Characterization of the 3' half of the human type IV collagen alpha 5 gene that is affected in the Alport syndrome

The clinical spectrum of type IV collagen mutations

Clinical manifestations of type IV collagen mutations can vary from the severe, clinically and genetically heterogeneous renal disorder, Alport syndrome, to autosomal dominant familial benign hematuria. The predominant form of Alport syndrome is X-linked; more than 160 different mutations have yet been identified in the type IV collagen alpha 5 chain (COL4A5) gene, located at Xq22-24 head to head to the COL4A6 gene. The autosomal recessive form of Alport syndrome is caused by mutations in the COL4A3 and COL4A4 genes, located at 2q35-37. Recently, the first mutation in the COL4A4 gene was identified in familial benign hematuria. This paper presents an overview of type IV collagen mutations, including eight novel COL4A5 mutations from our own group in patients with Alport syndrome. The spectrum of mutations is broad and provides insight into the clinical heterogeneity of Alport syndrome with respect to age at renal failure and accompanying features such as deafness, leiomyomatosis, and anti-GBM nephritis.

The COL4A5 gene in Japanese Alport syndrome patients: spectrum of mutations of all exons. The Japanese Alport Network

To determine the spectrum of mutations of the COL4A5 gene encoding type IV collagen among Japanese Alport syndrome (AS) patients, 60 unrelated patients (47 males and 13 females) from all over the country were recruited. Screening for mutations in all the exons (1 to 51) of the COL4A5 gene was carried out by PCR-SSCP analysis. A mobility shift was observed in 22 of 60 patients, and their genomic DNA were analyzed by the direct sequence method and using cloned ssDNA. Nine of these had missense mutations in the collagenous domain (in exons 39, 37, 31, 29, 28, 27, 21, 20, 19). Eight of these mutations were observed in a codon of glycine residue. Two were altered to arginine, two to valine, two to glutamic acid and two to aspartic acid. The other missense mutation was a change from isoleucine to serine in a interruption region. Five patients had small size base deletions and one had a 4 bp insertion resulting in frameshift (in exons 49, 41, 19, 14, 13). Three had a splice site mutation (in exons 49, 47, 27). One had a nonsense mutation (in exon 17). These mutations seemed to be pathogenic, but the phenotype, which includes extrarenal manifestations, can vary with respect to both expression and severity. The remaining mutations were three silent ones (in exons 19, 39, 46). In addition, major gene rearrangement seemed to be rare in Japanese AS patients.

A novel missense mutation in exon 3 of the COL4A5 gene associated with late-onset Alport syndrome

We have identified a novel missense transition (362G-->A) in exon 3 of the COL4A5 gene in a male patient with late-onset Alport syndrome. We used non-isotopic single strand conformation polymorphism, heteroduplex analysis, and automated DNA sequencing. The mutation changes a conserved glycine at codon 54 for an aspartic acid (Gly54Asp), which abolishes a BstNI site. Using restriction analysis, we identified the heterozygous carrier status in the two daughters of the proband. Our findings are in keeping with the hypothesis that slower progressive forms of Alport syndrome are more often associated with missense mutations rather than large deletions or frameshifts. This is the first mutation described in the N-terminus triple helical 7S domain of the COL4A5 gene in an Alport syndrome patient.

Splicing mutations in the COL4A5 gene in Alport's syndrome: different mRNA expression between leukocytes and fibroblasts

The COL4A5 gene from 40 patients with Alport's syndrome was examined using single-strand conformation substitution at the acceptor site (-2) of intron 50 and a G-to-C substitution at the donor site (+1) of intron 47, respectively. The transcript in peripheral leukocytes from the former had a 10-nucleotide deletion. This shortened transcript was derived from abnormal splicing in a cryptic acceptor site within exon 51. This could be translated into a protein with an alteration of three amino acids followed by premature termination, which eliminated 23 amino acids from the carboxyl end. Gene tracking revealed that the mother and a brother carried the mutant allele. In the latter, the transcript in leukocytes was normal, but that in cultured skin fibroblasts showed skipping of exon 47, the result being that 71 amino acids were absent. Glomerular basement membrane from the patient did not react with the anti-alpha 5(IV) antibody. His maternal grandmother, mother, and a sister, all with abnormal urinalysis, carried the mutant allele. Thus, the appearance of exons of the COL4A5 gene in leukocytes may differ from that in fibroblasts. If kidney mRNA is not available, mRNAs from cultured skin fibroblasts, in addition to leukocytes, can be used for gene analysis in subjects with Alport's syndrome.

