Structure of the human type IV collagen COL4A5 gene

Trimerization profile of type IV collagen COL4A5 exon deletion in X-linked Alport syndrome

BACKGROUND

Alport syndrome (AS) is a genetic kidney disease caused by a mutation in type IV collagen α3, α4, and α5, which are normally secreted as heterotrimer α345(IV). Nonsense mutation in these genes causes severe AS phenotype. We previously revealed that the exon-skipping approach to remove a nonsense mutation in α5(IV) ameliorated the AS pathology. However, the effect of removing an exon on trimerization is unknown. Here, we assessed the impact of exon deletion on trimerization to evaluate their possible therapeutic applicability and to predict the severity of mutations associated with exon-skipping.

METHODS

We produced exon deletion constructs (ΔExon), nonsense, and missense mutants by mutagenesis and evaluated their trimer formation and secretion activities using a nanoluciferase-based assay that we previously developed.

RESULTS

Exon-skipping had differential effects on the trimer secretion of α345(IV). Some ΔExons could form and secrete α345(IV) trimers and had higher activity compared with nonsense mutants. Other ΔExons had low secretion activity, especially for those with exon deletion near the C-terminal end although the intracellular trimerization was normal. No difference was noted in the secretion of missense mutants and their ΔExon counterpart.

CONCLUSION

Exon skipping is advantageous for nonsense mutants in AS with severe phenotypes and early onset of renal failure but applications may be limited to ΔExons capable of normal trimerization and secretion. This study provides information on α5(IV) exon-skipping for possible therapeutic application and the prediction of the trimer behavior associated with exon-skipping in Alport syndrome.

Abnormal mRNA Splicing Effect of COL4A3 to COL4A5 Unclassified Variants

Introduction

Genetic diagnosis of Alport syndrome (AS), which results from pathogenic variants in COL4A3, COL4A4, or COL4A5 genes, is hindered by large numbers of unclassified variants detected using next-generation sequencing (NGS). We examined the impact on splicing of variants of uncertain significance in COL4A3 to COL4A5.

Methods

Nine unrelated patients with clinical diagnosis or suspicion of AS were enrolled according to the criteria. Their clinical and genetic data were collected. Blood and urine samples were obtained from the patients and their family members. Sanger sequencing was used to confirm the 9 COL4A3 to COL4A5 unclassified variants identified by NGS. COL4A3 to COL4A5 mRNAs from urine were analyzed using targeted reverse transcription polymerase chain reaction and direct sequencing.

Results

Nine COL4A3 to COL4A5 unclassified variants were found to alter mRNAs splicing. Skipping of an exon or an exon fragment was induced by variants COL4A3 c.828+5G>A; COL4A4 c.3506-13_3528del; and COL4A5 c.451A>G (p. [Ile151Val]), c.2042-9 T>G, c.2689 G>C (p. [Glu897Gln]) and c.1033-10_1033-2delGGTAATAAA. Retention of an intron fragment was caused by variants COL4A3 c.3211-30G＞T, and COL4A5 c.4316-20T>A and c.1033-10 G>A, respectively. The 9 families in this study obtained genetic diagnosis of AS, including 3 with autosomal recessive AS and 6 with X-linked AS.

Conclusions

Our findings demonstrate that urine mRNA analysis facilitates the identification of abnormal splicing of unclassified variants in Alport genes, which provides evidence of routine use of RNA analysis to improve genetic diagnosis of AS.

Genetic Disorders of the Extracellular Matrix: From Cell and Gene Therapy to Future Applications in Regenerative Medicine

Metazoans have evolved to produce various types of extracellular matrix (ECM) that provide structural support, cell adhesion, cell-cell communication, and regulated exposure to external cues. Epithelial cells produce and adhere to a specialized sheet-like ECM, the basement membrane, that is critical for cellular homeostasis and tissue integrity. Mesenchymal cells, such as chondrocytes in cartilaginous tissues and keratocytes in the corneal stroma, produce a pericellular matrix that presents optimal levels of growth factors, cytokines, chemokines, and nutrients to the cell and regulates mechanosensory signals through specific cytoskeletal and cell surface receptor interactions. Here, we discuss laminins, collagen types IV and VII, and perlecan, which are major components of these two types of ECM. We examinegenetic defects in these components that cause basement membrane pathologies such as epidermolysis bullosa, Alport syndrome, rare pericellular matrix-related chondrodysplasias, and corneal keratoconus and discuss recent advances in cell and gene therapies being developed for some of these disorders.

