and CKD 11 and suggested later onset and/or slower progression of CKD in comparison to NPHP due to defects in other NPHP-associated genes, albeit this was a small cohort. 11 This aligns with earlier reports of NPHP4-related disease associating with kidney failure occurring at age ranges of 6 to 20 1 and 6 to 35 18 years, corresponding to median ages of 12.7 and 22 years, respectively. Another cohort of 250 patients with NPHP included 26 NPHP4 cases, 3 of whom 13 presented with an isolated renal phenotype. ...
... 2 We identified NPHP4 as an appreciable genetic cause for adultdiagnosed nonsyndromic NPHP, in keeping with previous reports that age of kidney failure extends to adulthood. 1,18 These cases highlight that this diagnosis should be considered among adults presenting with nonsyndromic kidney failure or progressive CKD. Further, this would be of particular interest among patients having a clinical phenotype consistent with tubulointerstitial kidney disease and a family history consistent with autosomal recessive inheritance, heightened if there is an affected sibling or cousin. ...
There is increasing appreciation of nephronophthisis (NPHP) as an autosomal recessive cause of kidney failure and earlier stages of chronic kidney disease among adults. We identified 2 families with presumed adult-diagnosed nonsyndromic NPHP and negative diagnostic genetic testing results from our Renal Genetics Clinic. Both had 2 affected siblings without extrarenal phenotypes. After informed consent, research whole-genome sequencing was undertaken. Biallelic NPHP4 variants were identified in trans and clinically confirmed in all 4 affected individuals, confirming a genetic diagnosis. Participant 1 of the first family (F1P1) had kidney failure diagnosed at 19 years of age. An affected younger sibling (F1P2) reached kidney failure at age 15 years after kidney biopsy suggested NPHP. Pathogenic variants detected in NPHP4 in this family were NM_015102.4:c.3766C>T (p.Gln1256*) and a 31-kb deletion affecting exons 12 to 16. In the second family, F2P3 reached kidney failure at age 27 years having undergone kidney biopsy suggesting NPHP. An affected younger sibling (F2P4) has chronic kidney disease stage 4 at age 39 years. The NPHP4 variants detected were NM_015102.4:c.1998_1999del (p.Tyr667Phefs*23) and c.3646G>T (p.Asp1216Tyr). The latter variant was initially missed in diagnostic sequencing due to inadequate NPHP4 coverage (94.3% exonic coverage). With these reports, we identify NPHP4 as an appreciable genetic cause for adult-diagnosed nonsyndromic NPHP that should be considered by adult nephrologists.
... Diagnosis of NPHC was based on US finding of normal or slightly reduced kidneys with increased echogenicity and/or combination of typical symptoms, such as polyuria, polydipsia, anemia [48][49][50][51][52][53][54][55][56]. The diagnosis was confirmed by genetic testing in all of the patients. ...
Introduction: Pediatric cystic kidney disease (CyKD) includes conditions characterized by renal cysts. Despite extensive research in this field, there are no reliable genetics or other biomarkers to estimate the phenotypic consequences. Therefore, CyKD in children heavily relies on clinical and diagnostic testing to predict the long-term outcomes. Aim: A retrospective study aimed to provide a concise overview of this condition and analyze real-life data from a single-center pediatric CyKD cohort followed during a 12-year period. Methods and Materials: Medical records were reviewed for extensive clinical, laboratory, and radiological data, treatment approaches, and long-term outcomes. Results: During the study period, 112 patients received a diagnosis of pediatric CyKD. Male patients were more involved than female (1:0.93). Fifty-six patients had a multicystic dysplastic kidney ; twenty-one of them had an autosomal dominant disorder; fifteen had an isolated renal cyst; ten had been diagnosed with autosomal recessive polycystic kidney disease; three had the tuberous sclerosis complex; two patients each had Bardet-Biedl, Joubert syndrome, and nephronophthisis; and one had been diagnosed with the trisomy 13 condition. Genetic testing was performed in 17.9% of the patients, revealing disease-causing mutations in three-quarters (75.0%) of the tested patients. The most commonly presenting symptoms were abdominal distension (21.4%), abdominal pain (15.2%), and oligohydramnios (12.5%). Recurrent urinary tract infections (UTI) were documented in one-quarter of the patients, while 20.5% of them developed hypertension during the long-term follow-up. Antibiotic prophylaxis and antihypertensive treatment were the most employed therapeutic modalities. Seventeen patients progressed to chronic kidney disease (CKD), with thirteen of them eventually reaching end-stage renal disease (ESRD). The time from the initial detection of cysts on an ultrasound (US) to the onset of CKD across the entire cohort was 59.0 (7.0-31124.0) months, whereas the duration from the detection of cysts on an US to the onset of ESRD across the whole cohort was 127.0 (33.0-141.0) months. The median follow-up duration in the cohort was 3.0 (1.0-7.0) years. The patients who progressed to ESRD had clinical symptoms at the time of initial clinical presentation. Conclusion: This study is the first large cohort of patients reported from Croatia. The most common CyKD was the multicystic dysplastic kidney disease. The most common clinical presentation was abdominal distention, abdominal pain, and oliguria. The most common long-term complications were recurrent UTIs, hypertension, CKD, and ESRD.
... NPHP4 (OMIM 606966) is a recessive gene causing Senior-Loken syndrome 4 [158] and it has been identified in a single consanguineous family with segregation of proteinuria and kidney phenotype in multiple siblings, with a single patient undergoing kidney biopsy and diagnosed with FSGS [159]. The mechanism of disease causing FSGS through NPHP genes remains unexplained, but it is possibly a secondary adaptive response to nephron loss or podocyte cytoskeleton dysfunction in TTC21B mutations. ...
Focal segmental glomerulosclerosis (FSGS) is a complex disease which describes different kinds of kidney defects, not exclusively linked with podocyte defects. Since nephrin mutation was first described in association with early-onset nephrotic syndrome (NS), many advancements have been made in understanding genetic patterns associated with FSGS. New genetic causes of FSGS have been discovered, displaying unexpected genotypes, and recognizing possible site of damage. Many recent large-scale sequencing analyses on patients affected by idiopathic chronic kidney disease (CKD), kidney failure (KF) of unknown origin, or classified as FSGS, have revealed collagen alpha IV genes, as one of the most frequent sites of pathogenic mutations. Also, recent interest in complex and systemic lysosomal storage diseases, such as Fabry disease, has highlighted GLA mutations as possible causes of FSGS. Tubulointerstitial disease, recently classified by KDIGO based on genetic subtypes, when associated with UMOD variants, may phenotypically gain FSGS features, as well as ciliopathy genes or others, otherwise leading to completely different phenotypes, but found carrying pathogenic variants with associated FSGS phenotype. Thus, glomerulosclerosis may conceal different heterogeneous conditions. When a kidney biopsy is performed, the principal objective is to provide an accurate diagnosis. The broad spectrum of phenotypic expression and genetic complexity is demonstrating that a combined path of management needs to be applied. Genetic investigation should not be reserved only to selected cases, but rather part of medical management, integrating with clinical and renal pathology records. FSGS heterogeneity should be interpreted as an interesting opportunity to discover new pathways of CKD, requiring prompt genotype–phenotype correlation. In this review, we aim to highlight how FSGS represents a peculiar kidney condition, demanding multidisciplinary management, and in which genetic analysis may solve some otherwise unrevealed idiopathic cases. Unfortunately there is not a uniform correlation between specific mutations and FSGS morphological classes, as the same variants may be identified in familial cases or sporadic FSGS/NS or manifest a variable spectrum of the same disease. These non-specific features make diagnosis challenging. The complexity of FSGS genotypes requires new directions. Old morphological classification does not provide much information about the responsible cause of disease and misdiagnoses may expose patients to immunosuppressive therapy side effects, mistaken genetic counseling, and misguided kidney transplant programs.
... However, little is known about the correlation between ACOT7 and ALL, and our research reported that the breakage form of ACOT7 gene was fused with NPHP4 gene, with retaining functional domains. In addition, NPHP4 gene is closely associated with nephronophthisis type 4, Senior-Loken syndrome type 4 [15], and tumorigenesis. To clarify the function of ACOT7-NPHP4, NALM-6 cells transfected with transcript ACOT7-NPHP4 presented significant chemoresistance to doxorubicin, indicating that the new fusion gene may contribute to the failure to the induction therapy, to some extent. ...
Background
Acute lymphoblastic leukemia (ALL) is a type of heterogeneous hematopoietic malignancy that accounts for approximately 20% of adult ALL. Although ALL complete remission (CR) rate has increased to 85–90% after induction chemotherapy, 40–50% of patients eventually relapsed. Therefore, it is necessary to improve the outcomes of ALL via accurate diagnosis and individualized treatments, which benefits in part from molecular biomarkers. Here, we identified a new fusion gene, Acyl-CoA Thioesterase 7–Nephrocystin 4 (ACOT7–NPHP4), in a 34-year-old patient with ALL. The fusion gene contributed to chemoresistance to doxorubicin and acted as a new molecular marker.
Case presentation
A 34-year-old male patient was diagnosed with ALL (common B cell) based on clinical manifestations and laboratory results. Although the patient received two cycles of the hyper-CVAD-L regimen as chemotherapy, the induction treatment failed. Because of the refusal of further treatments, the patient died of rapid progression of ALL one month later. Finally, a new fusion transcript, ACOT7–NPHP4, was detected in the patient’s lymphoblastic leukemia cells via RNA sequencing.
Conclusion
This is the first report of a patient with ALL carrying an ACOT7–NPHP4 fusion gene. These findings may help understand the impact of ACOT7–NPHP4 in clinical molecular monitoring and drug resistance to doxorubicin; furthermore, its leukemogenesis will be essential to explore in future.
... Defined nphp mutations produce ciliopathy phenotypes NPHP4 mutations cause End Stage Renal Disease (ESRD) with a variable onset (6-35 years), often associated with retinitis pigmentosa (31). Elimination of an ESS in zebrafish nphp4 sa38686 , predicted to truncate Nphp4 at amino acid 764, was not associated with glomerular cyst or cloaca malformation, while a nonsense mutation, inserting a stop codon at amino acid 444 revealed an increase in glomerular cyst formation that was statistically significant. ...
The zebrafish pronephros model, using morpholino oligonucleotides (MO) to deplete target genes, has been extensively used to characterize human ciliopathy phenotypes. Recently, discrepancies between MO and genetically defined mutants have questioned this approach. We analyzed zebrafish with mutations in the nphp1–4-8 module to determine the validity of MO-based results. While MO-mediated depletion resulted in glomerular cyst and cloaca malformation, these ciliopathy-typical manifestations were observed at a much lower frequency in zebrafish embryos with defined nphp mutations. All nphp1–4-8 mutant zebrafish were viable and displayed decreased manifestations in the next (F2) generation, lacking maternal RNA contribution. While genetic compensation was further supported by the observation that nphp4-deficient mutants became partially refractory to MO-based nphp4 depletion, zebrafish embryos, lacking one nphp gene, became more sensitive to MO-based depletion of additional nphp genes. Transcriptome analysis of nphp8 mutant embryos revealed an upregulation of the circadian clock genes cry1a and cry5. MO-mediated depletion of cry1a and cry5 caused ciliopathy phenotypes in wildtype embryos, while cry1a and cry5 depletion in maternal zygotic nphp8 mutant embryos increased the frequency of glomerular cysts compared to controls. Importantly, cry1a and cry5 rescued the nephropathy-related phenotypes in nphp1, nphp4 or nphp8-depleted zebrafish embryos. Our results reveal that nphp mutant zebrafish resemble the MO-based phenotypes, albeit at a much lower frequency. Rapid adaption through upregulation of circadian clock genes seems to ameliorate the loss of nphp genes, contributing to phenotypic differences.