YAC contigs mapping the human COL4A5 and COL4A6 genes and DXS118 within Xq21.3-q22

Sequence-tagged sites (STSs) were developed for three loci of uncertain X chromosomal localization (DXS122, DXS137, and DXS174) and were used to seed YAC contigs. Two contigs now total about 3.3 Mb formatted with 34 STSs. One contains DXS122 and DXS174 within 250 kb on single YACs; it is placed in Xq21.3-q22.1 by FISH analysis, which is consistent with somatic cell hybrid panel analyses and with the inclusion of a probe that detects polymorphism at the DXS118 locus already assigned to that general region. The other contig, which contains DXS137, is in Xq22.2 by FISH, consistent with cell hybrid analyses and with the finding that it covers the human COL4A5 and COL4A6 genes known to be in that vicinity. In addition to extending the cloned coverage of this portion of the X chromosome, these materials should aid, for example, in the further analysis of Alport syndrome.

Severe alport phenotype in a woman with two missense mutations in the same COL4A5 gene and preponderant inactivation of the X chromosome carrying the normal allele

The X-linked form of Alport disease, caused by mutations in the COL4A5 or the COL4A6 gene, usually leads to terminal renal failure in males, while affected females have a more variable and moderate phenotype. We detected in a female patient, with a severe Alport phenotype, two new missense mutations. One mutation (G289V) occurred in exon 15 and converted a glycine in a collagenous domain of COL4A5 to a valine. The second mutation, located in exon 46, substituted a cysteine proximal to the NC1 domain of COL4A5 for an arginine. In white blood cells and kidney both mutations were present on > 90% of the mRNA, while at the genomic level the patient was heterozygous for both mutations. The two mutations therefore occurred in the same COL4A5 allele. No mutation was found in the COL4A5 promoter region by sequencing nor was a major rearrangement of the normal allele detected. A skewed pattern of X inactivation was demonstrated in DNA isolated from the patient's kidney and white blood cells: > 90% of the X chromosomes with the normal COL4A5 allele was inactivated. It is suggested that this skewed inactivation pattern is responsible for the absence of detectable normal COL4A5 mRNA and hence the severe phenotype in this woman.

A nonsense mutation in the COL4A5 collagen gene in a family with X-linked juvenile Alport syndrome

The X-linked form of Alport syndrome is associated with mutations in the COL4A5 gene encoding the alpha 5-chain of type IV collagen. By using PCR-amplification and direct sequencing we identified a novel mutation involving a deletion of the last two bases in the codon GGA for Glycine-1479 in exon 47 of the COL4A5 gene in a patient with a juvenile form of X-linked Alport syndrome with deafness. This two base deletion caused a shift in the reading frame and introduced a premature stop codon which resulted in an alpha 5(IV)-chain shortened by 202 residues and lacking almost the entire NC1 domain. The mutation was found to co-segregate with the disease in the family. The information of the sequence variation in this family was used to perform carrier detection and prenatal diagnosis by allele-specific oligonucleotide hybridization analysis and direct sequencing of PCR amplified exon 47. Prenatal diagnosis on chorionic villi tissue, obtained from one of the female carriers in the family, revealed a male fetus hemizygous for the mutated allele. A subsequent prenatal test in her next pregnancy revealed a normal male fetus. Prenatal diagnosis of Alport syndrome has not previously been reported.

Detection of 12 novel mutations in the collagenous domain of the COL4A5 gene in Alport syndrome patients

A population of 35 Alport syndrome patients, defined by strict diagnostic criteria, was screened for mutations in 23 exons of the COL4A5 gene by SSCP analysis. Mobility shifts were observed in 12 out of 35 patients and were shown to represent genuine mutations. 9 of these were glycine substitutions in the collagenous domain (in exons 20, 25, 26, 29, 31, and 41), 2 were small deletions resulting in frameshifts (in exons 21 and 31), and one was a splice site mutation (in exon 12).

Mutations in the COL4A5 gene in Alport syndrome: a possible mutation in primordial germ cells

Using a combination of gene amplification with single strand conformation polymorphisms analysis and sequencing, we examined the COL4A5 gene in 37 patients with Alport syndrome. In patient A8, a single base insertion was noted at codon 1,597 tyrosine in exon 49. The premature terminal signal appeared and 89 amino acids (approximately one-third) of the non-collagenous domain were lost. The mutation was present in the mother, hence she is heterozygous. In patient A12, the nucleotide changed from C to T at codon 1,679 glutamine in exon 51, which created a termination codon, and 7 amino acids at the carboxyl terminus were lost. Gene tracking using peripheral leukocytes revealed that the parents did not carry the mutant allele, while the sister was heterozygous. DNA samples from hair roots and skin fibroblasts of the mother were normal and immunological examination of the epidermis of the mother indicated that the alpha 5(IV) chain was normally expressed. As these results suggest that somatic cells of the mother do not carry the mutant allele, the primordial germ cells possibly carry a fresh mutation in the mother of patient A12.