Organoprotective Effects of Spironolactone on Top of Ramipril Therapy in a Mouse Model for Alport Syndrome

Angiotensin-converting enzyme inhibitors (ACEi) delay progression of the inherited renal disease Alport syndrome. However, the effect of ACEis weakens gradually due to an “aldosterone escape”. Here, we investigate if an aldosterone antagonist can counteract loss of ACEi-efficacy. COL4A3−/− mice were treated with ramipril (ACEi), starting at 4.5 weeks of age, and spironolactone was added at 7 weeks of age. Lifespan until renal failure, as well as kidney function parameters, were investigated. Dual therapy decreased proteinuria levels compared to ACEi monotherapy. Matrix accumulation, as well as tubulointerstitial and glomerular scar-tissue formation, were significantly reduced compared to untreated mice and ACEi-monotherapy at 75 and 100 days. Lifespan in dual treated mice was extended compared to untreated mice. However, lifespan was not superior to ACEi monotherapy–despite improved urea-nitrogen levels in the dual therapy group. In conclusion, adding the aldosterone-antagonist spironolactone to ACEi therapy further improved kidney function and reduced proteinuria and fibrosis. However, survival was not improved further, possibly due to premature death from side effects of dual therapy such as hyperkalemia. Thus, dual therapy could offer an effective therapy option for Alport syndrome patients with progressive proteinuria. However, the risks of adverse events require close monitoring.

Reboot: a straightforward approach to identify genes and splicing isoforms associated with cancer patient prognosis

Nowadays, the massive amount of data generated by modern sequencing technologies provides an unprecedented opportunity to find genes associated with cancer patient prognosis, connecting basic and translational research. However, treating high dimensionality of gene expression data and integrating it with clinical variables are major challenges to perform these analyses. Here, we present Reboot, an integrative approach to find and validate genes and transcripts (splicing isoforms) associated with cancer patient prognosis from high dimensional expression datasets. Reboot innovates by using a multivariate strategy with penalized Cox regression (LASSO method) combined with a bootstrap approach, in addition to statistical tests and plots to support the findings. Applying Reboot on data from 154 glioblastoma patients, we identified a three-gene signature (IKBIP, OSMR, PODNL1) whose increased derived risk score was significantly associated with worse patients' prognosis. Similarly, Reboot was able to find a seven-splicing isoforms signature related to worse overall survival in 177 pancreatic adenocarcinoma patients with elevated risk scores after uni- and multivariate analyses. In summary, Reboot is an efficient, intuitive and straightforward way of finding genes or splicing isoforms signatures relevant to patient prognosis, which can democratize this kind of analysis and shed light on still under-investigated cancer-related genes and splicing isoforms.

A novel frameshift mutation of COL4A5 in a Chinese family with presumed IgA nephropathy and chronic glomerulonephritis

BACKGROUND

Alport syndrome (ATS) is a hereditary nephritis with hereditary and clinical heterogeneity; the early clinical symptoms are atypical, which can easily lead to misdiagnosis. The proband, a 6-year-old girl, was found to have microscopic hematuria, proteinuria, and visual impairment at about 5 years old; the results of renal pathological examination revealed mesangial hyperplasia and IgA deposition. The proband's father exhibited gross hematuria, eye swelling, and bilateral hearing loss after the age of 5, renal function progressively decreased, and he underwent right renal allograft at the age of 23 due to renal failure. The proband and her father were clinically diagnosed as IgA nephropathy and chronic glomerulonephritis, respectively.

METHODS

For proband, targeted exome capture sequencing was performed using the Targeted Exome Capture Kit; this kit targets 162 genes known to cause renal diseases. The identified mutation was confirmed and analyzed for cosegregation by Sanger sequencing in other family members whose gDNA was available.

RESULTS

Targeted exome capture sequencing revealed a novel heterozygous variant (NM_000495, c.697delG, p.G233fs) in the COL4A5 gene of the proband; the variant was inherited from her father. The variant was likely pathogenic according to the criteria of the American College of Medical Genetics and Genomics.

CONCLUSION

In this study, we first report a c.697delG mutation of COL4A5 in two patients presumed IgA nephropathy and chronic glomerulonephritis. This study emphasizes on the diagnostic value of next-generation sequencing for hereditary kidney diseases to help in their timely and cost-effective diagnosis, determine appropriate treatments, and promote genetic counseling.