... Molecular binding partners of NPHP4 are NPHP1, RP GTPase regulator interacting protein 1 (RPGRIP1) (Roepman et al., 2005), NPHP8 (alias of RPGRIP1L) (Delous et al., 2007) and Retinitis pigmentosa GTPase regulator (RPGR) (Murga-Zamalloa et al., 2010), proteins that regulate ciliary function. Homozygous missense or heterozygous frameshift mutations in NPHP4 have been associated with Nephronophthisis, an autosomal recessive kidney disease mainly affecting children and young adults (Strauss and Sommers, 1967) that presents with polyuria, polydipsia, and anemia (Wolf, 2015); it has been associated with different syndromes, including the Senior-Loken syndrome (SLSD) with retinitis pigmentosa (RP), Joubert syndrome with RP, cerebellar and brainstem malformations, and intellectual disability (Otto et al., 2002(Otto et al., , 2005Parisi et al., 2004). Mutant mice homozygous for a nonsense mutation in the Nphp4 gene present male infertility (Won et al., 2011) with reduced sperm counts (98% reduction compared to fertile controls), scarce motility, and virtually absent progressive motility (Won et al., 2011). ...
Spermatogenesis is a cell differentiation process that ensures the production of fertilizing sperm, which ultimately fuse with an egg to form a zygote. Normal spermatogenesis relies on Sertoli cells, which preserve cell junctions while providing nutrients for mitosis and meiosis of male germ cells. Several genes regulate normal spermatogenesis, some of which are not exclusively expressed in the testis and control multiple physiological processes in an organism. Loss-of-function mutations in some of these genes result in spermatogenesis and sperm functionality defects, potentially leading to the insurgence of rare genetic disorders. To identify genetic intersections between spermatogenesis and rare diseases, we screened public archives of human genetic conditions available on the Genetic and Rare Diseases Information Center (GARD), the Online Mendelian Inheritance in Man (OMIM), and the Clinical Variant (ClinVar), and after an extensive literature search, we identified 22 distinct genes associated with 21 rare genetic conditions and defective spermatogenesis or sperm function. These protein-coding genes regulate Sertoli cell development and function during spermatogenesis, checkpoint signaling pathways at meiosis, cellular organization and shape definition during spermiogenesis, sperm motility, and capacitation at fertilization. A number of these genes regulate folliculogenesis and oogenesis as well. For each gene, we review the genotype–phenotype association together with associative or causative polymorphisms in humans, and provide a description of the shared molecular mechanisms that regulate gametogenesis and fertilization obtained in transgenic animal models.
... 112,113 NPHP4 interacts with NPHP1, and loss-of-function protein truncating mutations were found in SLSN type 4 patients with retinitis pigmentosa (RP). 114 Mutations in NPHP5 present RP together with renal tubular abnormalities. The same gene is implicated in SLSN type 5 with X-linked RP, emerging from interactions between the 2 IQ domains of NPHP5 with the GTPase regulator of RP; these proteins colocalize both at photoreceptor connecting cilia and renal primary cilia in epithelial cells. ...
Context.—Cystic diseases of the kidney are a very heterogeneous group of renal inherited conditions, with more than 33 genes involved and encompassing X-linked, autosomal dominant, and autosomal recessive inheritance. Although mostly monogenic with mendelian inheritance, there are clearly examples of oligogenic inheritance, such as 3 mutations in 2 genes, while the existence of genetic modifiers is perhaps the norm, based on the extent of variable expressivity and the broad spectrum of symptoms.
Objectives.—To present in the form of a mini review the major known cystic diseases of the kidney for which genes have been mapped or cloned and characterized, with some information on their cellular and molecular biology and genetics, and to pay special attention to commenting on the issues of molecular diagnostics, in view of the genetic and allelic heterogeneity.
Data Sources.—We used major reviews that make excellent detailed presentation of the various diseases, as well as original publications.
Conclusions.—There is already extensive genetic heterogeneity in the group of cystic diseases of the kidney; however, there are still many more genes awaiting to be discovered that are implicated or mutated in these diseases. In addition, the synergism and interaction among this repertoire of gene products is largely unknown, while a common unifying aspect is the expression of nearly all of them at the primary cilium or the basal body. A major interplay of functions is anticipated, while mutations in all converge in the unifying phenotype of cyst formation.
... Mutations in NPHP4 caused nephronophthisis and Senior-Løken syndrome (a combination of nephronophthisis and RP; Mollet et al., 2002;Otto et al., 2002). NPHP4 is localized to the connecting cilium of photoreceptors, a localization that is dependent on RPGRIP1 (Patil et al., 2012;Roepman et al., 2005;Won et al., 2011). ...
Mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene are the predominant cause of retinitis pigmentosa. RPGR plays a critical role as a scaffold protein in the regulation of protein trafficking from the basal body to the axoneme, where the cargoes are transported to the outer segments (OSs) of photoreceptors. This trafficking process is controlled directly by intraflagellar transport complexes and regulated by the RPGR protein complex, although the precise mechanisms have yet to be defined. We used an Rpgr conditional knockout (cko) mouse model to investigate the disease mechanisms during retinal degeneration and to evaluate the protective effects of tauroursodeoxycholic acid (TUDCA). Rhodopsin, cone opsins and transducin were mislocalized in Rpgr cko photoreceptors, while localization of NPHP4 to connecting cilia was absent, suggesting that RPGR is required for ciliary protein trafficking. Microglia were activated in advance of retinal degeneration in Rpgr cko mouse retinas. TUDCA treatment suppressed microglial activation and inflammation and prevented photoreceptor degeneration in Rpgr cko mice. Our data demonstrated that TUDCA has therapeutic potential for RPGR-associated RP patients.
... adolescents and most gene products linked to NPHP localize to primary cilia and/or centrosomes, rendering NPHP a ciliopathy [3]. Consistent with the near ubiquitous existence of the primary cilium in the human body, individuals with NPHP often exhibit additional, extrarenal symptoms such as retinal degeneration, cerebellar hypoplasia, and liver fibrosis [4][5][6][7][8][9][10][11][12]. NPHP with extra-renal symptoms are classified as NPHP-related ciliopathies (NPHP-RC). ...
Nephronophthisis-related ciliopathies (NPHP-RC) are a group of disorders that present with end-stage renal failure in childhood/adolescence, kidney cysts, retinal degeneration, and cerebellar hypoplasia. One disorder that shares clinical features with NPHP-RC is Bardet-Biedl Syndrome (BBS). Serologically defined colon cancer antigen 8 (SDCCAG8; also known as NPHP10 and BBS16) is an NPHP gene that is also associated with BBS. To better understand the patho-mechanisms of NPHP and BBS caused by loss of SDCCAG8 function, we characterized an SDCCAG8 mouse model (Sdccag8Tn(sb-Tyr)2161B.CA1C2Ove) generated by Sleeping Beauty Transposon (SBT)-mediated insertion mutagenesis. Consistent with the previously reported, independent SDCCAG8 mouse models, our mutant mice display pre-axial polydactyly in their hind limbs. In addition, we report patterning defects in the secondary palate, brain abnormalities, as well as neonatal lethality associated with developmental defects in the lung in our mouse model. The neonatal lethality phenotype is genetic background dependent and rescued by introducing 129S6/SvEvTac background. Genetic modifier(s) responsible for this effect were mapped to a region between SNPs rs3714172 and rs3141832 on chromosome 11. While determining the precise genetic lesion in our mouse model, we found that SBT insertion resulted in a deletion of multiple exons from both Sdccag8 and its neighboring gene Akt3. We ascribe the patterning defects in the limb and the secondary palate as well as lung abnormalities to loss of SDCCAG8, while the developmental defects in the brain are likely due to the loss of AKT3. This mouse model may be useful to study features not observed in other SDCCAG8 models but cautions are needed in interpreting data.
... RPGRIP1 has an interaction not only with RPGR, but also with NPHP4 and SDCCAG8, Rpgrip1 nmf247 mice without RPGRIP1 expression lack NPHP4 and RPGR in photoreceptor cilia, whereas the SDCCAG8 and acetylated-a-tubulin ciliary localizations are strongly decreased, even though the NPHP4 and SDCCAG8 expression levels are normal and those of acetylated-a-tubulin and c-tubulin are upregulated [9]. Mutations in NPHP4 and SDCCAG8 would cause Senior-Loken syndrome and Bardet-Biedl syndrome, these two disorders are characterized by LCA/RP and other systemic features including kidney conditions [10][11]. These studies suggest that RPGRIP1 is important in visual pathway and has an essential function in eye development, and when mutated, it may cause RP disease. ...
As the most common inherited retinal degenerations, retinitis pigmentosa (RP) is clinically and genetically heterogeneous. Some of the RP genes are also associated with other retinal diseases, such as LCA (Leber's congenital amaurosis) and CORD (cone-rod dystrophy). Here, in our molecular diagnosis of 99 Chinese RP patients using targeted gene capture sequencing, three probands were found to carry mutations of RPGRIP1, which was known to be associated with pathogenesis of LCA and CORD. By further clinical analysis, two probands were confirmed to be RP patients and one was confirmed to be LCA patient. These novel mutations were co-segregated with the disease phenotype in their families. Our result not only expands the mutational spectrum of the RPGRIP1 gene but also gives supports to clinical diagnosis and molecular treatment of RP patients.
... About 10% of NPHP patients also have retinal degeneration (Otto et al. 2005;Mockel et al. 2011). So far, eight genes are associated with SLS (CEP164, CEP290, IQCB1, NPHP1, NPHP4, SDCCAG8, TRAF3IP1, WDR19), although other NPHP-associated genes are mutated in different syndromes involving the retina (Caridi et al. 1998;Otto et al. 2002Otto et al. , 2005Otto et al. , 2010Sayer et al. 2006;Chaki et al. 2012;Coussa et al. 2013;Bizet et al. 2015). There is a considerable overlap between SLS and other ciliopathies, where almost all SLS genes are associated with other diseases (Fig. 3). ...
Photoreceptors are sensory neurons designed to convert light stimuli into neurological responses. This process, called phototransduction, takes place in the outer segments (OS) of rod and cone photoreceptors. OS are specialized sensory cilia, with analogous structures to those present in other nonmotile cilia. Deficient morphogenesis and/or dysfunction of photoreceptor sensory cilia (PSC) caused by mutations in a variety of photoreceptor-specific and common cilia genes can lead to inherited retinal degenerations (IRDs). IRDs can manifest as isolated retinal diseases or syndromic diseases. In this review, we describe the structure and composition of PSC and different forms of ciliopathies with retinal involvement. We review the genetics of the IRDs, which are monogenic disorders but genetically diverse with regard to causality.
... NPHP4: NPHP4 which encodes nephrocystin-4 or nephroretinin has a mutation frequency of 2 to 3% in genetically confirmed NPHP with the abnormality located in 1p36.22 [39,40]. Nephrocystin -4 localizes to the primary cilium and interacts with other proteins namely nephrocystin 1,3,8 and inversin. ...