High resolution platinum-carbon replication of freeze-dried basement membrane

High angle platinum/carbon (Pt/C) replication has proved to be a valuable tool in analyzing basement membrane structure in human amnion, bovine lens capsule, and the Engelbreth-Holm-Swarm (EHS) tumor. High resolution replicas for transmission electron microscopy (TEM) have been achieved by depositing 1.0 +/- 0.1 nm thick Pt/C films backed with rotary deposited 12.5 +/- 2.5 nm thick carbon films. The basement membrane collagen IV network was observed to consist of fine branching filaments containing globular domains intrinsic to the filaments. A second quasi-regular network is formed by laminin. Unidirectional 45 degree angle Pt/C replication was used for most of this work. The merits and deficiencies of unidirectional vertical replication (80 degree angle), unidirectional 45 degree angle, and 20 degrees low angle rotary replication are discussed. Vertical replication produces the highest resolution replicas and has the potential for revealing the overall pattern of basement membrane structural assembly if basement membrane preparations freeze-dried in low salt can faithfully maintain their in vivo structure.

Canine X chromosome-linked hereditary nephritis: a genetic model for human X-linked hereditary nephritis resulting from a single base mutation in the gene encoding the alpha 5 chain of collagen type IV

Many families with X-chromosome linked hereditary nephritis (HN) have mutations in the gene on the X chromosome that codes for the alpha 5 chain of collagen type IV. Canine X-linked HN is an animal model for human X-linked HN. To study the alpha 5(IV) gene in this model, we used the nucleotide sequence published for the human alpha 5(IV) cDNA to construct sets of primers covering approximately 95% of the complete cDNA. cDNA from both affected and normal dog kidneys was amplified by PCR in nine overlapping regions. The nucleotide sequence encoding the noncollagenous domain NC1 hybridized to the human X chromosome and was 93% identical at the DNA level and 97% identical at the protein level to the human alpha 5(IV) NC1 domain, confirming that the canine alpha 5(IV) cDNA had been amplified. Sequence analysis of the alpha 5(IV) cDNA detected a single nucleotide substitution, G-->T, in affected dogs, changing a codon for a conserved glycine residue (GGA) to a stop codon (TGA). When genomic DNA was amplified, the same abnormality was found in exon 35. Using the canine NC1 domain cDNA as a probe for Northern analysis, two transcripts of approximately 8.6 kb and approximately 6.7 kb were identified in both normal and affected male dog kidney RNA. However, the abundance of both transcripts was decreased by a factor of approximately 10 in the affected dog. These results establish at the molecular level that canine X-linked HN is a model for human X-linked HN. This model provides an opportunity to determine the efficacy of new therapies and to investigate the role of the alpha 5(IV) chain in type IV collagen assembly.

COL4A5 gene deletion and production of post-transplant anti-alpha 3(IV) collagen alloantibodies in Alport syndrome

Mutations in the COL4A5 gene encoding the alpha 5(IV) chain of type IV collagen have been implicated as the primary defect in X-linked Alport syndrome. Several kinds of mutations have been reported so far, spanning point mutations to complete gene deletions. About 5% of Alport patients, who undergo renal transplantation, develop anti-glomerular basement membrane (GBM) nephritis, causing loss of allograft function. In one such patient, COL4A5 gene deletion was recently identified. In the present study, the GBM constituent, targeted by the anti-GBM alloantibodies from the patient who had complete COL4A5 gene deletion was identified. Its identity was determined on the basis of circulating antibody binding to various GBM constituents, domains of bovine type IV collagen and recombinant NC1 domain of human type IV collagen. These results establish, for the first time, the absence of the alpha 5(IV) chain in Alport GBM and, in the same patient, the production of an alloantibody that is targeted to a different chain of type IV collagen, the alpha 3(IV) chain. These findings provide further support for the hypothesis that: (1) anti-alpha 3(IV) collagen alloantibodies mediate the allograft glomerulonephritis; and (2) COL4A5 gene mutations cause defective assembly of the alpha 3(IV) collagen alloantibodies mediate the allograft glomerulonephritis; and (2) COL4A5 gene mutations cause defective assembly of the alpha 3(IV) chain in Alport GBM, as reflected by the production of anti-alpha 3(IV) alloantibodies.

Deletions in the COL4A5 collagen gene in X-linked Alport syndrome. Characterization of the pathological transcripts in nonrenal cells and correlation with disease expression

The type IV collagen alpha 5 chain (COL4A5) gene of 88 unrelated male patients with X-linked Alport syndrome was tested for major gene rearrangements by Southern blot analysis, using COL4A5 cDNA probes. 14 different deletions were detected, providing a 16% deletion rate in the COL4A5 gene in the patient population. The deletions are dispersed all over the gene with different sizes, ranging from 1 kb to the complete absence of the gene (> 250 kb) in one patient. In four patients with intragenic deletions, absence of the alpha 3 (IV) chain in the glomerular basement membrane was demonstrated by immunohistochemical studies. This finding supports the hypothesis that abnormalities in the alpha 5 (IV) chain may prevent normal incorporation of the alpha 3 (IV) chain into the glomerular basement membrane. Direct sequencing of cDNA amplified from lymphoblast mRNA of four patients with internal gene deletions, using appropriate combinations of primers amplifying across the predicted boundaries of the deletions, allowed us to determine the effect of the genomic rearrangements on the transcripts and, by inference, on the alpha 5 (IV) chain. Regardless of the extent of deletion and of the putative protein product, the 14 deletions occur in patients with juvenile-type Alport syndrome.