DNA variant databases improve test accuracy and phenotype prediction in Alport syndrome

X-linked Alport syndrome is a form of progressive renal failure caused by pathogenic variants in the COL4A5 gene. More than 700 variants have been described and a further 400 are estimated to be known to individual laboratories but are unpublished. The major genetic testing laboratories for X-linked Alport syndrome worldwide have established a Web-based database for published and unpublished COL4A5 variants ( https://grenada.lumc.nl/LOVD2/COL4A/home.php?select_db=COL4A5 ). This conforms with the recommendations of the Human Variome Project: it uses the Leiden Open Variation Database (LOVD) format, describes variants according to the human reference sequence with standardized nomenclature, indicates likely pathogenicity and associated clinical features, and credits the submitting laboratory. The database includes non-pathogenic and recurrent variants, and is linked to another COL4A5 mutation database and relevant bioinformatics sites. Access is free. Increasing the number of COL4A5 variants in the public domain helps patients, diagnostic laboratories, clinicians, and researchers. The database improves the accuracy and efficiency of genetic testing because its variants are already categorized for pathogenicity. The description of further COL4A5 variants and clinical associations will improve our ability to predict phenotype and our understanding of collagen IV biochemistry. The database for X-linked Alport syndrome represents a model for databases in other inherited renal diseases.

Skin biopsy is a practical approach for the clinical diagnosis and molecular genetic analysis of X-linked Alport's syndrome

A total of 209 unrelated patients of predominantly Han Chinese ethnicity and with X-linked Alport's syndrome, a clinically heterogeneous hereditary nephritis, were enrolled in the present study to evaluate the ability to make a clinical diagnosis and perform molecular genetics analysis using skin biopsy. A negative or mosaic α5(IV) chain staining in the epidermal basement membrane was detected in 86.2% of male and 93.5% of female patients. COL4A5 mutations were identified in 85% of male patients with a negative α5(IV) chain staining pattern in the epidermal basement membrane. With use of skin biopsy and immunostaining, 16.4% of our patients were diagnosed before 3 years of age, and the youngest was diagnosed at 1 year of age. COL4A5 mutations were detected in 22 patients with normal epidermal basement membrane staining for the α5(IV) chain. Analysis of COL4A5 cDNA fragments from skin fibroblasts yielded a mutation detection rate of 83%, which was particularly valuable for identification of cryptic splicing mutations. Furthermore, 83% of COL4A5 mutations identified in the present study were novel. Thus, skin biopsy is a practical approach for the clinical diagnosis and molecular genetic analysis of X-linked Alport's syndrome.

Twenty-one novel mutations identified in the COL4A5 gene in Chinese patients with X-linked Alport's syndrome confirmed by skin biopsy

BACKGROUND

The clinical and pathological features of Alport syndrome are characterized by abnormalities in the basement membrane collagen network which are composed of the α3, α4 and α5 chains of type IV collagen and usually associated with hearing loss and ocular lesions. The predominant form (85% of AS) is inherited as X-linked mode (XLAS) caused by mutations encoding the α5 chain of type IV collagen gene, COL4A5. Different mutations in the COL4A5 gene have been reported widely, but only a few mutations were identified in Chinese patients.

METHODS

We studied 71 Chinese patients from 35 unrelated families with XLAS confirmed by skin biopsy. Genomic DNA was extracted from peripheral blood of all patients. All 51 exons of the COL4A5 gene were screened by direct sequencing for the probands.

RESULTS

A total of twenty-five identified gene mutations were considered to be pathogenic, including 1 nonsense, 1 splice-site, 1 complex rearrangement, 5 small deletions, 2 small insertions and 15 missense mutations. Twenty-one mutations have not been reported previously.

CONCLUSIONS

We have identified 25 pathogenic mutations in 35 Chinese families with XLAS. Skin biopsy is effective for the diagnosis of XLAS.

X-linked Alport syndrome in Hellenic families: phenotypic heterogeneity and mutations near interruptions of the collagen domain in COL4A5

The X-linked Alport syndrome (ATS) is caused by mutations in COL4A5 and exhibits a widely variable expression. Usually ATS is heralded with continuous microhematuria which rapidly progresses to proteinuria, hypertension and chronic or end-stage renal disease (ESRD) by adolescence, frequently accompanied by sensorineural deafness and ocular complications. Milder forms of ATS also exist. We studied 42 patients (19M, 23F) of nine Hellenic families suspected clinically of X-linked ATS who presented with marked phenotypic heterogeneity. We identified mutations in COL4A5 in six families. Two males with nonsense mutation E228X reached ESRD by ages 14 and 18. Frameshift mutation 2946delT followed the same course with early onset renal involvement and deafness. However, two males with the milder missense mutation G624D, reached ESRD after 39 years and one patient showed thin basement membrane nephropathy (TBMN). Another 5/8 affected males with missense mutation P628L also developed ESRD between 30 and 57 years, while three exhibit only mild chronic renal failure (CRF). The data support previous findings that certain mutations are associated with milder phenotypes and confirm that mutation G624D may be expressed as TBMN with familial hematuria. Similar conclusions apply for missense mutation P628L. Interestingly, mutations G624D and P628L are near the 12th natural interruption of COL4A5 triple helical domain, which may explain the milder phenotype.