Data sources: A literature review was conducted using pubmed database. English language articles published over the past 25 years in peer reviewed journals were reviewed – search terms used " Nephronophthisis " , " Cilia " , " Ciliopathy " and " Cystic Kidney disease ". A total of 34 articles were available of which 8 were review articles and 26 were that of clinical and animal trials. Additional information was also obtained from the references in select review articles. 4 articles (clinical trials) were excluded as they pertained to adult medullary cystic kidney disease. Nephronophthisis (NPHP) is an autosomal recessive cystic renal disease which presents with chronic tubulointerstitial nephritis and progressive renal failure. If extrarenal symptoms are present in addition to NPHP, these disorders are classified as NPHP-related ciliopathies (NPHP-RC). Recent identification of many disease causing genes have improved our understanding of ciliopathies and their varied presentation involving multiple organ systems. The pleiotropy in NPHP is explained by the fact that almost all NPHP gene products share expression in primary cilia, a sensory organelle present in most mammalian cells. Genetic testing for the most common affected genes is readily available making the diagnosis process easier and without the need for invasive procedures such as renal biopsy. Even though major breakthrough has been achieved in identifying new pathogenic genes, still known genetic diagnosis is available only in about 30 to 40% of NPHP-RC. Current treatment options are only supportive and all children with NPHP will progress to ESRD requiring renal replacement at some point in their life. The challenge still remains to understand the biological function of nephrocystins and the molecular mechanism behind cyst formation. Further research to understand the biology of cyst formation at a cellular level and the molecular role of the other pathogenic genes will help improve our understanding of this complex disease. This could hopefully provide us with tools to delay progression or even reverse the process of cyst formation and hence renal failure in NPHP. We report here a case of a young adolescent boy diagnosed with NPHP, his clinical presentation and management with a brief literature review on this rare genetic cause of ESRD. Case Study The patient is a 12 year old Caucasian boy who presented to his primary care physician with h/o fatigue, lethargy, low grade fevers and vomiting. His past medical history was significant for primary nocturnal enuresis and constipation. For the enuresis patient has seen an urologist and was started on desmopressin about 4 years back. Prior lab works included a urine analysis which showed low specific gravity at 1.005 but no protein or blood. For constipation, patient uses stool softener on and off. No other significant health issues were identified by family. He was one of four siblings and there was no significant family h/o renal disease, dialysis or kidney transplant. The pediatrician did lab work including a complete blood count and chemistry panel which showed the following values. Hemoglobin 8.2 g/dl, Hematocrit 23%. Sodium 140 meq/L, potassium 4 meq/L, chloride 109 meq/L, bicarbonate 20 meq/L , blood urea nitrogen 90 mg/dl, creatinine 4.1 mg/dl, calcium 8.1 mg/dl and phosphorus 6.1 mg/dl. Patient got admitted under pediatric nephrology service in Children's hospital for further evaluation. Physical examination showed a height of 146 cm, body weight of 34 kg, and blood pressure of 114/66 mm Hg with a regular heart rate of 90 beats per minute. On exam no edema was appreciated. Visual acuity was normal and an ophthalmologist assessment did not show any retinal abnormalities. Neurological exam was intact and no skin rash or joint swelling appreciated. Further work up included complements (C3 & C4) which were in the normal limits, Parathyroid hormone elevated at 966 pg/ml indicating chronic kidney damage and vitamin D level was adequate at 27 ng/ml. Urine analysis was repeated and showed bland urine with low specific gravity 1.005 and no protein or blood. Urine protein/Creatinine ratio was normal at 0.2 and fractional excretion of sodium was elevated at 7.6% indicating intrinsic renal injury. Imaging studies included a renal ultrasound which showed both kidneys to measure around 10 cm (normal for age) with increased echogenicity and no hydronephrosis. A voiding cysto urethrogram (VCUG) did not reveal any reflux. Radionuclide studies included a MAG3 scan which showed slow uptake of the radiotracer with cortical retention and slow delayed excretion compatible with chronic medical renal disease. A clinical diagnosis of cystic kidney disease was made and molecular testing for NPHP 1 gene done. Patient's acidosis was corrected with bicarbonate supplementation and epogen was started for anemia. The molecular testing did come back positive for NPHP1 homozygous deletion confirming the diagnosis of nephronophthisis. Patient was placed on a preemptive renal transplant list and is now s/p a diseased donor kidney transplant with normal renal function. Screening on his other siblings showed that one of his younger brothers, an eight year old boy also has NPHP with elevated creatinine and is currently getting medically managed for his chronic kidney disease.
... Both proteins are required for ciliogenesis and Cep164 can also participate in the DNA damage response, a function it can share with other NPHP proteins (Graser et al. 2007;Chaki et al. 2012;Tanos et al. 2013;Daly et al. 2016). As noted above, C. elegans orthologs of the NPHP proteins Nphp1 and Nphp4 localize in both TFs and TZ (Hildebrandt et al. 1997;Mollet et al. 2002;Otto et al. 2002;Jensen et al. 2015). However, whether the mammalian orthologs are also present or function at TFs is unclear. ...
Cilia are plasma membrane protrusions that act as cellular propellers or antennae. To perform these functions, cilia must maintain a composition distinct from those of the contiguous cytosol and plasma membrane. The specialized composition of the cilium depends on the ciliary gate, the region at the ciliary base separating the cilium from the rest of the cell. The ciliary gate's main structural features are electron dense struts connecting microtubules to the adjacent membrane. These structures include the transition fibers, which connect the distal basal body to the base of the ciliary membrane, and the Y-links, which connect the proximal axoneme and ciliary membrane within the transition zone. Both transition fibers and Y-links form early during ciliogenesis and play key roles in ciliary assembly and trafficking. Accordingly, many human ciliopathies are caused by mutations that perturb ciliary gate function.
... Nephronophthisis-related ciliopathies (NPHP-RC) are associated with mutations in a variety of genes [32][33][34][35][36][37][38][39]. A recent study of 100 consanguine patients with NPHP-RC identified a homozygous truncating mutation in DCDC2 (the same as that in our patient 1) in a single patient who also had liver disease. ...
Background & aims:
Neonatal sclerosing cholangitis (NSC) is a severe neonatal-onset cholangiopathy commonly leading to liver transplantation (LT) for end-stage liver disease in childhood. Liver-biopsy findings histopathologically resemble those in biliary atresia (BA); however, in NSC extrahepatic bile ducts are patent, whilst in BA their lumina are obliterated. NSC is commonly seen in consanguineous kindreds, suggesting autosomal recessive inheritance.
Methods:
From 29 NSC patients (24 families) identified, DNA was available in 24 (21 families). Thirteen (7 male) patients (12 families) of consanguineous parentage were selected for whole exome sequencing. Sequence variants were filtered for homozygosity, pathogenicity, minor allele frequency, quality score, and encoded-protein expression pattern.
Results:
Four of 13 patients were homozygous and two were compound heterozygous for mutations in DCDC2, encoding doublecortin domain containing 2 (DCDC2), expressed in cholangiocyte cilia. Another 11 patients were sequenced: one (with one sibling pair) was compound heterozygous for DCDC2 mutations. All mutations were protein-truncating. In available liver tissue from patients with DCDC2 mutations, immunostaining for human DCDC2 and the ciliary protein acetylated alpha-tubulin (ACALT) showed no expression (n=6) and transmission electron microscopy found that cholangiocytes lacked primary cilia (n=5). DCDC2 and ACALT were expressed in NSC patients without DCDC2 mutations (n=22). Of the DCDC2, one patient died awaiting LT; five came to LT, of whom one died 2 years later. The other 4 are well.
Conclusion:
Among 24 NSC patients with available DNA, 7 had mutations in DCDC2 (6 of 19 families). NSC patients in substantial proportion harbour mutations in DCDC2. Their disease represents a novel liver-based ciliopathy.
Lay summary:
Neonatal sclerosing cholangitis (NSC) is a rare genetic form of liver disease presenting in infancy. Through Next Generation Sequencing we identified mutations in the gene encoding for doublecortin domain containing 2 (DCDC2) protein in a group of NSC children. DCDC2 is a signalling and structural protein found in primary cilia of cholangiocytes. Cholangiocytes are the cells forming the biliary system which is the draining system of the liver.
... The characteristic histological findings in NPHP are renal interstitial infiltration with fibrosis, tubular atrophy with basement membrane disruption, and cyst development at the corticomedullary renal border (2). A combination of positional cloning and functional candidate gene approaches have led to the identification of 10 causative NPHP genes (NPHP1-NPHP9 and NPHP11) (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). The products of each gene localize to primary cilia, basal bodies, and centrosomes, supporting a theory that describes cystic kidney diseases as "ciliopathies" (5,6,14,15). ...
... Mutations in human NPHP4 cause nephronophthisis, either with or without retinal degeneration [48,49]. To test whether the genetic interactions detected in C. elegans with MKS complex genes could contribute to the expressivity of NPHP4, we investigated whether the same genetic interactions occur in mammals. ...
Mutations in genes encoding cilia proteins cause human ciliopathies, diverse disorders affecting many tissues. Individual genes can be linked to ciliopathies with dramatically different phenotypes, suggesting that genetic modifiers may participate in their pathogenesis. The ciliary transition zone contains two protein complexes affected in the ciliopathies Meckel syndrome (MKS) and nephronophthisis (NPHP). The BBSome is a third protein complex, affected in the ciliopathy Bardet-Biedl syndrome (BBS). We tested whether mutations in MKS, NPHP and BBS complex genes modify the phenotypic consequences of one another in both C. elegans and mice. To this end, we identified TCTN-1, the C. elegans ortholog of vertebrate MKS complex components called Tectonics, as an evolutionarily conserved transition zone protein. Neither disruption of TCTN-1 alone or together with MKS complex components abrogated ciliary structure in C. elegans. In contrast, disruption of TCTN-1 together with either of two NPHP complex components, NPHP-1 or NPHP-4, compromised ciliary structure. Similarly, disruption of an NPHP complex component and the BBS complex component BBS-5 individually did not compromise ciliary structure, but together did. As in nematodes, disrupting two components of the mouse MKS complex did not cause additive phenotypes compared to single mutants. However, disrupting both Tctn1 and either Nphp1 or Nphp4 exacerbated defects in ciliogenesis and cilia-associated developmental signaling, as did disrupting both Tctn1 and the BBSome component Bbs1. Thus, we demonstrate that ciliary complexes act in parallel to support ciliary function and suggest that human ciliopathy phenotypes are altered by genetic interactions between different ciliary biochemical complexes.
... Le gène NPHP2 code pour l'inversine des mutations au sein de ce gène (Olbrich et al., 2003) sont responsables de la forme infantile. Des mutations du gène NPHP3 (Otto et al., 2002) ont été décrites dans une grande famille du Vénézuela et sont responsables de la forme tardive. Des mutations du gène NPHP4 ont été mises en évidence dans plusieurs familles dont certaines ont une atteinte rétinienne associée (syndrome de Senior-Loken) et enfin des mutations ont été identifiées au niveau du gène NPHP5 qui code pour une protéine ayant un domaine de liaison à la calmoduline . ...