Differential splicing of COL4A5 mRNA in kidney and white blood cells: a complex mutation in the COL4A5 gene of an Alport patient deletes the NC1 domain

PCR conditions were optimized to amplify the COL4A5 cDNA from lymphoblasts and kidney tissue. Sequencing of the COL4A5 mRNA isolated from the kidney of an Alport syndrome patient revealed two differences with the published sequence. One divergence, the insertion of an 18 bp sequence between exon 11 and 10 of the COL4A5 mRNA added two Gly-X-Y triplets to the COL4A5 sequence and was subsequently found in the mRNA of four normal kidney mRNA samples. This sequence was absent in all white blood cell RNA samples sequenced by us, indicating tissue specific splicing with the presence of an additional exon in kidney COL4A5 mRNA. This finding of differential splicing of COL4A5 mRNA in kidney and white blood cells might affect the use of white blood cell mRNA for the analysis of Alport mutations. Second, a complex mutation was detected in the mRNA from the AS patient introducing a premature stop codon in the message, deleting part of the triple helical domain and the complete NC domain. The mother of the patient was shown to be heterozygous for this mutation.

Alport syndrome: from bedside to genome to bedside

Alport syndrome is a genetic disorder of basement membranes manifested clinically by a progressive nephropathy and, in many families, sensorineural hearing loss and ocular lesions. During the 1980s evidence was amassed indicating type IV (basement membrane) collagen as the defective protein in Alport This hypothesis was confirmed in 1990 by the cloning of the X-chromosomal gene COL4A5, which encodes the alpha 5 chain of type IV collagen, and the discovery of mutations in this gene in many Alport kindreds. The results of results of recent studies suggest that the alpha 5(IV) chain forms a distinct collagenous network with the alpha 3 and alpha 4 chains of type IV collagen and that mutations in alpha 5(IV) may prevent the normal incorporation of alpha 3(IV) and alpha 4(IV) into basement membranes. Renal biopsy remains an important modality for making the diagnosis of Alport syndrome, but may eventually be replaced by molecular genetic techniques. Posttransplant anti-glomerular basement membrane nephritis occurs rarely in Alport patients and may be restricted to a subgroup with particular COL4A5 mutations. It is not clear why COL4A5 mutations result in glomerulosclerosis and renal failure, or whether this process may be slowed through dietary or pharmacologic intervention.

Identification of a single base insertion in the COL4A5 gene in Alport syndrome

We identified a novel mutation in the COL4A5 gene of a Japanese patient with Alport syndrome. A combination of in vitro amplification of the exons with single strand conformation polymorphisms (SSCP) analysis suggested the presence of a mutation in exon 48. Sequencing of the amplified DNA revealed a single base (T) insertion which was between nucleotides T 4750 and G 4751 within the methionine 1516. This mutation caused a shift in the reading frame of nine amino acids and introduced a premature termination signal that would be expected to lack about two-thirds of the noncollagenous (NC1) domain. This mutation may interfere with type IV collagen assembly leading to increased permeability and play a causative role in the glomerular basement membrane abnormality of this patient with typical Alport syndrome. Gene tracking by restriction enzyme NlaIII digestion revealed that the patient's mother is heterozygous whereas the patient's brother and one sister are normal, albeit they have hematuria and proteinuria. Without gene analysis, they would have been misdiagnosed. We propose that the diagnosis of Alport syndrome should be made on the basis of both clinical phenotypes and molecular defects.

Small frameshift deletions within the COL4A5 gene in juvenile-onset Alport syndrome

Small frameshift deletions within the COL4A5 gene were identified in three Alport syndrome Italian families by non-isotopic single-strand conformation polymorphism (SSCP) screening: in family RMA, a 7-bp deletion (GGGTGAA) in exon 39; in family DGR, a 4-bp deletion (TGGA) in exon 41; in family MIB, deletion of a G in exon 50. The phenotype was characterized by juvenile-onset renal failure with sensorineural hearing loss in males, and a milder clinical pattern in heterozygous females.

cDNA isolation and partial gene structure of the human alpha 4(IV) collagen chain

A novel collagen IV chain, alpha 4(IV), has recently been identified in basement membranes. We describe part of the primary structure of the human alpha 4(IV) polypeptide for the first time, which has been determined by cloning and sequencing of cDNAs encoding 241 amino acid residues of the COL domain and 231 residues of the NC1 domain. We also characterized a genomic DNA fragment containing 4 exons coding for the entire NC1 domain. Among five known alpha chains of collagen IV, the alpha 4(IV) chain is distinct from the other four chains. However, it is more similar to the alpha 2(IV) chain than to the alpha 1(IV), alpha 3(IV) and alpha 5(IV) chains in terms of amino acid sequence homology, domain structure of polypeptides and exon/intron structure of the genes, suggesting the presence of two phylogenetically distinct subclasses of collagen IV alpha chains; one composed of alpha 2 and alpha 4 chains and the other of alpha 1, alpha 3 and alpha 5 chains.

