A 1-Mb BAC/PAC-based physical map of the autosomal recessive polycystic kidney disease gene (PKHD1) region on chromosome 6

Molecular genetics of autosomal recessive polycystic kidney disease

Autosomal recessive polycystic kidney disease (ARPKD) is a severe form of inherited childhood nephropathy ( approximately 1:20,000 live births) characterized by fusiform dilatation of collecting ducts and congenital hepatic fibrosis. Up to 30% die as neonates due to respiratory insufficiency and the majority of surviving infants develop hypertension. Progression to end stage renal disease occurs in 20-45% of cases within 15 years but a proportion maintain renal function into adulthood where complications of liver disease predominate. The ARPKD disease gene, PKHD1, has recently been identified through analysis of an orthologous animal model, the PCK rat. PKHD1 is a large gene ( approximately 470 kb) with 67 exons from which multiple transcripts may be generated by alternative splicing. It is highly expressed in kidney, with lower levels in liver and pancreas. The ARPKD protein, fibrocystin (4074 aa and 447 kDa), is predicted to be an integral membrane, receptor-like protein containing multiple copies of an Ig-like domain (TIG). Fibrocystin is localized to the branching ureteric bud, collecting and biliary ducts, consistent with the disease phenotype, and often absent from ARPKD tissue. In common with other PKD-related proteins, fibrocystin is localized to the primary cilia of renal epithelial cells, reinforcing the link between ciliary dysfunction and cyst development. Screens of PKHD1 have revealed 119 different mutations of various types spread throughout the gene. Several ancestral changes have been described, some localized to specific geographic populations. The majority of patients are compound heterozygotes and preliminary genotype/phenotype studies associate two truncating mutations with severe disease. The complexities of PKHD1, marked allelic heterogeneity and high level of missense changes complicate gene-based diagnostics.

A complete mutation screen of PKHD1 in autosomal-recessive polycystic kidney disease (ARPKD) pedigrees

BACKGROUND

Autosomal-recessive polycystic kidney disease (ARPKD) is an important neonatal nephropathy characterized by fusiform dilation of collecting ducts, congenital hepatic fibrosis, and in some cases Caroli's disease. The ARPKD gene, PKHD1, has recently been identified. Herein we describe an effective method for PKHD1 mutation screening and the results from analysis of a novel ARPKD cohort.

METHODS

The coding region of PKHD1 was amplified as 79 fragments and analyzed for base pair changes by denaturing high-performance liquid chromatography (DHPLC). Forty-seven ARPKD and 14 pedigrees with congenital hepatic fibrosis and/or Caroli's disease, were screened for PKHD1 mutations.

RESULTS

Thirty-three different mutations were detected on 57 alleles (51.1% ARPKD, 32.1% congenital hepatic fibrosis/Caroli's disease). In the 22 pedigrees where both mutations were identified, two were homozygous for 9689delA and the remainder were compound heterozygotes; a combination of truncating, missense and splicing changes. Patients with two truncating mutations all died in the perinatal period. Two frequent truncating mutations were identified: 9689delA (9 alleles) and 5896insA (8 alleles) plus some more common missense changes; haplotype analysis indicated most were ancestral mutations.

CONCLUSION

DHPLC has been established as a rapid mutation screening method for ARPKD. The mutation detection rate was high in severely affected patients (85%), lower in those with moderate ARPKD (41.9%), and low, but significant, in adults with congenital hepatic fibrosis/Caroli's disease (32.1%). The prospects for gene-based diagnostics are complicated by the large gene size, marked allelic heterogeneity, and clinical diversity of the ARPKD phenotype. Identification of some common mutations, especially in specific populations, will aid mutation screening.

Refinement of the autosomal recessive polycystic kidney disease (PKHD1) interval and exclusion of an EF hand-containing gene as a PKHD1 candidate gene

Autosomal recessive polycystic kidney disease (ARPKD) is an often devastating form of polycystic kidney disease that presents primarily in infancy. The locus, PKHD1 (polycystic kidney and hepatic disease 1), on chromosome 6p21.1-p12, has been linked to all classical forms of this disorder. In previous studies, we cloned the PKHD1 interval in a set of overlapping YACs, converted this YAC-based framework into a BAC/PAC contig, and delimited the critical interval to a region flanked by the markers D6S1714 and D6S1024. We now have refined the genetic interval using new polymorphic markers developed from our BAC/PAC resources. In addition, we have evaluated a recently identified, EF hand-containing gene that maps to the interval of interest, established its transcript sequence, defined its genomic organization, and excluded this new gene as a PKHD1 candidate. Therefore, this study has narrowed the PKHD1 interval and excluded a potentially relevant gene as a PKHD1 candidate gene. This further refinement of the PKHD1 interval will facilitate efforts to identify the PKHD1 gene by positional cloning. These data also provide additional, highly polymorphic markers for haplotype-based diagnostic testing for ARPKD.