About 15% of couples are confronted with infertility problems. In half of the cases, a male factor component is found, often with abnormal semen parameters. The etiology of the large majority of male infertility remains unknown and genetic origin is probably responsible of a significant proportion of spermatogenesis disorders. This work comprises two parts: in the first part, the analysis of a large cohort of patients (n = 87), allowed us to identify two new mutations in AURKC gene. A splice site mutation [c.36-2A> G] was identified in only two brothers and the second variant identified [p.Y248*] is a recurrent mutation found in 11 unrelated patients. The second part of our study was carried out on 20 infertile patients with flagellar abnormalities associated with asthenozoospermia. We have applied the strategy of homozygosity by descent who has bring out two regions of homozygosity: the first region, located on chromosome 3, is common for 9/20 patients and the second one, located on chromosome 20, is common for 13/20 patients. Three candidate genes present in these regions were selected: KIF9, SPAG4 and DNAH1. Sequencing of DNAH1 gene has bring out three type of mutations: missense mutation [c.3877G> A], run-on mutation [c.12796 T> C] and splice site mutation [c.5094 +1 G> A] [c.11958-1G> A]. The absence of dnah1 protein has been shown by immunostaining of spermatozoa of a patient carrier the mutation [c.11958-1G> A] and confirms the degradation of the mutated transcript by NMD. An electron microscopic analysis of spermatozoa of one patient of the cohort reveals axoneme abnormalities. This study clarifies the diagnosis of male infertility and broadens the knowledge of the genes involved in spermatogenesis.
With the increased availability of genomic sequencing technologies, the molecular bases for kidney diseases such as nephronophthisis and mitochondrially inherited and autosomal-dominant tubulointerstitial kidney diseases (ADTKD) has become increasingly apparent. These tubulointerstitial kidney diseases (TKD) are monogenic diseases of the tubulointerstitium and result in interstitial fibrosis and tubular atrophy (IF/TA). However, monogenic inheritance alone does not adequately explain the highly variable onset of kidney failure and extra-renal manifestations. Phenotypes vary considerably between individuals harbouring the same pathogenic variant in the same putative monogenic gene, even within families sharing common environmental factors. While the extreme end of the disease spectrum may have dramatic syndromic manifestations typically diagnosed in childhood, many patients present a more subtle phenotype with little to differentiate them from many other common forms of non-proteinuric chronic kidney disease (CKD). This review summarises the expanding repertoire of genes underpinning TKD and their known phenotypic manifestations. Furthermore, we collate the growing evidence for a role of modifier genes and discuss the extent to which these data bridge the historical gap between apparently rare monogenic TKD and polygenic non-proteinuric CKD (excluding polycystic kidney disease).
Meckel syndrome, nephronophthisis, Joubert syndrome and Bardet–Biedl syndrome are caused by mutations in proteins that localize to the ciliary transition zone (TZ). The phenotypically distinct syndromes suggest that these TZ proteins have differing functions. However, mutations in a single TZ gene can result in multiple syndromes, suggesting that the phenotype is influenced by modifier genes. We performed a comprehensive analysis of ten zebrafish TZ mutants, including mks1, tmem216, tmem67, rpgrip1l, cc2d2a, b9d2, cep290, tctn1, nphp1 and nphp4, as well as mutants in ift88 and ift172. Our data indicate that variations in phenotypes exist between different TZ mutants, supporting different tissue-specific functions of these TZ genes. Further, we observed phenotypic variations within progeny of a single TZ mutant, reminiscent of multiple disease syndromes being associated with mutations in one gene. In some mutants, the dynamics of the phenotype became complex with transitory phenotypes that are corrected over time. We also demonstrated that multiple-guide-derived CRISPR/Cas9 F0 ‘crispant’ embryos recapitulate zygotic null phenotypes, and rapidly identified ciliary phenotypes in 11 cilia-associated gene candidates (ankfn1, ccdc65, cfap57, fhad1, nme7, pacrg, saxo2, c1orf194, ttc26, zmynd12 and cfap52).
Inherited cystic diseases of the kidneys are some of the most significant monogenic causes of renal disorders causing significant morbidity and mortality in both the pediatric and adult populations. There have been considerable advances in the past few decades in identifying and characterizing the genes responsible for these diseases. The genetic aspects, molecular pathogenesis, clinical features, and management of these disorders will be highlighted in this chapter.
Background
Nephronophthisis (NPHP) 4 gene encoding nephrocystin-4, which contributes to end-stage renal disease in children and young adults, is involved in the development of the heart and kidneys. Cardiorenal syndrome (CRS), which consists of bidirectional dysfunction of the heart and kidneys, is a risk factor for cardiovascular events. Single-nucleotide polymorphisms (SNPs) within the NPHP4 gene are reportedly associated with kidney function, even in adults. However, the association of NPHP4 gene variability with CRS and cardiovascular events remains unknown.Methods and resultsThis prospective cohort study included 2946 subjects who participated in a community-based health study with a 16-year follow-up period. We genotyped 11 SNPs within the NPHP4 gene whose minor allele frequency was greater than 0.1 in the Japanese population. The SNP rs12058375 was significantly associated with CRS and cardiovascular events. Multivariate logistic analysis demonstrated a significant association between the homozygous A-allele of rs12058375 with the presence of CRS. Haplotype analysis identified the haplotype with the A-allele of rs12058375 as an increased susceptibility factor for CRS. Kaplan–Meier analysis demonstrated that homozygous A-allele carriers of rs12058375 had the greatest risk of developing cardiovascular events among the NPHP4 variants. Multivariate Cox proportional hazard regression analysis revealed that the homozygous A-allele and heterozygous carriers of rs12058375 were associated with cardiovascular events after adjusting for confounding factors. The net reclassification index and integrated discrimination index were significantly improved by the addition of rs12058375 as a cardiovascular risk factor.Conclusion
Genetic variations in the NPHP4 gene were associated with CRS and cardiovascular events in the general population, suggesting that it may facilitate the early identification of high-risk subjects with CRS and cardiovascular events.
Bright light exposure in animals results in the selective degeneration of the outer retina, known as “retinal photic injury” (RPI). The susceptibility to RPI differs among rat strains. WKY rats display susceptibility to RPI with extensive retinal degeneration observed in the sagittal eye specimen, whereas LEW strain rats are resistant to it, showing only slight or no degeneration. In the present study, we first established an ethological screening method using the Morris water maze to discern differential susceptibility among the living rats. WKY and LEW were crossed to produce the first filial generation (F1) offspring. Maze-trained individuals were exposed to bright, white light. The screening test results demonstrated that the susceptibility to light-induced visual impairment in rats is a dominant Mendelian susceptibility trait, as F1 rats were susceptible to visual impairment like WKY rats. Therefore, F1 rats were backcrossed with recessive LEW to produce the first backcross offspring (BC1). Subsequent recurrent backcrossing while selecting for the susceptibility, indicated a segregation ratio of ca. 24% in BC1 and BC2 generations, indicating the involvement of two or more genes in the susceptibility. Further, microsatellite analysis of BC1-to-BC4 individuals using microsatellite markers mapped two susceptibility loci on chromosome segments 5q36 and 19q11-q12, named RPI susceptibility (Rpi)1 and Rpi2, respectively. This study provides an insight into mechanisms underlying differential susceptibility, which could help decipher the mechanism underlying the onset/progression of human age-related macular degeneration.
Renal hypodysplasia and cystic kidney diseases, the common non-glomerular causes of pediatric chronic kidney disease (CKD), are usually diagnosed by their clinical and imaging characteristics. The high degree of phenotypic heterogeneity, in both conditions, makes the correct final diagnosis dependent on genetic testing. It is not clear, however, whether the frequencies of damaged alleles vary among different ethnicities in children with non-glomerular CKD, and this will influence the strategy used for genetic testing. In this study, 69 unrelated children (40 boys, 29 girls) of predominantly Han Chinese ethnicity with stage 2–5 non-glomerular CKD caused by suspected renal hypodysplasia or cystic kidney diseases were enrolled and assessed by molecular analysis using proband-only targeted exome sequencing and array-comparative genomic hybridization. Targeted exome sequencing discovered genetic etiologies in 33 patients (47.8%) covering 10 distinct genetic disorders. The clinical diagnoses in 13/48 patients (27.1%) with suspected renal hypodysplasia were confirmed, and two patients were reclassified carrying mutations in nephronophthisis (NPHP) genes. The clinical diagnoses in 16/20 patients (80%) with suspected cystic kidney diseases were confirmed, and one patient was reclassified as carrying a deletion in the hepatocyte nuclear factor-1-beta gene (HNF1B). The diagnosis of one patient with unknown non-glomerular disease was elucidated. No copy number variations were identified in the 20 patients with negative targeted exome sequencing results. NPHP genes were the most common disease-causing genes in the patients with disease onsets above 6 years of age (14/45, 31.1%). The children with stage 2 and 3 CKD at onset were found to carry causative mutations in paired box gene 2 (PAX2) and HNF1B gene (11/24, 45.8%), whereas those with stage 4 and 5 CKD mostly carried causative mutations in NPHP genes (19/45, 42.2%). The causative genes were not suspected by the kidney imaging patterns at disease onset. Thus, our data show that in Chinese children with non-glomerular renal dysfunction caused by renal hypodysplasia and cystic kidney diseases, the common causative genes vary with age and CKD stage at disease onset. These findings have the potential to improve management and genetic counseling of these diseases in clinical practice.
Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and characterized by cysts. NPH is caused by mutations in over 20 different genes, most of which encode components of the primary cilium, an organelle in which important cellular signaling pathways converge. Ciliary signal transduction plays a critical role in kidney development and tissue homeostasis, and disruption of ciliary signaling has been associated with cyst formation, epithelial cell dedifferentiation and kidney function decline. Drugs have been identified that target specific signaling pathways (for example cAMP/PKA, Hedgehog, and mTOR pathways) and rescue NPH phenotypes in in vitro and/or in vivo models. Despite identification of numerous candidate drugs in rodent models, there has been a lack of clinical trials and there is currently no therapy that halts disease progression in NPH patients. This review covers the most important findings of therapeutic approaches in NPH model systems to date, including hypothesis-driven therapies and untargeted drug screens, approached from the pathophysiology of NPH. Importantly, most animal models used in these studies represent the cystic infantile form of NPH, which is less prevalent than the juvenile form. It appears therefore important to develop new models relevant for juvenile/adult NPH. Alternative non-orthologous animal models and developments in patient-based in vitro model systems are discussed, as well as future directions in personalized therapy for NPH.
Renal ciliopathies are a heterogenous group of inherited disorders leading to an array of phenotypes that include cystic kidney disease and renal interstitial fibrosis leading to progressive chronic kidney disease and end-stage kidney disease. The renal tubules are lined with epithelial cells that possess primary cilia that project into the lumen and act as sensory and signalling organelles. Mutations in genes encoding ciliary proteins involved in the structure and function of primary cilia cause ciliopathy syndromes and affect many organ systems including the kidney. Recognised disease phenotypes associated with primary ciliopathies that have a strong renal component include autosomal dominant and recessive polycystic kidney disease and their various mimics, including atypical polycystic kidney disease and nephronophthisis. The molecular investigation of inherited renal ciliopathies often allows a precise diagnosis to be reached where renal histology and other investigations have been unhelpful and can help in determining kidney prognosis. With increasing molecular insights, it is now apparent that renal ciliopathies form a continuum of clinical phenotypes with disease entities that have been classically described as dominant or recessive at both extremes of the spectrum. Gene-dosage effects, hypomorphic alleles, modifier genes and digenic inheritance further contribute to the genetic complexity of these disorders. This review will focus on recent molecular genetic advances in the renal ciliopathy field with a focus on cystic kidney disease phenotypes and the genotypes that lead to them. We discuss recent novel insights into underlying disease mechanisms of renal ciliopathies that might be amenable to therapeutic intervention.