Genotype-phenotype correlation in X-linked Alport syndrome

Mutations in the COL4A5 gene cause X-linked Alport syndrome (XLAS). Understanding the correlation between clinical manifestations and the underlying mutations adds prognostic value to genetic testing, which is increasingly available. Our aim was to determine the association between genotype and phenotype in 681 affected male participants with XLAS from 175 US families. Hearing loss and ocular changes were present in 67 and 30% of participants, respectively. Average age of participants at onset of ESRD was 37 years for those with missense mutations, 28 years for those with splice-site mutations, and 25 years for those with truncating mutations (P < 0.0001). We demonstrated a strong relationship between mutation position and age at onset of ESRD, with younger age at onset of ESRD associated with mutations at the 5' end of the gene (hazard ratio 0.766 [95% confidence interval 0.694 to 0.846] per 1000 bp toward the 3' end; P < 0.0001). Affected participants with splice mutations or truncating mutations each had two-fold greater odds of developing eye problems than those with missense mutations; development of hearing impairment showed a similar trend. Hearing loss and ocular changes associated with mutations located closer to the 5; end of the gene. These strong genotype-phenotype correlations could potentially help in the evaluation and counseling of US families with XLAS.

Biological responses of ligament fibroblasts and gene expression profiling on micropatterned silicone substrates subjected to mechanical stimuli

In this study, ligament fibroblasts were cultivated on micropatterned silicone substrates and subjected to cyclic stretching to simulate the in vivo biomechanical environment during ligament healing. Without stretching, ligament fibroblasts were aligned parallel to the microgrooves on the silicone substrate surface. However, we previously reported that uniaxial cyclic stretching induces alignment perpendicular to the stretching axis. With stretching on a microgrooved surface, cell proliferation and collagen production were greatly enhanced. The exact functions of the micropatterned surface and mechanical stimuli are unknown. Therefore, in gene expression microarray experiments, genes whose expression is inhibited by subculture from passage 0 (P0) to passage 8 (P8) and enhanced by micropatterning and stretching were sought out. The following six genes were selected: MGP, GADD45A, UNC5B, TGFB1, COL4A1, and COL4A2. The selected genes play fundamental roles in cell proliferation, differentiation, apoptosis, and structural maintenance. On the basis of the obtained gene expression profiles, we identified candidate genes that might be involved in responses to a micropatterned surface and mechanical stretching.

Bifunctional promoter of type IV collagen COL4A5 and COL4A6 genes regulates the expression of alpha5 and alpha6 chains in a distinct cell-specific fashion

Type IV collagen is present ubiquitously in basement membranes. A bifunctional promoter regulates the expression of the alpha1/alpha2 genes, and the alpha3/alpha4 and the alpha5/alpha6 genes are also considered to be regulated by putative bifunctional promoters. Unlike the other type IV collagen chains, the alpha5(IV) and alpha6(IV) chains do not always co-localize and are present in distinct basement membranes. To address such dichotomy in the alpha5(IV) and alpha6(IV) gene regulation, we cloned a mouse genomic DNA fragment containing the promoter region between the two transcription start sites of these genes and we then placed this putative promoter sequence between the chloramphenicol acetyltransferase and Luciferase reporter genes, so that these genes would be transcribed in opposite directions in this unique construct. Glomerular endothelial cells and mesangial cells generate the kidney glomerular basement membrane, which always contains the alpha5(IV) chain but not the alpha6(IV) chain. In contrast, the basement membranes of Bowman's capsule and distal tubuli (produced by the tubular epithelial cells) contain the alpha6(IV) chain. We demonstrate that, in response to TGF-beta (transforming growth factor beta), epidermal growth factor, vascular endothelial growth factor and platelet-derived growth factor, expression from the alpha5(IV) gene is significantly enhanced in the glomerular endothelial cells and mesangial cells, but not expression from the alpha6(IV) gene. In contrast, the expression from the alpha6(IV) gene, and not that from the alpha5(IV) gene, was significantly enhanced in response to growth factors in the tubular epithelial cells. Our results demonstrate that the proximal bifunctional promoter regulates the expression of the alpha5(IV) and alpha6(IV) genes in a cell-specific manner and offers the first demonstration of the promoter plasticity in growth factor regulation of type IV collagen genes in different tissues of the body.