A novel gene encoding a TIG multiple domain protein is a positional candidate for autosomal recessive polycystic kidney disease

Autosomal recessive polycystic kidney disease (ARPKD) is a common hereditary renal cystic disease in infants and children. By genetic linkage analyses, the gene responsible for this disease, termed polycystic kidney and hepatic disease 1 (PKHD1), was mapped on human chromosome 6p21.1-p12, and has been further localized to a 1-cM genetic interval flanked by the D6S1714/D6S243 (telomeric) and D6S1024 (centromeric) markers. We recently identified a novel gene in this genetic interval from kidney cDNA, using cloning strategies. The gene PKHD1 (PKHD1-tentative) encodes a novel 3396-amino-acid protein with no apparent homology with any known proteins. We named its gene product "tigmin" because it contains multiple TIG domains, which usually are seen in proteins containing immunoglobulin-like folds. PKHD1 encodes an 11.6-kb transcript and is composed of 61 exons spanning an approximately 365-kb genomic region on chromosome 6p12-p11.2 adjacent to the marker D6S1714. Northern blot analyses demonstrated that the gene has discrete bands with one peak signal at approximately 11 kb, indicating that PKHD1 is likely to have multiple alternative transcripts. PKHD1 is highly expressed in adult and infant kidneys and weakly expressed in liver in northern blot analysis. This expression pattern parallels the tissue involvement observed in ARPKD. In situ hybridization analysis further revealed that the expression of PKHD1 in the kidney is mainly localized to the epithelial cells of the collecting duct, the specific tubular segment involved in cyst formation in ARPKD. These features of PKHD1 make it a strong positional candidate gene for ARPKD.

PKHD1, the polycystic kidney and hepatic disease 1 gene, encodes a novel large protein containing multiple immunoglobulin-like plexin-transcription-factor domains and parallel beta-helix 1 repeats

Autosomal recessive polycystic kidney disease (ARPKD) is a severe form of polycystic kidney disease that presents primarily in infancy and childhood and that is characterized by enlarged kidneys and congenital hepatic fibrosis. We have identified PKHD1, the gene mutated in ARPKD. PKHD1 extends over > or =469 kb, is primarily expressed in human fetal and adult kidney, and includes a minimum of 86 exons that are variably assembled into a number of alternatively spliced transcripts. The longest continuous open reading frame encodes a 4,074-amino-acid protein, polyductin, that is predicted to have a single transmembrane (TM)-spanning domain near its carboxyl terminus, immunoglobulin-like plexin-transcription-factor domains, and parallel beta-helix 1 repeats in its amino terminus. Several transcripts encode truncated products that lack the TM and that may be secreted if translated. The PKHD1-gene products are members of a novel class of proteins that share structural features with hepatocyte growth-factor receptor and plexins and that belong to a superfamily of proteins involved in regulation of cell proliferation and of cellular adhesion and repulsion.

Molecular basis of polycystic kidney disease: PKD1, PKD2 and PKHD1

Recent developments have helped elucidate the function of the autosomal dominant polycystic kidney disease proteins, polycystin-1 and polycystin-2, and have revealed the primary defect in autosomal recessive polycystic kidney disease, by positional cloning of the gene, PKHD1. Several studies demonstrating that polycystin-2 can act as a calcium-ion-permeable cation channel, and that polycystin-1 may be involved in regulating/localizing this channel, have provided compelling evidence of the function of these proteins. A role in regulating intracellular calcium levels seems likely, with the many cellular abnormalities associated with cystogenesis due to a disruption of calcium homeostasis. Improved mutation analysis in autosomal dominant polycystic kidney disease has led to the finding of genotype/phenotype correlations which could be related to possible cleavage of polycystin-1. A major recent breakthrough has revealed the primary defect in autosomal recessive polycystic kidney disease. Genetic analysis showed that the PCK rat model is orthologous to autosomal recessive polycystic kidney disease, and allowed the human gene, PKHD1, to be precisely localized and identified. PKHD1 is a large gene, encoding a protein, fibrocystin, of 4074 amino acids, which is predicted to have a large extracellular region, a single transmembrane domain and a short cytoplasmic tail. Fibrocystin may act as a receptor with critical roles in collecting-duct and biliary development.