Diverse human ciliopathies, including nephronophthisis (NPHP), Meckel syndrome (MKS) and Joubert syndrome (JBTS), can be caused by mutations affecting components of the transition zone, a ciliary domain near its base. The transition zone controls the protein composition of the ciliary membrane, but how it does so is unclear. To better understand the transition zone and its connection to ciliopathies, we defined the arrangement of key proteins in the transition zone using two-color stochastic optical reconstruction microscopy (STORM). This mapping revealed that NPHP and MKS complex components form nested rings comprised of nine-fold doublets. The NPHP complex component RPGRIP1L forms a smaller diameter transition zone ring within the MKS complex rings. JBTS-associated mutations in RPGRIP1L disrupt the architecture of the MKS and NPHP rings, revealing that vertebrate RPGRIP1L has a key role in organizing transition zone architecture. JBTS-associated mutations in TCTN2 , encoding an MKS complex component, also displace proteins of the MKS and NPHP complexes from the transition zone, revealing that RPGRIP1L and TCTN2 have interdependent roles in organizing transition zone architecture. To understand how altered transition zone architecture affects developmental signaling, we examined the localization of the Hedgehog pathway component SMO in human fibroblasts derived from JBTS-affected individuals. We found that diverse ciliary proteins, including SMO, accumulate at the transition zone in wild type cells, suggesting that the transition zone is a way station for proteins entering and exiting the cilium. JBTS-associated mutations in RPGRIP1L disrupt SMO accumulation at the transition zone and the ciliary localization of SMO. We propose that the disruption of transition zone architecture in JBTS leads to a failure of SMO to accumulate at the transition zone, disrupting developmental signaling in JBTS.
Background:
The clinical diagnosis of genetic renal diseases may be limited by the overlapping spectrum of manifestations between diseases or by the advancement of disease where clues to the original process are absent. The objective of this study was to determine whether genetic testing informs diagnosis and facilitates management of kidney disease patients.
Methods:
We developed a comprehensive genetic testing panel (KidneySeq) to evaluate patients with various phenotypes including cystic diseases, congenital anomalies of the kidney and urinary tract (CAKUT), tubulointerstitial diseases, transport disorders and glomerular diseases. We evaluated this panel in 127 consecutive patients ranging in age from newborns to 81 years who had samples sent in for genetic testing.
Results:
The performance of the sequencing pipeline for single-nucleotide variants was validated using CEPH (Centre de'Etude du Polymorphism) controls and for indels using Genome-in-a-Bottle. To test the reliability of the copy number variant (CNV) analysis, positive samples were re-sequenced and analyzed. For patient samples, a multidisciplinary review board interpreted genetic results in the context of clinical data. A genetic diagnosis was made in 54 (43%) patients and ranged from 54% for CAKUT, 53% for ciliopathies/tubulointerstitial diseases, 45% for transport disorders to 33% for glomerulopathies. Pathogenic and likely pathogenic variants included 46% missense, 11% nonsense, 6% splice site variants, 23% insertion-deletions and 14% CNVs. In 13 cases, the genetic result changed the clinical diagnosis.
Conclusion:
Broad genetic testing should be considered in the evaluation of renal patients as it complements other tests and provides insight into the underlying disease and its management.
Nephronophthisis (NPHP) is a renal ciliopathy and an autosomal recessive cause of cystic kidney disease, renal fibrosis, and end-stage renal failure, affecting children and young adults. Molecular genetic studies have identified more than 20 genes underlying this disorder, whose protein products are all related to cilia, centrosome, or mitotic spindle function. In around 15% of cases, there are additional features of a ciliopathy syndrome, including retinal defects, liver fibrosis, skeletal abnormalities, and brain developmental disorders. Alongside, gene identification has arisen molecular mechanistic insights into the disease pathogenesis. The genetic causes of NPHP are discussed in terms of how they help us to define treatable disease pathways including the cyclic adenosine monophosphate pathway, the mTOR pathway, Hedgehog signaling pathways, and DNA damage response pathways. While the underlying pathology of the many types of NPHP remains similar, the defined disease mechanisms are diverse, and a personalized medicine approach for therapy in NPHP patients is likely to be required.
Ciliopathies, including nephronophthisis (NPHP), Meckel syndrome (MKS) and Joubert syndrome (JBTS), can be caused by mutations affecting components of the transition zone, a domain near the base of the cilium that controls the protein composition of its membrane. We defined the three-dimensional arrangement of key proteins in the transition zone using two-colour stochastic optical reconstruction microscopy (STORM). NPHP and MKS complex components form nested rings comprised of nine-fold doublets. JBTS-associated mutations in RPGRIP1L or TCTN2 displace certain transition-zone proteins. Diverse ciliary proteins accumulate at the transition zone in wild-type cells, suggesting that the transition zone is a waypoint for proteins entering and exiting the cilium. JBTS-associated mutations in RPGRIP1L disrupt SMO accumulation at the transition zone and the ciliary localization of SMO. We propose that the disruption of transition-zone architecture in JBTS leads to a failure of SMO to accumulate at the transition zone and cilium, disrupting developmental signalling in JBTS.
Nephronophthisis comprises a clinically and genetically heterogenous group of autosomal recessive inherited tubulointerstitial cystic disorders. It represents the most frequent genetic cause of end-stage renal disease in children and young adults. Up to date mutations in 18 different genes (NPHP1-18) have been identified. Almost all gene products localize either to primary cilia or the ciliary base which leads to the classification of nephronophthisis as a ciliopathy. Nephronophthisis is often accompanied by anomalies in other organs. Several well described complex clinical syndromes can feature the renal picture of nephronophthisis, including Senior-Løken syndrome, Joubert syndrome, COACH syndrome, Jeune syndrome, Meckel-Gruber syndromea and others. Autosomal dominant interstitial kidney disease (ADIKD) is a rare genetic disorder characterized by a slowly progressive tubulo-interstitial nephropathy leading to end-stage renal disease in late adulthood. Although there is major clinical and histological overlap with nephronophthisis, autosomal dominant inheritance as well as progressive renal failure later in life are two main differences. So far three genes could be identified in which mutations lead to ADIKD: (1) UMOD, (2) REN and (3) MUC1.
Nephronophthisis-related ciliopathies (NPHP-RC) are a group of inherited diseases that affect genes encoding proteins that localize to primary cilia or centrosomes. With few exceptions, ciliopathies are inherited in an autosomal recessive manner, and affected individuals manifest early during childhood or adolescence. NPHP-RC are genetically very heterogeneous, and, currently, mutations in more than 90 genes have been described as single-gene causes. The phenotypes of NPHP-RC are very diverse, and include cystic-fibrotic kidney disease, brain developmental defects, retinal degeneration, skeletal deformities, facial dimorphism, and, in some cases, laterality defects, and congenital heart disease. Mutations in the same gene can give rise to diverse phenotypes depending on the mutated allele. At the same time, there is broad phenotypic overlap between different monogenic genes. The identification of monogenic causes of ciliopathies has furthered the understanding of molecular mechanism and cellular pathways involved in the pathogenesis.
Medullary cystic kidney disease (MCKD) is a hereditary disease associated with bilateral medullary polycysts and interstitial fibrosis. MCKD is typically associated with slowly progressive renal dysfunction. We herein report two rare elderly cases with enlarged kidneys and rapidly progressive renal dysfunction without myeloperoxidase anti-neutrophil cytoplasmic antibody (MPO-ANCA), PR3-ANCA, or anti-glomerular basement membrane (GBM) antibodies. Renal biopsies revealed extensive tubular dilatation and atrophy with interstitial fibrosis consistent with MCKD. Both patients began hemodialysis therapy a few months later. Our cases suggest a MCKD subgroup among elderly patients with an undefined genetic background, rapidly progressive renal dysfunction, and enlarged kidneys.
Nephronophthisis (NPHP) is a childhood cystic kidney disease, which almost invariably leads to end-stage renal disease in those affected. Recognition and diagnosis requires clinical suspicion, biochemical evaluation, renal imaging and historically, renal biopsy. Modern molecular genetics now allows a diagnosis to be made in a significant proportion of cases. Mutations in NPHP1 account for 20% of cases, but the disease is genetically heterogeneous with at least 20 different genes associated with NPHP. Recent developments in the fields of genetics and proteomics have led to increased understanding of the underlying pathogenetic defects. Almost all NPHP genes encode proteins, which localize to the primary cilia, basal body and centrosome. NPHP is a therefore considered to be a ciliopathy, and can be part of a broad spectrum of clinical disease that includes extra-renal manifestations including retinal degeneration, cerebellar ataxia, liver fibrosis and situs inversus. In this review, we discuss the historical descriptions of NPHP in the context of more recent developments in our understanding of this disease.
Nephronophthisis-related ciliopathy (NPHP-RC) is a common genetic cause of end-stage renal failure during childhood and adolescence and exhibits an autosomal recessive pattern of inheritance. Genetic diagnosis is quite limited owing to genetic heterogeneity in NPHP-RC. We designed a novel approach involving the step-wise screening of Sanger sequencing and targeted exome sequencing for the genetic diagnosis of 55 patients with NPHP-RC. First, five NPHP-RC genes were analyzed by Sanger sequencing in phenotypically classified patients. Known pathogenic mutations were identified in 12 patients (21.8%); homozygous deletions of NPHP1 in 4 juvenile nephronophthisis patients, IQCB1/NPHP5 mutations in 3 Senior–Løken syndrome patients, a CEP290/NPHP6 mutation in 1 Joubert syndrome patient, and TMEM67/MKS3 mutations in 4 Joubert syndrome patients with liver involvement. In the remaining undiagnosed patients, we applied targeted exome sequencing of 34 ciliopathy-related genes to detect known pathogenic mutations in 7 (16.3%) of 43 patients. Another 18 likely damaging heterozygous variants were identified in 13 NPHP-RC genes in 18 patients. In this study, we report a variety of pathogenic and candidate mutations identified in 55 patients with NPHP-RC in Korea using a step-wise application of two genetic tests. These results support the clinical utility of targeted exome sequencing to resolve the issue of allelic and genetic heterogeneity in NPHP-RC.
Die im Kindesalter vorkommenden zystischen Nierenkrankheiten sind in der folgenden Übersicht aufgelistet.
Nephronophthisis (NPHP) is an autosomal recessive cause of end-stage renal failure, typically within the first three decades of life. The condition may present insidiously with symptoms suggesting a urinary concentrating defect. Increased echogenicity seen on renal ultrasound is typical and corticomedullary cysts may also be evident. Renal histopathology demonstrates interstitial fibrosis, corticomedullary cysts and tubular basement membrane thinning and thickening. NPHP is a ciliopathy and is associated with extra-renal manifestations in 10–15% of patients. Features include retinal dystrophy and retinal degeneration, neurodevelopmental abnormalities, and a variety of other organ involvement. A molecular genetic diagnosis of NPHP should be sought, and will solve around 30% of cases. This avoids the need for renal biopsies in index cases and at risk siblings. All NPHP genes identified to date encode protein products that are expressed in the primary cilium or basal body/centrosome.
The primary causes of chronic kidney disease (CKD) in children differ from those of CKD in adults. In the USA the most common diagnostic groups of renal disease that manifest before the age of 25 years are congenital anomalies of the kidneys and urinary tract, steroid-resistant nephrotic syndrome, chronic glomerulonephritis and renal cystic ciliopathies, which together encompass >70% of early-onset CKD diagnoses. Findings from the past decade suggest that early-onset CKD is caused by mutations in any one of over 200 different monogenic genes. Developments in high-throughput sequencing in the past few years has rendered identification of causative mutations in this high number of genes feasible. Use of genetic analyses in patients with early onset-CKD will provide patients and their families with a molecular genetic diagnosis, generate new insights into disease mechanisms, facilitate aetiology-based classifications of patient cohorts for clinical studies, and might have consequences for personalized approaches to the prevention and treatment of CKD. In this Review, we discuss the implications of next-generation sequencing in clinical genetic diagnostics and the discovery of novel genes in early-onset CKD. We also delineate the resulting opportunities for deciphering disease mechanisms and the therapeutic implications of these findings.