Alport syndrome caused by inversion of a 21 Mb fragment of the long arm of the X-chromosome comprising exon 9 through 51 of the COL4A5 gene

The X-linked form of Alport syndrome (AS) is caused by mutation in the COL4A5 gene located at Xq22.3 and encoding the alpha5-chain of type IV-collagen. More than 400 different mutations have so far been detected in the COL4A5 gene. Not all mutations, however, will be detected using an exon-by-exon mutation detection strategy such as SSCP analysis or direct sequencing. We have previously reported the results of SSCP analysis of 81 patients suspected of X-linked AS. Genomic DNA from these 81 patients was also analyzed for larger genomic rearrangements, using Southern blotting analysis. Abnormal band patterns were found in three patients, two of which were caused by single base substitutions in the coding region, also detected by the SSCP analysis. Here we report the results of the analysis of a larger structural COL4A5 rearrangement that escaped the SSCP analysis. The rearrangement was found to be an inversion of a 21 Mb fragment of the COL4A5 gene comprising exon 9 through 51 with proximal breakpoint within intron 8 at Xq22.3 and a distal breakpoint 56 kb upstream to the initiation codon in the RAB33A gene at Xq25. The inversion of exon 9 through 51 is expected to result in a truncated or absent alpha5(IV)-chain and has not previously been associated with AS. These findings emphasize the need for a supplement to mutation detection strategies such as SSCP analysis and direct sequencing, in order to detect more complicated structural COL4A5 rearrangements. Larger structural rearrangements constitute 2.3% (1/43) of the mutations in the present material.

Detection of mutations in the COL4A5 gene by analyzing cDNA of skin fibroblasts

BACKGROUND

Alport syndrome is a progressive hereditary glomerulonephritis that is characterized by hematuria, sensorineural deafness, ocular lesions, and progressive renal failure. The majority of cases (about 85%) are caused by mutations in the COL4A5 gene on the X chromosome which encodes the type IV collagen alpha5 chain (X-linked Alport syndrome).

METHODS

In this study we performed a systematic analysis of the entire coding region of COL4A5 mRNA in 31 unrelated Chinese X-linked Alport syndrome patients and four controls by using reverse transcription-polymerase chain reaction (RT-PCR) and direct sequencing methods. The mRNA analyzed was isolated from cultured skin fibroblasts of Alport syndrome patients.

RESULTS

The entire sequences of mRNA of the controls corresponded exactly to the published sequence. There were 28 variants detected by analyzing mRNA of COL4A5 in 28/31 patients. Of those, a total of 25 functionally significant COL4A5 mutations was confirmed in 25/31 patients by using RT-PCR method and subsequently confirmed at genomic DNA level, which included seven different mutations described in previous reports, and 18 novel mutations. The mutation detection rate was 80.6% (25/31), which is comparable with the highest previous detection sensitivity of COL4A5 mutations in evident X-linked Alport syndrome using genomic DNA. Furthermore, three splicing mutations that occurred at the cryptic splice sites and would be overlooked or simply considered as intronic sequence variations by solely analyzing genomic DNA were identified in this study.

CONCLUSION

RT-PCR and direct sequencing using cultured skin fibroblasts RNA is a practical approach with high sensitivity for genetic analysis in X-linked Alport syndrome patients.

A large tandem duplication within the COL4A5 gene is responsible for the high prevalence of Alport syndrome in French Polynesia

A large tandem duplication within the COL4A5 gene is responsible for the high prevalence of Alport syndrome in French Polynesia. Background. The prevalence of X-linked Alport syndrome, a progressive inherited nephropathy associated with mutations in the type IV collagen gene COL4A5, is remarkably high in French Polynesia. Methods. A vast clinical, genealogic, and molecular study was undertaken in Polynesia, based on public records, patients' interviews, linkage analysis, and mutation screening. Results and Conclusions. We show that the high frequency of Alport syndrome in this region is due to a founder mutation that occurred onto a common haplotype shared by affected and unaffected individuals, the presence of which precludes indirect molecular diagnosis. We have characterized the mutation as a tandem duplication of 35 COL4A5 exons, resulting in a approximately 65% increase in the length of the collagenous domain of the alpha 5(IV) chain, which is still able to assemble into type IV collagen network as shown by immunofluorescence analysis. That mutation is associated with severe and highly penetrant ocular symptoms and with uniformly thin glomerular basement membrane (GBM) in male adult patients. However, the rate of progression of the renal disease is very variable from one male patient to another, demonstrating the importance of strong modifier factors. Our results suggest that the 20% to 50% of "missing"COL4A5 mutations in X-linked Alport syndrome may be rearrangements similar to that reported here, which was not detectable by sequencing of either individual COL4A5 exons or overlapping cDNA fragments. Finally, we provide the basis for a polymerase chain reaction (PCR) assay that accurately identifies female carriers and allows adequate genetic counseling in this population.