A splicing mutation in the alpha 5(IV) collagen gene of a family with Alport's syndrome

DNA sequence analysis of the alpha 5(IV) collagen chain gene (COL4A5) was carried out between exon 47 and 51, which encode the noncollagenous (NC) domain, in eight Japanese families with Alport's syndrome. In one family with X-linked inheritance of the disease, a point mutation (G to C) was found at the 3' end of exon 49 in the COL4A5. This mutation converted the codon of a conserved methionine-1601 to the codon for isoleucine, and also altered the normal splicing process. The polymerase chain reaction (PCR) product amplified between exons 47 and 51 of cDNA in the affected male (hemizygote) of this family contained four fragments with various molecular weights, whereas that of a normal control contained one with the expected molecular weight. Sequence analysis of the PCR fragments of the male patient revealed various types of alternative splicing between the exons, reflecting the various sizes of PCR fragments. The PCR amplified product of the cDNA of the affected female (heterozygote), on the other hand, contained a fragment with the same molecular weight as the normal control. Sequence analysis of the PCR fragments of her cDNA revealed normal splicing and no point mutation at the 3' end of exon 49. These findings indicate that this point mutation at the consensus sequence not only converted the codon but also altered the splicing between these exons encoding the NC domain of the COL4A5. Resulting in missense of the alpha 5(IV) chain, changing a large portion of the carboxyl terminal crosslinking NC domain, this mutation can alter the normal structure of the type IV collagen network.(ABSTRACT TRUNCATED AT 250 WORDS)

Mutations in the codon for a conserved arginine-1563 in the COL4A5 collagen gene in Alport syndrome

We have screened 110 unrelated Alport syndrome kindreds for mutations in the exon 48 region of the COL4A5 collagen gene. Denaturing gradient gel electrophoresis (DGGE) of the PCR-amplified region of exon 48 revealed sequence variants in DNA from affected males and carriers of three unrelated kindreds. All three kindreds have classical Alport syndrome of the juvenile type. DNA-sequencing analyses demonstrated two different single base changes in the codon for arginine-1563 located in exon 48. In Utah kindred 2103, there was a substitution of C by T resulting in the change of the CGA codon for arginine to the translation stop codon TGA. In Utah kindred 2123 and in the Danish kindred A13, there was a C-->T mutation in the noncoding strand changing the same codon to CAA for glutamine. Both mutations were confirmed by allele-specific hybridization on PCR-amplified DNA from other family members.

COL4A5 splice site mutation and alpha 5(IV) collagen mRNA in Alport syndrome

Mutations affecting the COL4A5 gene encoding the alpha 5 chain of type IV collagen, are involved in the pathogenesis of X-linked Alport syndrome. We used denaturing gradient gel electrophoresis (DGGE) to screen PCR amplified exons of COL4A5 for point mutations in a set of 18 Alport patients previously characterized by Southern blotting. One sequence variant was identified in the exon 38 region of a male Alport patient. Sequence analysis revealed a G to C transversion in the 5' intron splice donor site downstream from exon 38 (GT to CT). To determine the effect of the mutation on mRNA splicing, alpha 5(IV) cDNA was generated from total RNA of peripheral blood lymphocytes. Subsequent cDNA PCR yielded a product 81 base pairs shorter in the affected Alport patient, compared to normal controls. The absence of exon 38 from the alpha 5(IV) cDNA was confirmed by sequence analysis. The results demonstrated that the mutation leads to skipping of exon 38 in the processing of alpha 5(IV) pre-mRNA. The shortened transcript lacked 27 codons encoding a Gly-X-Y-repeat sequence with a preserved reading frame, enabling the translation of codons further downstream. Clinically, the patient presented with juvenile onset Alport syndrome, end-stage renal failure, and deafness. He had no ocular lesions. Typical ultrastructural changes of the glomerular basement membrane (GBM) were shown on electron microscopy. The patient developed anti-GBM antibodies after renal transplantation, however, renal function deteriorated only moderately.