Nephronophthisis (NPHP) is an autosomal recessive cystic kidney disease that represents the most frequent monogenic cause of end-stage renal disease (ESRD). Three clinical forms of NPHP that have been distinguished by onset of ESRD include infantile, juvenile, and adolescent NPHP, which manifest with ESRD at the median ages of 1 year, 13 years, and 15 years, respectively. Five different genes that are identified by positional cloning as mutated in NPHP include NPHP1, NPHP2/inversin, NPHP3, NPHP4,and NPHP5,defining NPHP types 1, 2, 3, 4, and 5, respectively. NPHP can occur in combination with extrarenal associations involving retina, cerebellum, liver, bones, and other organs. It can be associated with ocular motor apraxia type Cogan, with retinitis pigmentosa in about 10% of cases, with liver fibrosis, with cone-shaped epiphyses in Mainzer-Saldino syndrome, and with cerebellar vermis aplasia and coloboma of the optic nerve in Joubert syndrome type B. In Joubert syndrome type B (JBTS), a developmental disorder with multiple organ involvement, NPHP occurs in association with coloboma of the eye (or retinal degeneration), aplasia/hypoplasia of the cerebellar vermis with ataxia, and the facultative symptoms of psychomotor retardation, polydactyly, occipital encephalocele, and episodic neonatal tachy/dyspnea. A pathognomonic diagnostic feature of JBTS on axial magnetic resonance imaging (MRI) of the brain is prominent superior cerebellar peduncles, termed the "molar tooth sign" (MTS) of the midbrain-hindbrain junction. The presence of situs inversusis reported in a patient with infantile NPHP and mutations in the NPHP2/inversingene. The association of NPHP with cone shaped epiphyses of the phalanges (types 28 and 28A) is known as Mainzer-Saldino syndrome.
Cystic diseases of the kidney are some of the most significant monogenic causes of renal morbidity and mortality in both the pediatric and adult populations. There have been considerable advances in the past decade in identifying and characterizing the genes responsible for these disorders. The genetic aspects, molecular pathogenesis, clinical features, and management of these disorders will be highlighted in this chapter. Although cystic renal disease can be acquired, the primary aim of this chapter will be to focus on those forms that are inherited.
Studies in Chlamydomonas have illuminated the basic biology of many ciliary and basal body proteins involved in human diseases and developmental disorders, including PCD, hydrocephalus, epilepsy, situs inversus, and PKD. This chapter reviews past work on Chlamydomonas that has provided important insights into these diseases, and discusses additional diseases for which Chlamydomonas has the potential to be very informative in the future. Frequently, the human genes causing a disease have been identified by positional cloning, and the proteins they encode have been shown to be localized to cilia or basal bodies by immunofluorescence microscopy, but the functions of the proteins are understood poorly or not at all. ChlamydomonasIn many of these cases, Chlamydomonas offers the best opportunity for a detailed analysis that could lead to an understanding of the basic biology of the human disease protein. Diseases associated with them usually involve defects in the ciliary assembly machinery or ciliary signaling. These diseases include polycystic kidney disease (PKD), retinal degeneration and blindness, and several syndromes that usually involve kidney disease and/or blindness plus other symptoms. These diseases are explained in detail. Genomic stability is dependent on correct centriole duplication and function and control of the cell cycle may involve the primary cilium, so defects in cilia and basal bodies/centrioles also may lead to cancer, which is also covered here.
Next-generation sequencing (NGS) has transformed genomic research by decreasing the cost of sequencing and increasing the throughput. NGS platforms have evolved to provide an accurate and comprehensive means for the detection of molecular mutations, and the recent focus is on using NGS technology in clinical diagnosis. NGS analysis has three major components: enrichment, sequencing, and analysis. In the last several years, enrichment technologies based on hybridization or amplification principles have emerged. Similarly, sequencing platforms have continued to improve by increasing the sequencing output and decreasing the sequencing time and cost. Various enrichment and sequencing platform combinations have been utilized for the diagnosis of genetically heterogeneous disorders, and it is the topic of discussion for this chapter. We describe the employment of NGS approaches to the diagnosis of genetically heterogeneous disorders and mention advantages and challenges of these technologies in a clinical laboratory setting.
Nephronophthisis, an autosomal-recessive cystic kidney disease, is the most frequent monogenic cause for renal failure in childhood. Infantile and juvenile forms of nephronophthisis are known to originate from separate gene loci. We describe here a new disease form, adolescent nephronophthisis, that is clearly distinct by clinical and genetic findings. In a large, 340-member consanguineous Venezuelan kindred, clinical symptoms and renal pathology were evaluated. Onset of terminal renal failure was compared with that in a historical sample of juvenile nephronophthisis. Onset of terminal renal failure in adolescent nephronophthisis occurred significantly later (median age 19 years, quartile borders 16.0 and 25.0 years) than in juvenile nephronophthisis (median age 13.1 years, quartile borders 11.3 and 17.3 years; Wilcoxon test P=.0069). A total-genome scan of linkage analysis was conducted and evaluated by LOD score and total-genome haplotype analyses. A gene locus for adolescent nephronophthisis was localized to a region of homozygosity by descent, on chromosome 3q22, within a critical genetic interval of 2.4 cM between flanking markers D3S1292 and D3S1238. The maximum LOD score for D3S1273 was 5.90 (maximum recombination fraction .035). This locus is different than that identified for juvenile nephronophthisis. These findings will have implications for diagnosis and genetic counseling in hereditary chronic renal failure and provide the basis for identification of the responsible gene.
Juvenile nephronophthisis (NPH), an autosomal recessive cystic kidney disease, is the primary genetic cause of chronic renal failure in children. About two thirds of patients with NPH carry a large homozygous deletion at the gene locus NPH1 on 2q13. We here identify a novel gene. NPHP1, which extends over most of this common deletion. The 4.5-kb transcript encodes a protein with an SH3 domain, which is highly conserved throughout evolution. The 11-kb interval between the 3' end of NPHP1 and an inverted repeat containing the distal deletion breakpoint was found to contain the first exon of a second gene, MALL. In patients with a hemizygous deletion of the NPH1 region, additional point mutations were found in NPHP1 but not in MALL.
A database (SpliceDB) of known mammalian splice site sequences has been developed. We extracted 43 337 splice pairs from mammalian divisions of the gene-centered Infogene database, including sites from incomplete or alternatively spliced genes. Known EST sequences supported 22 815 of them. After discarding sequences with putative errors and ambiguous location of splice junctions the verified dataset includes 22 489 entries. Of these, 98.71% contain canonical GT-AG junctions (22 199 entries) and 0.56% have non-canonical GC-AG splice site pairs. The remainder (0.73%) occurs in a lot of small groups (with a maximum size of 0.05%). We especially studied non-canonical splice sites, which comprise 3.73% of GenBank annotated splice pairs. EST alignments allowed us to verify only the exonic part of splice sites. To check the conservative dinucleotides we compared sequences of human non-canonical splice sites with sequences from the high throughput genome sequencing project (HTG). Out of 171 human non-canonical and EST-supported splice pairs, 156 (91.23%) had a clear match in the human HTG. They can be classified after sequence analysis as: 79 GC-AG pairs (of which one was an error that corrected to GC-AG), 61 errors corrected to GT-AG canonical pairs, six AT-AC pairs (of which two were errors corrected to AT-AC), one case was produced from a non-existent intron, seven cases were found in HTG that were deposited to GenBank and finally there were only two other cases left of supported non-canonical splice pairs. The information about verified splice site sequences for canonical and non-canonical sites is presented in SpliceDB with the supporting evidence. We also built weight matrices for the major splice groups, which can be incorporated into gene prediction programs. SpliceDB is available at the computational genomic Web server of the Sanger Centre: http://genomic.sanger.ac. uk/spldb/SpliceDB.html and at http://www.softberry. com/spldb/SpliceDB.html.
Juvenile nephronophthisis type 1 is caused by mutations of NPHP1, the gene encoding for nephrocystin. The function of nephrocystin is presently unknown, but the presence of a Src homology 3 domain and its recently described interaction with p130(Cas) suggest that nephrocystin is part of the focal adhesion signaling complex. We generated a nephrocystin-specific antiserum and analyzed the interaction of native nephrocystin with endogenous proteins. Immunoprecipitation of nephrocystin revealed that nephrocystin forms protein complexes with p130(Cas), proline-rich tyrosine kinase 2 (Pyk2), and tensin, indicating that these proteins participate in a common signaling pathway. Expression of nephrocystin resulted in phosphorylation of Pyk2 on tyrosine 402 as well as activation of downstream mitogen-activated protein kinases, such as ERK1 and ERK2. Our findings suggest that nephrocystin helps to recruit Pyk2 to cell matrix adhesions, thereby initiating phosphorylation of Pyk2 and Pyk2-dependent signaling. A lack of functional nephrocystin may compromise Pyk2 signaling in a subset of renal epithelial cells.
Nephrocystin is the protein product of the gene mutated in juvenile nephronophthisis, an autosomal recessive cystic kidney disease afflicting children and young adults. Because the normal cellular function of nephrocystin is largely unknown, the molecular defects underlying disease pathogenesis remain obscure. Analysis of nephrocystin amino acid sequences from human and other species revealed three distinct conserved domains including Src homology 3 and coil-coil domains in the N-terminal region, as well as a large highly conserved C-terminal region bearing no obvious homology to other proteins and hence referred to as the "nephrocystin homology domain" (NHD). The objective of this study was to gain insight into nephrocystin function by defining functional properties of the conserved domains. We analyzed a series of nephrocystin deletion mutants expressed in Madin-Darby canine kidney and COS-7 cells. This analysis revealed previously unrecognized functional attributes of the NHD, including abilities to promote both self-association and epithelial cell-cell junctional targeting. We further observed that Madin-Darby canine kidney cell lines stably expressing a nephrocystin mutant with a deletion of the Src homology 3 domain have reduced ability to establish tight junctions as measured by transepithelial electrical resistance. Finally, from a two-hybrid screen and coimmunoprecipitation studies we identified members of the filamin family of actin-binding proteins as having the capacity to interact with the NHD. These findings support a functional role for nephrocystin as a docking protein involved in organizing a protein complex to regulate the actin cytoskeleton at sites of epithelial cell-cell adhesion and further suggest that these properties are important for establishing epithelial cell polarity.
Determination of recombination rates across the human genome has been constrained by the limited resolution and accuracy of existing genetic maps and the draft genome sequence. We have genotyped 5,136 microsatellite markers for 146 families, with a total of 1,257 meiotic events, to build a high-resolution genetic map meant to: (i) improve the genetic order of polymorphic markers; (ii) improve the precision of estimates of genetic distances; (iii) correct portions of the sequence assembly and SNP map of the human genome; and (iv) build a map of recombination rates. Recombination rates are significantly correlated with both cytogenetic structures (staining intensity of G bands) and sequence (GC content, CpG motifs and poly(A)/poly(T) stretches). Maternal and paternal chromosomes show many differences in locations of recombination maxima. We detected systematic differences in recombination rates between mothers and between gametes from the same mother, suggesting that there is some underlying component determined by both genetic and environmental factors that affects maternal recombination rates.