Effect of glycine substitutions on alpha5(IV) chain structure and structure-phenotype correlations in Alport syndrome

The phenotype variety caused by glycine substitutions in alpha5(IV) chain in X-linked Alport syndrome (XLAS) prompted the complexity of structure changes of alpha5(IV) chain that was little to know now. In this study, we expressed a domain of alpha5(IV) chain containing different glycine substitutions (G1015V and G1030S, respectively) which were revealed in two XLAS pedigrees with different phenotype severities and the corresponding domain of a control in Escherichia coli. The recombinant proteins were characterized by immunoblot and mass spectrometry and analyzed the secondary structure by using circular dichroism (CD) spectroscopy. CD analysis showed that the recombinant protein containing G1015V mutation identified in the pedigree of juvenile-onset XLAS exhibited 12.9% alpha-helix that was not found in the control recombinant protein. The spectrum of the recombinant protein containing G1030S mutation identified in the pedigree of adult-onset XLAS was slightly different from that of the control, that is, mostly with the random coil and the beta-sheet, while without alpha-helix. These results demonstrated that two kinds of glycine substitutions, although in the same domain of alpha5(IV) chain, displayed the distinctly different secondary structures. The changes of the secondary structure could explain the phenotypic diversities of XLAS, which would be hardly understood solely by analyzing genomic DNA or mRNA of alpha5(IV) chain.

Detection of COL4A5 gene mutations in Chinese patients with Alport's syndrome

BACKGROUND

Mutations in the COL4A5 gene, encoding the alpha 5 chain of type IV collagen, are responsible for X-linked Alport's syndrome (XLAS), a progressive nephropathy characterized by glomerular basement membrane abnormalities and usually associated with progressive hearing loss and ocular lesions.

METHODS

In this study, we analysed all 51 exons of the COL4A5 gene in 20 Chinese patients with XLAS or suspected XLAS from 16 families by using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) DNA sequencing.

RESULTS

Five gene mutations identified in five families were considered to be pathogenic, including one nonsense mutation in exon 1 (266C-->T, Gln22Term), two missense mutations in exons 31 (2757G-->T, Gly852Val) and 43 (4142C-->T, Pro1314Ser), and two splice site mutations in introns 1 and 25 just next to the 3' end of their respective exons (283+1G-->T, 2150+1G-->T). According to GenBank, these five mutations have not been reported previously. All male patients have typical clinical manifestations and pathological findings that closely correspond to the effects of the mutations. Furthermore, seven gene polymorphisms were detected in introns 18 and 10 and exons 20, 27, 29, 39 and 46. Only the substitution in intron 18 (1234+25G-->A) had a gene frequency significantly higher in patients than in normal individuals.

CONCLUSION

Our study demonstrated the critical role of COL4A5 gene mutations in the pathogenesis of XLAS. The linkage of the polymorphism to AS is still unknown.

Tissue- and developmental stage-specific activation of α5 and α6(IV) collagen expression in the upper gastrointestinal tract of transgenic mice

Little is known about mechanisms regulating gene expression for the alpha chains of basement membrane type IV collagen, arranged head-to-head in transcription units COL4A1-COL4A2, COL4A3-COL4A4, and COL4A5-COL4A6, and implicated broadly in genetic diseases. To investigate these mechanisms, we generated transgenic mouse lines bearing 5'-flanking sequences of COL4A5 and COL4A6, cloned upstream of a lacZ reporter gene. A 3.8-kb fragment upstream of COL4A6 directs reporter gene expression in the esophagus, stomach, and duodenum, whereas a 13.8-kb fragment directs expression in the esophagus only. A 10.6-kb fragment upstream of COL4A5 directs expression in the esophagus. Coupled with evidence of long-range conservation between human and mouse non-coding sequences, described herein, our findings provide the first indication that highly specialized patterns characteristic of COL4A5-COL4A6 expression in vivo arise from effects of distributed cis-acting regulatory elements on a bidirectional proximal promoter, itself transcriptionally competent.

Transfer of the alpha 5(IV) collagen chain gene to smooth muscle restores in vivo expression of the alpha 6(IV) collagen chain in a canine model of Alport syndrome

X-linked Alport syndrome is a progressive renal disease caused by mutations in the COL4A5 gene, which encodes the alpha 5(IV) collagen chain. As an initial step toward gene therapy for Alport syndrome, we report on the expression of recombinant alpha 5(IV) collagen in vitro and in vivo. A full-length cDNA-encoding canine alpha 5(IV) collagen was cloned and expressed in vitro by transfection of HEK293 cells that synthesize the alpha1(IV) and alpha2(IV), but not the alpha 3(IV) to alpha 6(IV) collagen chains. By Northern blotting, an alpha 5(IV) mRNA transcript of 5.2 kb was expressed and the recombinant protein was detected by immunocytochemistry. The chain was secreted into the medium as a 190-kd monomer; no triple helical species were detected. Transfected cells synthesized an extracellular matrix containing the alpha1(IV) and alpha2(IV) chains but the recombinant alpha 5(IV) chain was not incorporated. These findings are consistent with the concept that the alpha 5(IV) chain requires one or more of the alpha 3(IV), alpha 4(IV), or alpha 6(IV) chains for triple helical assembly. In vivo studies were performed in dogs with X-linked Alport syndrome. An adenoviral vector containing the alpha 5(IV) transgene was injected into bladder smooth muscle that lacks both the alpha 5(IV) and alpha 6(IV) chains in these animals. At 5 weeks after injection, there was expression of both the alpha 5(IV) and alpha 6(IV) chains by smooth muscle cells at the injection site in a basement membrane distribution. Thus, this recombinant alpha 5(IV) chain is capable of restoring expression of a second alpha(IV) chain that requires the presence of the alpha 5(IV) chain for incorporation into collagen trimers. This vector will serve as a useful tool to further explore gene therapy for Alport syndrome.