Molecular genetics of Alport syndrome

Alport syndrome is a progressive hereditary kidney disease characterized by hematuria, sensorineural hearing loss and ocular lesions with structural defects in the glomerular basement membrane (GBM). The gene frequency has been estimated to be 1:5000. The disease is primarily X chromosome-linked, but autosomal forms have also been reported. The X-linked form has been shown to be caused by mutations in a recently identified alpha 5(IV) collagen chain gene (COL4A5). We have isolated cDNA clones for providing the entire primary structure of the human alpha 5(IV) chain. The gene has been located to the Xq22 region. Using antibodies against synthetic peptides, the alpha 5(IV) chain was shown to be located in the kidney only in the glomerular basement membrane. Thus far, the exon-intron structure has been determined for a large portion of the gene which probably has a size of over 200 kb. Numerous different mutations have been identified in the COL4A5 gene. The mutations include single base mutations, large deletions and other major rearrangements such as inversion and duplication. The consequences of the mutations observed can be considered sufficient to cause structural and functional defects in the type IV collagen molecule and, therefore, also the GBM network. This, in turn can explain the disruption of the GBM and hematuria occurring in these Alport patients. Alport syndrome is the first genetic basement membrane and kidney disease whose gene has been cloned. These recent results have enabled the development of antibodies and DNA probes for accurate diagnosis of Alport syndrome.

Alport syndrome: a genetic study of 31 families

Thirty one families with Alport syndrome including 3 families with associated syndromes were studied. The location of the COL4A5 gene, responsible for the Alport syndrome, was determined by linkage analysis with eight probes of the Xq arm and by a radiation hybrid panel. Concordant data indicated the localization of the Alport gene between DXS17 and DXS11. Four deletions and one single base mutation of the COL4A5 gene were detected. Homogeneity tests failed to show any evidence of genetic heterogeneity superimposed on clinical heterogeneity for ophthalmic signs and end-stage renal disease age.

Deletions of the COL4A5 gene in patients with Alport syndrome

Mutations in the COL4A5 gene encoding the alpha 5 chain of type IV collagen have been found in linkage with X-chromosomal Alport syndrome (AS). To identify COL4A5 mutations in patients from Germany with clinically defined AS, DNA from 20 unrelated patients was analyzed by conventional Southern blotting. By using full length alpha 5(IV) cDNA probes, large COL4A5 deletions could be detected in two patients. In one case, a 34 kb deletion affecting the 14 most 3' exons of the gene was observed. The second patient harbored a complete COL4A5 deletion. In both cases, functional alpha 5(IV) mRNA was unlikely to be present. Clinically, both patients developed end-stage renal failure before age 30. Furthermore, they had characteristic retinal flecks, and sensorineural hearing loss with typical changes on the audiogram. The patient with the complete deletion of COL4A5 lost the renal allograft due to an anti-GBM mediated glomerulonephritis.

DNA rearrangements in the alpha 5(IV) collagen gene (COL4A5) of individuals with Alport syndrome: further refinement using pulsed-field gel electrophoresis

Alport syndrome (AS), an X-linked kidney disorder, has been shown to be caused by mutations in the gene for the alpha 5-chain of type IV collagen (COL4A5), which maps to Xq22. On the basis of the results of conventional Southern blot analysis of AS patient DNAs, we employed pulsed-field gel electrophoresis to characterize further three gene rearrangements at the 3'-end of alpha 5(IV). We were able to construct long-range restriction maps for all three of these patients and deduce the extent and nature of each rearrangement. One of these mutations is a 450-kb simple deletion that includes 12 kb of the alpha 5(IV) gene. A second mutation has been shown to be a direct duplication of 35 kb of alpha 5(IV) genomic DNA, and a third mutation involves a complex insertion/deletion event resulting in an overall loss of 25 kb.

Construction of a yeast artificial chromosome contig encompassing the human alpha 5(IV) collagen gene (COL4A5)

A PCR-based screening approach was used to isolate six yeast artificial chromosome (YAC) clones containing segments of the human alpha 5(IV) collagen gene (COL4A5). This gene is located at Xq22 and is known to be involved in the kidney disorder known as Alport syndrome (AS). By analyzing sequence-tagged sites, cDNA content, and rare-cutting restriction site patterns in these YAC clones, a contig that spans the entirety of the alpha 5(IV) gene was constructed. This contig may contain as much as 690 kb of DNA from the alpha 5(IV) locus. On the basis of the information obtained from these YAC clones, the genomic map and gene structure of the alpha 5(IV) gene have been refined. This study has also provided a valuable resource for subsequent studies of the alpha 5(IV) gene and its flanking DNA sequences.

Different mutations in the COL4A5 collagen gene in two patients with different features of Alport syndrome

Alport syndrome is a hereditary renal disease in which progressive renal failure is often accompanied by sensorineural deafness and ocular abnormalities. Recently, mutations were detected in the type IV collagen alpha 5 chain gene in Alport syndrome patients. We searched for mutations in this gene in 18 unrelated patients, and in two patients abnormalities were detected. In the gene of patient BB we identified a complex deletion, which included the exons encoding the non-collagenous domain and part of the collagenous region. This patient showed early onset nephritis (end-stage renal disease at 17 years) with deafness. Within a year after receiving a kidney from an unrelated donor, he developed an antiglomerular basement membrane nephritis. In patient WJ a point-mutation was detected, changing a tryptophane into a serine in the non-collagenous domain. His clinical features are milder (renal failure at 33 years, no hearing loss), and a recent renal allograft did not provoke antiglomerular basement membrane disease. These initial data suggest that differences in the extent of disruption of the non-collagenous domain may correlate with the severity and/or heterogeneity of Alport syndrome and with the development of nephritis in renal allografts.