In 1951 Fanconi and co-workers described seven children from two families suffering from progressive renal insufficiency due to a chronic tubulointerstitial nephropathy. The disorder was termed “familial juvenile nephronophthisis”. A clinically and morphologically very similar sporadic case had been reported previously by Smith and Graham (1945). At autopsy they found numerous cysts in the renal medulla which they designated as “congenital medullary cysts of the kidney”.
This paper reports a rare congenital lesion of the kidneys in a child with intractable anemia. The anemia was not explained until routine examination revealed severe and unexpected azotemia, despite minimal urinary changes. Chronic progressive anemia and nitrogen retention continued to be the outstanding features during the subsequent period of eight months. Exhaustive clinical, roentgenographic and urologic studies during life could not be correlated with the unusual pathologic condition found in the kidneys on postmortem examination.
REPORT OF A CASE History.–The history comprises six hospital admissions from Sept. 12, 1942 to May 22, 1943. Brief summaries of each hospitalization follow, with inclusion of only the more significant results of laboratory examinations.First Hospitalization: M. L., a white girl 8 years old, was admitted to the Children's Clinic of the New York Hospital on Sept. 12, 1942 for study of a profound anemia of one year's duration. She was well until
Two siblings, a boy and a girl, with congenital blindness died at 8 and 9 years of age from renal failure. Autopsy was performed in one case. The kidneys showed evidence of dysplasia and of pyelonephritis. Earlier suggestions that renal dysplasia might be the primary cause in cases of chronic pyelonephritis in children are supported. Examination of the eyes indicated a congential defect, retinal aplasia.
Two siblings, a boy and a girl, with congenital blindness died at 8 and 9 years of age from renal failure. Autopsy was performed in one case. The kidneys showed evidence of dysplasia and of pyelonephritis. Earlier suggestions that renal dysplasia might be the primary cause in cases of chronic pyelonephritis in children are supported. Examination of the eyes indicated a congential defect, retinal aplasia.
The clinical and morphological findings are described in 27 children with nephronophthisis. Seventeen children were considered as sporadic cases. In 10 familial cases the presumed mode of inheritance was autosomal recessive. The clinical picture was rather uniform: polyuria-polydipsia, hyposthenuria, anemia, growth retardation, and azotemia with progressive renal failure. Six patients presented with tapeto-retinal degeneration. In a further seven children other ocular changes were detected. Two female siblings showed additional non-renal manifestations: mental retardation, pulmonary emphysema, skeletal anomalies, and congenital hepatic fibrosis.
Renal histology displayed a chronic sclerosing tubulo-interstitial nephropathy with extensive tubular atrophy and dedifferentiation. Medullary cysts were frequently found in end-stage kidneys. Immunofluorescence was either non-specific or completely negative. On electron microscopy, the tubular basement membrane changes predominated: thickening, lamellation, splitting, and deposition of microfibrils within the increased basement membrane substance. Detailed light- and electron microscopic findings were non-specific but the overall morphologic picture was characteristic and even diagnostic in conjunction with the clinical presentation.
A recurrence of nephronophthisis in transplanted kidneys has not been observed.
The pathogenesis of nephronophthisis is obscure but with respect to the morphologic findings a primary or secondary tubular basement membrane defect seems very likely.
Our experience suggests that nephronophthisis is a frequent cause of chronic renal failure in children and commonly associated with non-renal abnormalities. To avoid the separation of different syndromes presenting with a uniform renal disease but various non-renal manifestations, we suggest that the term “nephronopthisis complex” be used.
Familial juvenile nephronophthisis (NPH) is an autosomal recessive kidney disease that leads to end-stage renal failure in adolescence and is associated with the formation of cysts at the cortico-medullary junction of the kidneys. NPH is responsible for about 15% of end-stage renal disease in children, as shown by Kleinknecht and Habib. NPH in combination with autosomal recessive retinitis pigmentosa is known as the Senior-Løken syndrome (SLS) and exhibits renal pathology that is identical to NPH. We had excluded 40% of the human genome from linkage with a disease locus for NPH or SLS when antignac et al. first demonstrated linkage for an NPH locus on chromosome 2. We present confirmation of linkage of an NPH locus to microsatellite markers on chromosome 2 in nine families with NPH. By linkage analysis with marker AFM262xb5 at locus D2S176, a maximum lod score of 5.05 at a θmax = .03 was obtained. In a large NPH family that yielded at D2S176 a maximum lod score of 2.66 at θmax = .0, markers AFM172xc3 and AFM016yc5, representing loci D2S135 and D2S110, respectively, were identified as flanking markers, thereby defining the interval for an NPH locus to a region of approximately 15 cM. Furthermore, the cytogenetic assignment of the NPH region was specified to 2p12-(2q13 or adjacent bands) by calculation of linkage between these flanking markers and markers with known unique cytogenetic assignment. The refined map may serve as a genetic framework for additional genetic and physical mapping of the region.
The association of nephronophthisis and tapeto-retional degeneration was described by both Senior and Loken in 1961, but prior to 1974 only 28 cases had been published. This report describes 8 new cases in 27 members of 5 families. The severe juvenile type produces blindness in infancy and death from renal failure before the age of ten. The adult type is characterized by later onset, slower progression of the renal disease and milder ocular manifestations. The eye disease may be congenital amaurosis of Leber type, pigmentary retinal degeneration or retinitis punctata albescens and the electroretinogram (ERG) is of value in the diagnosis of these varieties of hereditary tapeto-retinal degeneration. Renal involvement is often asymptomatic. Defective urinary concentration leading to polyuria and polydipsia is the earliest sign. Proteinuria is inconstant and urinary sediment is often normal. Two patients had aminoaciduria. The disease progresses inexorably to chronic renal failure. One patient has been successfully transplanted and two others are on chronic hemodialysis. Renal histological changes are those of nephronophthisis with tubulointerstitial lesions and multiple cysts. Senior-Loken syndrome appears to be transmitted by a single autosomal recessive pleotropic gene of variable expression. Degeneration of neuroepithelium and renal tubular epithelium, both tissues of ectodermal origin, may represent a genetically determined enzyme abnormality.
An efficient strategy for mapping human genes that cause recessive traits has been devised that uses mapped restriction fragment
length polymorphisms (RFLPs) and the DNA of affected children from consanguineous marriages. The method involves detection
of the disease locus by virtue of the fact that the adjacent region will preferentially be homozygous by descent in such inbred
children. A single affected child of a first-cousin marriage is shown to contain the same total information about linkage
as a nuclear family with three affected children. Calculations show that it should be practical to map a recessive disease
gene by studying DNA from fewer than a dozen unrelated, affected inbred children, given a complete RFLP linkage map. The method
should make it possible to map many recessive diseases for which it is impractical or impossible to collect adequate numbers
of families with multiple affected offspring.
We conducted electro-oculographic and electroretinographic studies of six families with the autosomal recessively inherited Senior-Loken syndrome (juvenile familial nephronophthisis or medullary cystic disease in association with tapetoretinal degeneration). Sixteen patients had both renal and ocular involvement. In two families consanguinity between the patients was established. Routine ophthalmologic examination of relatives without renal involvement showed no retinal abnormalities, but electro-oculographic and electroretinographic studies were helpful in detecting 16 asymptomatic family members who carried the gene.
Familial juvenile nephronophthisis (NPH) is a chronic autosomal recessive kidney disease responsible for 15% of end stage renal failure in children. NPH is frequently (16% of cases) associated with Leber amaurosis (termed Senior-Løken syndrome, SLS). Linkage analyses, performed in 22 multiplex NPH families (18 without and 4 with ocular abnormalities), have localized the gene to a region between D2S48 and D2S51 on chromosome 2p. This was confirmed using adjacent microsatellite markers, one of which (AFM220ze3 at the D2S160 locus) gave a lod score of 4.78 at theta = 0.05 in the 18 families with isolated NPH, whereas the same marker excluded linkage with SLS. These results demonstrate linkage of the purely renal form of NPH to chromosome 2p, and suggest that there may be genetic heterogeneity between NPH and SLS.
Familial juvenile nephronophthisis (NPH) is an autosomal recessive kidney disease that leads to end-stage renal failure in adolescence and is associated with the formation of cysts at the cortico-medullary junction of the kidneys. NPH is responsible for about 15% of end-stage renal disease in children, as shown by Kleinknecht and Habib. NPH in combination with autosomal recessive retinitis pigmentosa is known as the Senior-Løken syndrome (SLS) and exhibits renal pathology that is identical to NPH. We had excluded 40% of the human genome from linkage with a disease locus for NPH or SLS when Antignac et al. first demonstrated linkage for an NPH locus on chromosome 2. We present confirmation of linkage of an NPH locus to microsatellite markers on chromosome 2 in nine families with NPH. By linkage analysis with marker AFM262xb5 at locus D2S176, a maximum lod score of 5.05 at a theta max = .03 was obtained. In a large NPH family that yielded at D2S176 a maximum lod score of 2.66 at theta max = .0, markers AFM172xc3 and AFM016yc5, representing loci D2S135 and D2S110, respectively, were identified as flanking markers, thereby defining the interval for an NPH locus to a region of approximately 15 cM. Furthermore, the cytogenetic assignment of the NPH region was specified to 2p12-(2q13 or adjacent bands) by calculation of linkage between these flanking markers and markers with known unique cytogenetic assignment. The refined map may serve as a genetic framework for additional genetic and physical mapping of the region.
The great increase in successful linkage studies in a number of higher eukaryotes during recent years has essentially resulted from major improvements in reference genetic linkage maps, which at present consist of short tandem repeat polymorphisms of simple sequences or microsatellites. We report here the last version of the Généthon human linkage map. This map consists of 5,264 short tandem (AC/TG)n repeat polymorphisms with a mean heterozygosity of 70%. The map spans a sex-averaged genetic distance of 3,699 cM and comprises 2,335 positions, of which 2,032 could be ordered with an odds ratio of at least 1,000:1 against alternative orders. The average interval size is 1.6 cM; 59% of the map is covered by intervals of 2 cM at most and 1% remains in intervals above 10 cM.
A novel type of infantile nephronophthisis was identified in an extended Bedouin family from Israel. This disease has an autosomal recessive mode of inheritance, with the phenotypic presentation ranging from a Potter-like syndrome to hyperechogenic kidneys, renal insufficiency, hypertension, and hyperkalemia. Affected individuals show rapid deterioration of kidney function, leading to end-stage renal failure within 3 years. Histopathologic examination of renal tissue revealed variable findings, ranging from infantile polycystic kidneys to chronic tubulointerstitial nephritis, fibrosis, and cortical microcysts. A known familial juvenile nephronophthisis locus on chromosome 2q13 and autosomal recessive polycystic kidney disease on chromosome 6p21.1-p12 were excluded by genetic linkage analysis. A genomewide screen for linkage was conducted by searching for a locus inherited by descent in all affected individuals. Pooled DNA samples from parents and unaffected siblings and individual DNA samples from four affected individuals were used as PCR templates with trinucleotide- and tetranucleotide-repeat polymorphic markers. Using this approach, we identified linkage to infantile nephronophthisis for markers on chromosome 9q22-31. The disorder maps to a 12.9-cM region flanked by markers D9S280 and GGAT3G09.