Efficient detection of Alport syndrome COL4A5 mutations with multiplex genomic PCR-SSCP

We have performed effective mutation screening of COL4A5 with a new method of direct, multiplex genomic amplification that employs a single buffer condition and PCR profile. Application of the method to a consecutive series of 46 United States patients with diverse indications of Alport syndrome resulted in detection of mutations in 31 cases and of five previously unreported polymorphisms. With a correction for the presence of cases that are not likely to be due to changes at the COL4A5 locus, the mutation detection sensitivity is greater than 79%. The test examines 52 segments, including the COL4A6/COL4A5 intergenic promoter region, all 51 of the previously recognized exons and two newly detected exons between exons 41 and 42 that encode an alternatively spliced mRNA segment. New genomic sequence information was generated and used to design primer pairs that span substantial intron sequences on each side of all 53 exons. For SSCP screening, 16 multiplex PCR combinations (15 4-plex and 1 3-plex) were used to provide complete, partially redundant coverage of the gene. The selected combinations allow clear resolution of products from each segment using various SSCP gel formulations. One of the 29 different mutations detected initially seemed to be a missense change in exon 32 but was found to cause exon skipping. Another missense variant may mark a novel functional site located in the collagenous domain.

Structure of the human type IV collagen gene COL4A3 and mutations in autosomal Alport syndrome

Mutations in either the COL4A3 or the COL4A4 genes, encoding the alpha3 and alpha4 chains of type IV collagen, are responsible for the autosomal-recessive form of Alport syndrome, a progressive hematuric nephropathy characterized by glomerular basement membrane abnormalities. Reported here are the complete COL4A3 exon-intron structure and a comprehensive screen for mutations of the 52 COL4A3 exons in 41 unrelated patients diagnosed as having autosomal Alport syndrome. This resulted in the identification of 21 mutations that are expected to be causative. Furthermore, it is shown that heterozygous COL4A3 missense mutations, when symptomatic, can be associated with a broad range of phenotypes, from familial benign hematuria to the complete features of Alport syndrome nephropathy.

Alport syndrome: a review

Alport syndrome, a hereditary nephritis accompanied by high-tone sensorineural deafness and distinctive ocular signs was first noted in the literature during the early 1900s. This disease is caused by a genetic defect in Type IV collagen which makes up basement membranes in many body systems. The patient will usually have bilateral anterior lenticonus causing varied refractive errors. You may also note yellow-white to silver flecks within the macular and midperipheral regions of the retina. The treatment of the visual problems is an important but secondary concern due to the seriousness of the systemic disease. Dual sensory loss, however, creates an urgent need for appropriate vision care. Due to the high risk for developmental delay and decreased social integration, early intervention should be considered in the treatment plan. Coping strategies for the patient (and the family) need to be addressed because of the chronicity of this syndrome. The primary care optometrist will be challenged by the individual with Alport syndrome since a balance between oculo-visual, developmental/psycho-educational and systemic care is required. A multi-disciplinary approach by the healthcare management team will enhance the quality of life and positive outcomes for these patients.

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.

Detection of mutations in COL4A5 in patients with Alport syndrome

Alport syndrome (AS) can be caused by mutations in COL4A5, one of the six type IV collagen genes. For the purposes of confirming diagnoses, carrier screening and correlating genotype to phenotype, we have screened all 51 exons of this gene by SSCP analysis in 153 families with suspected AS. Mutations were identified in 77 families (of which 20 have previously been reported) and are reported with all available clinical information. All types of mutation were found (missense, nonsense, splicing, small and large deletions and insertions), with the commonest type being those affecting glycine residues in the collagen triple helix. Our 50% detection rate is similar to that of other groups and may imply the presence of mutations outside of the COL4A5 coding region or the existence of a second X-linked AS gene.