Distribution of the alpha 1 and alpha 2 chains of collagen IV and of collagens V and VI in Alport syndrome

We compared the distribution of the alpha 1 and alpha 2 chains of collagen IV and of collagens V and VI in glomeruli of males with Alport syndrome to their distribution in normal glomeruli and glomeruli from patients with non-Alport renal diseases. alpha 1(IV), alpha 2(IV), collagen V and collagen VI are normally restricted to the mesangium and the subendothelial aspect of the glomerular basement membrane (GBM). In contrast, these proteins were present throughout the entire width of the GBM in Alport glomeruli. These alterations were apparent in "early" Alport glomeruli, that is, those exhibiting minimal abnormalities by light microscopy, and they were further accentuated in sclerosing Alport glomeruli. Obsolescent Alport glomeruli, in which the capillary tuft had collapsed and few remaining cell nuclei were present, exhibited nearly complete loss of alpha 1(IV) and alpha 2(IV), like obsolescent glomeruli in non-Alport diseased kidneys. However, the matrix of obsolescent Alport glomeruli stained intensely for collagen V and collagen VI, while these collagen types were not prominent in obsolescent glomeruli of non-Alport diseases kidneys. These observations suggest that the process of glomerulosclerosis in Alport kidneys has attributes unique to this disease. It would also appear that mutations affecting the Alport gene product have secondary effects on the distribution of other GBM constituents.

The pathogenesis of Alport syndrome involves type IV collagen molecules containing the alpha 3(IV) chain: evidence from anti-GBM nephritis after renal transplantation

Mutations in the COL4A5 collagen gene have been implicated as the primary defect in Alport syndrome, a heritable disorder characterized by sensorineural deafness and glomerulonephritis that progresses to end-stage renal failure. In the present study, the molecular nature of the defect in Alport glomerular basement membrane (GBM) was explored using anti-GBM alloantibodies (tissue-bound and circulating) produced in three Alport patients subsequent to renal transplantation. The alloantibodies bound to the alpha 3(IV)NC1 domain of type IV collagen and not to any other basement membrane component. In tissue sections, the alloantibodies bound specifically to peripheral GBM in normal kidney and the affected renal transplant but not to that of Alport kidney. These results establish that: the alpha 3 chain in type IV collagen molecules, the Goodpasture autoantigen, is the target alloantigen in post-transplant anti-GBM nephritis in patients with Alport syndrome, and that a molecular commonality exists in the pathogenesis of anti-GBM nephritis causing loss of renal allografts in patients with Alport syndrome and renal failure in patients with Goodpasture syndrome. These findings implicate: (1) defective assembly of type IV collagen molecules containing the alpha 3(IV) chain in Alport GBM; and (2) the existence of a mechanism linking the assembly of molecules containing the alpha 3(IV) chain with those containing the alpha 5(IV) chain.

Immunochemical studies of the Alport antigen

The Alport antigen, a component of normal glomerular basement membranes (GBM) which is absent in Alport familial nephritis, is characterized as a 26 kD non-collagenous (NC1) peptide identified by a monoclonal antibody (Mab A7) and an Alport alloantibody. Both antibodies discriminate X-linkage of the Alport defect using indirect immunofluorescence of hemizygous and heterozygous Alport GBM and epidermal basement membrane (EBM). Immunoblotting of SDS-PAGE gels of collagenase-digested Alport renal BM shows absence of monomeric and dimeric components of the Alport antigen, alpha 3(IV) NC1, and alpha 4(IV) NC1. By immunoprecipitation experiments with specific antibodies, the Alport antigen is distinct from the 26 kD NC1 peptide derived from alpha 1(IV). The monoclonal antibody to the Alport antigen and rabbit antiserum to a non-consensus sequence of alpha 5(IV) NC1 react similarly by immunofluorescence with normal kidney and both fail to bind to Alport renal BM. Two dimension Western blots of collagenase-digested BM show that the anti-Alport antigen and the ant-alpha 5(IV) NC1 react similarly with monomeric and dimeric components of BM collagen. These studies are consistent with the likelihood that the Alport antigen and alpha 5(IV) NC1 are the same or are highly homologous molecules. The precise relationship will require characterization of alpha 5(IV) NC1 protein and determination of the nucleotide sequence of the Alport antigen. The associated absence of alpha 3(IV) NC1 and alpha 4(IV) (NC1) from Alport BM is consistent with other observations for a molecular association of these chains in a novel collagen network.