A new mouse model for autosomal recessive polycystic kidney disease

In the course of large-scale mutagenesis studies, we discovered a mutant that provides a new mouse model for human autosomal recessive polycystic kidney disease. Animals homozygous for this mutation, T(2;10)67Gso, present evidence of grossly cystic renal and hepatic tissue at birth and a limited survival time of 3-4 days. The recessively expressed phenotype is associated with inheritance of a reciprocal translocation involving mouse chromosomes 2 and 10. Here we describe the pathology and phenotype of this new mutation. The mapping of the chromosomal breakpoint to the 1.0-cM critical region defined for another mouse autosomal recessive polycystic kidney disease model, juvenile congenital polycystic kidney disease (jcpk), led us to undertake the complementation testing that confirmed T(2;10)67Gso and jcpk are allelic. Because of the strong resemblance between the phenotype associated with these mouse mutations and early childhood polycystic kidney disease, and because of advantages offered by reciprocal translocations for gene mapping and cloning, T(2;10)67Gso should prove a valuable asset for studies concerning this fatal disease.

The gene mutated in autosomal recessive polycystic kidney disease encodes a large, receptor-like protein

Autosomal recessive polycystic kidney disease (ARPKD) is characterized by dilation of collecting ducts and by biliary dysgenesis and is an important cause of renal- and liver-related morbidity and mortality. Genetic analysis of a rat with recessive polycystic kidney disease revealed an orthologous relationship between the rat locus and the ARPKD region in humans; a candidate gene was identified. A mutation was characterized in the rat and screening the 66 coding exons of the human ortholog (PKHD1) in 14 probands with ARPKD revealed 6 truncating and 12 missense mutations; 8 of the affected individuals were compound heterozygotes. The PKHD1 transcript, approximately 16 kb long, is expressed in adult and fetal kidney, liver and pancreas and is predicted to encode a large novel protein, fibrocystin, with multiple copies of a domain shared with plexins and transcription factors. Fibrocystin may be a receptor protein that acts in collecting-duct and biliary differentiation.

Phenotypic analysis of conditionally immortalized cells isolated from the BPK model of ARPKD

To study the pathophysiology of autosomal recessive polycystic kidney disease (ARPKD), we sought to develop conditionally immortalized control and cystic murine collecting tubule (CT) cell lines. CT cells were isolated from intercross breedings between BPK mice (bpk(+/-)), a murine model of ARPKD, and the Immorto mice (H-2K(b)-ts-A58(+/+)). Second-generation outbred offspring (BPK x Immorto) homozygous for the BPK mutation (bpk(-/-); Im(+/+/-); cystic BPK/H-2K(b)-ts-A58), were phenotypically indistinguishable from inbred cystic BPK animals (bpk(-/-)). Cystic BPK/H-2K(b)-ts-A58 mice developed biliary ductal ectasia and massively enlarged kidneys, leading to renal failure and death by postnatal day 24. Principal cells (PC) were isolated from outbred cystic and noncystic BPK/H-2K(b)-ts-A58 littermates at specific developmental stages. Epithelial monolayers were under nonpermissive conditions for markers of epithelial cell polarity and PC function. Cystic and noncystic cells displayed several properties characteristic of PCs in vivo, including amiloride-sensitive sodium transport and aquaporin 2 expression. Cystic cells exhibited apical epidermal growth factor receptor (EGFR) mislocalization but normal expression of ZO-1 and E-cadherin. Hence, these cell lines retain the requisite characteristics of PCs, and cystic BPK/H-2K(b)-ts-A58 PCs retained the abnormal EGFR membrane expression characteristic of ARPKD. These cell lines represent important new reagents for studying the pathogenesis of ARPKD.

Role of CFTR in autosomal recessive polycystic kidney disease

An extensive body of in vitro data implicates epithelial chloride secretion, mediated through cystic fibrosis transmembrane conductance regulator (CFTR) protein, in generating or maintaining fluid filled cysts in MDCK cells and in human autosomal dominant polycystic kidney disease (ADPKD). In contrast, few studies have addressed the pathophysiology of fluid secretion in cyst formation and enlargement in autosomal recessive polycystic kidney disease (ARPKD). Murine models of targeted disruptions or deletions of specific genes have created opportunities to examine the role of individual gene products in normal development and/or disease pathophysiology. The creation of a murine model of CF, which lacks functional CFTR protein, provides the opportunity to determine whether CFTR activity is required for renal cyst formation in vivo. Therefore, this study sought to determine whether renal cyst formation could be prevented by genetic complementation of the BPK murine model of ARPKD with the CFTR knockout mouse. The results of this study reveal that in animals that are homozygous for the cystic gene (bpk), the lack of functional CFTR protein on the apical surface of cystic epithelium does not provide protection against cyst growth and subsequent decline in renal function. Double mutant mice (bpk -/-; cftr -/-) developed massively enlarged kidneys and died, on average, 7 d earlier than cystic, non-CF mice (bpk -/-; cftr +/+/-). This suggests fundamental differences in the mechanisms of transtubular fluid secretion in animal models of ARPKD compared with ADPKD.