Tapeto-retinal degeneration is frequent in patients with nephronophthisis. Association of the most severe forms of tapeto-retinal dystrophy with NPH identifies a syndrome described first by Senior et al and Loken et al. This syndrome is distinct on molecular grounds from pure renal nephronophthisis (NPH1), which has its gene locus mapped on chromosome 2q13. We describe three families with large homozygous deletion of the NPH1 locus in which mild to moderate ocular lesions due to tapeto-retinal degeneration coexisted and were correlated to renal defects. This new association of NPH1 with retinal dystrophy is characterized by focal lesions of retina and is pauci-symptomatic in clinical presentation. For this reason it may remain unrecognized in most NPH1 patients.
Juvenile nephronophthisis, an autosomal recessive cystic kidney disease, is the primary genetic cause for chronic renal failure in children. The gene (NPHP1) for nephronophthisis type 1 has recently been identified. Its gene product, nephrocystin, is a novel protein of unknown function, which contains a src-homology 3 domain. To study tissue expression and analyze amino acid sequence conservation of nephrocystin, the full-length murine Nphp1 cDNA sequence was obtained and Northern and in situ hybridization analyses were performed for extensive expression studies. The results demonstrate widespread but relatively weak NPHP1 expression in the human adult. In the adult mouse there is strong expression in testis. This expression occurs specifically in cell stages of the first meiotic division and thereafter. In situ hybridization to whole mouse embryos demonstrated widespread and uniform expression at all developmental stages. Amino acid sequence conservation studies in human, mouse, and Caenorhabditis elegans show that in nephrocystin the src-homology 3 domain is embedded in a novel context of other putative domains of protein-protein interaction, such as coiled-coil and E-rich domains. It is concluded that for multiple putative protein-protein interaction domains of nephrocystin, sequence conservation dates back at least to Caenorhabditis elegans. The previously described discrepancy between widespread tissue expression and the restriction of symptoms to the kidney has now been confirmed by an in-depth expression study.
Crk-associated substrate (p130(Cas), Cas) is a docking protein first recognized as having elevated phosphotyrosine content in mammalian cells transformed by v-Src and v-Crk oncoproteins. Subsequent studies have implicated Cas in the control of normal cell behavior through its roles in integrin-mediated signal transduction and organization of the actin cytoskeleton at sites of cell adhesion. In this study, we sought to gain new insight into normal Cas function by identifying previously unrecognized interacting proteins. A yeast two-hybrid screen using the C-terminal region of Cas as a bait identified the Src homology 3 (SH3) domain of the mouse "nephrocystin" protein-orthologous to a human protein whose loss of function leads to the cystic kidney disease familial juvenile nephronophthisis. The putative full-length mouse and partial canine nephrocystin sequences were deduced from cDNA clones. Additional studies using epitope-tagged mouse nephrocystin indicated that nephrocystin and Cas can interact in mammalian cells and revealed that both proteins prominently localize at or near sites of cell-cell contact in polarized Madin-Darby canine kidney epithelial cells. Our findings provide novel insight into the normal cellular activities regulated by both Cas and nephrocystin, and raise the possibility that these proteins have a related function in polarized epithelial cells.
Nephronophthisis (NPH) and medullary cystic kidney disease (MCKD) constitute a group of renal cystic diseases that share the macroscopic feature of cyst development at the corticomedullary border of the kidneys. The disease variants also have in common a characteristic renal histologic triad of tubular basement membrane disintegration, tubular atrophy with cyst development, and interstitial cell infiltration with fibrosis. NPH and, in most instances, MCKD lead to chronic renal failure with an onset in the first two decades of life for recessive NPH and onset in adult life for autosomal dominant MCKD. There is extensive genetic heterogeneity with at least three different loci for NPH (NPHP1, NPHP2, and NPHP3) and two different loci for MCKD (MCKD1 and MCKD2). Juvenile nephronophthisis, in addition, can be associated with extrarenal organ involvement. As a first step toward understanding the pathogenesis of this disease group, the gene (NPH1) for juvenile nephronophthisis (NPH1) has been identified by positional cloning. Its gene product, nephrocystin, is a novel protein of unknown function that contains a src-homology 3 domain. It is hypothesized that the pathogenesis of NPH might be related to signaling processes at focal adhesions (the contact points between cells and extracellular matrix) and/or adherens junctions (the contact points between cells). This hypothesis is based on the fact that most src-homology 3-containing proteins are part of focal adhesion signaling complexes, on animal models that exhibit an NPH-like phenotype, and on the recent finding that nephrocystin binds to the protein p130(cas), a major mediator of focal adhesion signaling.
Tubulointerstitial fibrosis invariably accompanies the course of chronic renal failure towards end-stage renal disease. Tubular epithelial cells, the predominant cell type in the tubulointerstitium, are increasingly being recognized for playing a dominant role as mediators of renal fibrogenesis. Tubular epithelial cells become activated either by the glomerular ultrafiltrate from their apical side or by mononuclear cells from their basolateral side. They initiate the scarring process by secreting chemokines, which in return attract mononuclear cells as well as growth factors that stimulate interstitial fibroblasts. In later phases of renal fibrogenesis, cellular changes of tubular epithelial cells contribute to the chronic impairment of renal function. Whereas tubular epithelial cells react by proliferation or hypertrophy to initial stimuli, they may undergo apoptosis or transdifferentiate into fibroblasts, and thus contribute to tubular atrophy in later stages of progressive renal disease. Resident interstitial fibroblasts are also important in renal fibrogenesis, and recent research has demonstrated that these cells are much more heterogeneous than expected. Cytokines such as fibroblast growth factor type 2 and epithelial growth factor have been shown to be pro-fibrogenic, whereas hepatocyte growth factor and bone morphogenic protein type 7 may inhibit fibrogenesis. Despite recent progress, further research is mandatory for a better understanding and the development of novel therapeutic approaches.
Senior-Løken syndrome is an autosomal recessive disease with the main features of nephronophthisis (NPH) and Leber congenital amaurosis. The gene for adolescent nephronophthisis (NPHP3) was recently localized to chromosome 3q21-q22. The hypothesis was tested that Senior-Løken syndrome (SLS) might localize to the same region by studying a kindred of German ancestry with extended consanguinity and typical findings of SLS. Twenty highly polymorphic markers located in the vicinity of the NPHP3 genetic region were tested. Haplotype analysis revealed homozygosity by descent in affected individuals, and linkage analysis yielded a parametric maximum multipoint logarithm of likelihood of odds (LOD) score of 3.14, thus identifying the first locus for SLS. The SLS1 locus is flanked by D3S1587 and D3S621 and contains a 14-cM interval that contains the whole critical NPHP3 region. Three additional families with SLS were studied, and evidence for genetic heterogeneity in one of them was found. Localization of a SLS locus to the region of NPHP3 opens the possibilities of both diseases arising by mutations within the same pleiotropic gene or two adjacent genes.
For nephronophthisis (NPHP), the primary genetic cause of chronic renal failure in young adults, three loci have been mapped. To identify a new locus for NPHP, we here report on total-genome linkage analysis in seven families with NPHP, in whom we had excluded linkage to all three known NPHP loci. LOD scores >1 were obtained at nine loci, which were then fine mapped at 1-cM intervals. Extensive total-genome haplotype analysis revealed homozygosity in one family, in the region of the PCLN1 gene. Subsequent mutational analysis in this gene revealed PCLN1 mutations, thereby allowing exclusion of this family as a phenocopy. Multipoint linkage analysis for the remaining six families with NPHP together yielded a maximum LOD score (Z(max)) of 8.9 (at D1S253). We thus identified a new locus, NPHP4, for nephronophthisis. Markers D1S2660 and D1S2642 are flanking NPHP4 at a 2.9-cM critical interval. In one family with NPHP4, extensive genealogical studies were conducted, revealing consanguinity during the 17th century. On the basis of haplotype sharing by descent, we obtained a multipoint Z(max) of 5.8 for D1S253 in this kindred alone. In addition, we were able to localize to the NPHP4 locus a new locus for Senior-Løken syndrome, an NPHP variant associated with retinitis pigmentosa.
A family is described in which at least four and probably six of the 13 children had a nephropathy closely resembling juvenile familial nephronophthisis. All six of these patients also had tapetoretinal degeneration.
Neph-rocystin forms a multimeric protein complex with Pyk2, p130cas and tensin, and triggers phosphorylation and acti-vation of Pyk2 SpliceDB data-base of canonical and non-canonical mammaliansplicesites
- T Benzing
- P Gerke
- F Hildebrandt
- E Kim
- Walz
Nat Genet 3:342–345 Benzing T, Gerke P, Hildebrandt F, Kim E, Walz G (2001)Neph-rocystin forms a multimeric protein complex with Pyk2, p130cas and tensin, and triggers phosphorylation and acti-vation of Pyk2. Proc Natl Acad Sci USA 98:9784–9789 Burset M, Seledtsov IA, Solovyev VV (2001) SpliceDB data-base of canonical and non-canonical mammaliansplicesites
Juvenile familial nephropathy with tapetoretinal degeneration: a new ocu-lorenal dystrophy Congenital medullary cysts of the kidneys with severe refractory anemia
- B Ai Friedmann
- Braudo
- Ch Smith
- Graham
- Jb
B, Friedmann AI, Braudo JL (1961) Juvenile familial nephropathy with tapetoretinal degeneration: a new ocu-lorenal dystrophy. Am J Ophthalmol 52:625–633 Smith CH, Graham JB (1945) Congenital medullary cysts of the kidneys with severe refractory anemia. Am J Dis Child 69:369–377
Nephrocystin forms a multimeric protein complex with Pyk2, p130cas and tensin, and triggers phosphorylation and activation of Pyk2
- T Benzing
- P Gerke
- F Hildebrandt
- E Kim
- G Walz
Benzing T, Gerke P, Hildebrandt F, Kim E, Walz G (2001) Nephrocystin forms a multimeric protein complex with Pyk2,
p130cas and tensin, and triggers phosphorylation and activation of Pyk2. Proc Natl Acad Sci USA 98:9784-9789
Die familiä re juvenile Nephronophthise
- G E Hanhart
- A Albertini
- E Uhlinger
- G Dolivo
- Prader
G, Hanhart E, Albertini A, Uhlinger E, Dolivo G, Prader A (1951) Die familiä re juvenile Nephronophthise. Helv Paediatr Acta 6:1–49
Juvenile nephronophthisis Pediatric nephrology Molecular genetics of the neph-ronophthisis-medullary cystic disease complex
- Williams Wilkins
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Juvenile nephronophthisis
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Hildebrandt F (1999) Juvenile nephronophthisis. In: Avner E,
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contained the following error in the Electronic-Database Information section: Preliminary BankIt numbers should have been replaced by permanent GenBank numbers for full-length NPHP4 cDNAs in human, mouse, and Caenorhabditis elegans (acession numbers AF537130, AF537131, and Z81579, respectively)
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Erratum
In the November 2002 issue of the Journal, the article "A
Gene Mutated in Nephronophthisis and Retinitis Pigmentosa Encodes a Novel Protein, Nephroretinin, Conserved in
Evolution," by Otto et al. (71:1161-1167), contained the
following error in the Electronic-Database Information section: Preliminary BankIt numbers should have been replaced
by permanent GenBank numbers for full-length NPHP4
cDNAs in human, mouse, and Caenorhabditis elegans (acession numbers AF537130, AF537131, and Z81579, respectively). The authors regret this error.
Nephrocystin forms a multimeric protein complex with Pyk2, p130cas and tensin, and triggers phosphorylation and activation of Pyk2
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Die familiäre juvenile Nephronophthise
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A comprehensive genetic map of the human genome based on 5,264 microsatellites
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