Alport syndrome caused by a 5' deletion within the COL4A5 gene

Fourteen Italian patients affected with X-linked Alport syndrome were analyzed by Southern blotting, using cDNA probes of the COL4A5 gene. One proband was shown to carry a large deletion (greater than 38 kb) that included the 5' part of the gene.

Sensorineural deafness inherited as a tissue specific mitochondrial disorder

We present here a large Israeli-Arab kindred with hereditary deafness. In this family 55 deaf subjects (29M, 26F), who are otherwise healthy, have been identified and traced back five generations to one common female ancestor. The deafness is progressive in nature, usually presenting in infancy and childhood. Audiometry on six deaf and seven unaffected subjects was consistent with severe to profound sensorineural hearing loss. Based on formal family segregation analysis, the inheritance of deafness in this family closely fits the expectation of a two locus model owing to the simultaneous mutation of a mitochondrial gene and an autosomal recessive gene. Thus, this disorder appears to have the unusual features of being an inherited tissue specific mitochondrial disease and apparently requiring the homozygous presence of a nuclear gene for clinical expression. Most importantly, this disorder presents a unique opportunity to investigate the molecular basis of hereditary non-syndromic deafness and normal hearing.

Long-range mapping of the gene for the human alpha 5(IV) collagen chain at Xq22-q23

The X-linked kidney disorder known as Alport syndrome (AS) has been shown to be due to mutations in the gene for an alpha 5 chain of type IV collagen that maps to Xq22-23. Using overlapping cDNA clones that represent approximately 90% of this gene and pulsed-field gel electrophoresis, we have constructed a 2.4-Mb long-range restriction map around the locus. All of the cDNA clones lie within a 360-kb segment of DNA bounded by CpG islands that contain sites for the rare-cutting enzymes BssHII, MluI, NotI, NruI, SalI, and SfiI. High-resolution PFGE mapping with XhoI shows that the gene is at least 110 kb in size and is one of the largest collagen genes characterized to date. This map will prove useful in the characterization of mutations in individuals affected with AS and will also provide information as to the location of other genes in the region.

Three-dimensional structure of type IV collagen in the mammalian lens capsule

The anterior lens capsule provides a thick, easily handled model system for the study of the organization of type IV collagen, the main component of basement membranes. We have used the technique of rapid freezing, deep-etch, and rotary replication to study the three-dimensional organization of the collagen skeleton in mammalian lens capsule after a variety of extraction procedures. In all cases the collagen appeared as a densely packed three-dimensional branching network of fine microfibrils. The organization of the microfibrils appears to show some regularity, with branch points approximately 40 nm apart. Most junctions are three-way and the network forms predominantly five-sided figures. This closely resembles the collagenous network described by Yurchenco and Ruben (1987, 1988) in human amniotic basement membrane and EHS tumor matrix, but extends their findings to another system for which X-ray diffraction data are available. The three-dimensional network is discussed in terms of molecular packing of type IV collagen in light of the information available from the diffraction data.

Major rearrangements in the alpha 5(IV) collagen gene in three patients with Alport syndrome

The gene coding for the alpha 5 chian of type IV collagen (alpha 5(IV) collagen), which maps to Xq22, is a candidate gene for the X-linked dominant disease Alport syndrome (AS). Using three cDNA clones, covering the 3' end of the alpha 5(IV) collagen gene, 3 of 38 patients have been identified with mutations in this gene. Each of these patients shows a gross rearrangement of DNA: a deletion of at least 35 kb, an insertion/deletion event involving approximately 25 kb, and a duplication of at least 35 kb of DNA.

Single base mutation in alpha 5(IV) collagen chain gene converting a conserved cysteine to serine in Alport syndrome

We have identified a point mutation in the type IV collagen alpha 5 chain gene (COL4A5) in Alport syndrome. Variant PstI (Barker et al., 1990, Science 248, 1224-1227), and BglII restriction sites with complete linkage with the Alport phenotype have been found in the 3' end of the COL4A5 gene in the large Utah Kindred P. The approximate location of the variant sites was determined by restriction enzyme mapping, after which this region of the gene (1028 bp) was amplified with the polymerase chain reaction (PCR) from DNA of normal and affected individuals for sequencing analysis. The PCR products showed the absence or presence of the variant PstI and BglII sites in DNA from normal and affected individuals, respectively. DNA sequencing revealed a single base change in exon 3 (from the 3' end) in DNA from affected individuals, changing the TGT codon of cysteine to the TCT codon for serine. This single base mutation also generated new restriction sites for PstI and BglII. The mutation involves a cysteine residue that has remained conserved in the carboxyl-end noncollagenous domain (NC domain) of all known type IV collagen alpha chains from Drosophila to man. It is presumably crucial for maintaining the right conformation of the NC domain, which is important for both triple-helix formation and the formation of intermolecular cross-links of type IV collagen molecules.