Detection of mutations in the COL4A5 gene in over 90% of male patients with X-linked Alport's syndrome by RT-PCR and direct sequencing

X-linked Alport's syndrome is caused by mutations in the COL4A5 gene encoding the type IV collagen alpha5 chain (alpha5[IV]). Polymerase chain reaction-single-str and conformation polymorphism (PCR-SSCP) on genomic DNA has previously been used to screen for mutations in the COL4A5 gene, but this method was relatively insensitive, with mutations detected in less than 50% of patients. Here, we report a systematic analysis of the entire coding region of the COL4A5 gene, using nested reverse-transcription-polymerase chain reaction (RT-PCR) and the direct sequence method using leukocytes. This study examines twenty-two unrelated Japanese patients with X-linked Alport's syndrome showing abnormal expression of alpha5(IV) in the glomerular or epidermal basement membranes. Mutations that were predicted to be pathogenic were identified in 12 of the 13 male patients (92%) and five of the nine female patients (56%). Six patients had missense mutations, four had out-of-frame deletion mutations, three had nonsense mutations, and three had mutations causing exon loss of the transcript. The current study shows that nested RT-PCR and the direct sequence method using leukocytes are highly sensitive and offer a useful approach for systematic gene analysis in patients with X-linked Alport's syndrome.

Complete exon-intron organization and chromosomal location of the gene for mouse type XIII collagen (col13a1) and comparison with its human homologue

Recent findings indicate that type XIII collagen is a transmembrane protein with a short N-terminal sytocsolic domain, a single transmembrane domain and a large, mainly collagenous ectodomain. The complete exon-intron structure of the gene coding for the mouse alpha1(XIII) collagen chain, col13a1, has now been characterized from genomic clones spanning over 180 kilobases (kb) and shown to be approximately 135 kb in size and to contain 42 exons varying between 8 base pairs (bp), the shortest exon in the genes encoding the various collagens, and 836 bp. Nuclease S1 mapping and 5'RACE resulted in identification of multiple transcription initiation points in the mouse gene, ranging between 470 and 548 bp upstream from the initiation methionine. This is in good agreement with a recently identified human EST clone extending 537 bp upstream from the initiation methionine. The 836-bp first exon of the mouse gene covers both the long 5' untranslated region and also a 36-residue cytosolic portion, a 23-residue transmembrane domain, and 37 residues of the 60-residue non-collagenous ectodomain immediately adjacent to the plasma membrane. One striking feature of the exons encoding solely collagenous sequences is the abundance of 27-bp exons, half the ancestral 54-bp size characteristic of fibrillar collagen genes, while the others vary between 8 and 144 bp, including instances of 36-, 45- and 54-bp exons. Determination of approximately 2.6 kb of sequences upstream of the initiation methionine of both the mouse and human genes and the identification of a clone containing four exons and spanning a gap in the previously characterized human clones allowed detailed comparison of the two genes. The exon-intron structures were found to be completely conserved between the species, and both genes have their 5' untranslated region preceded by a highly homologous apparent promoter region of approximately 350 bp containing a modified TATAA motif and several GC boxes. The chromosomal location of the mouse gene was determined by SSCP and fluorescence in situ hybridization and found to be at chromosome 10, band 4, between markers D1OMit5 -2.3 +/- 1.6 cM -col13a1 - 3.4+/-1.9 cM - D1OMit15. This result indicates that the mouse type XIII collagen gene and its human counterpart are located in chromosomal segments with conserved syntenies (The GenBank accession numbers for the mouse gene are AF063666-AF063693. The new GenBank accession number for the 5' end of the human type XIII collagen gene is AF071009).

Expression of mRNA for type IV collagen alpha1, alpha5 and alpha6 chains by cultured dermal fibroblasts from patients with X-linked Alport syndrome

COL4A5 mutations causing X-linked Alport syndrome (XLAS) are frequently associated with absence of the alpha3, alpha4,alpha5 and alpha6 chains of type IV collagen from basement membranes and increased amounts of the alpha1(IV) and alpha2(IV) chains in glomerular basement membrane. Although many COL4A5 mutations have been described in XLAS, the mechanisms by which these mutations influence the basement membrane appearance of chains other than alpha5(IV) remain poorly understood. In this study, we used dermal fibroblasts from eight normal individuals and nine males with XLAS to test the hypotheses that COL4A5 mutations increase transcription of COL4A1 and suppress transcription of COL4A6. Ribonuclease protection assays revealed that alpha1(IV), alpha5(IV) and alpha6(IV) transcripts were expressed in cultures of dermal fibroblasts. The mRNA levels for alpha1(IV) in eight of nine patients with XLAS were not increased compared to controls; one patient with a large COL4A5 deletion showed significant elevation of alpha1(IV) mRNA levels. No differences in steady-state mRNA levels for alpha6(IV) were found when XLAS fibroblasts were compared with controls, even though little or no alpha6(IV) protein was detectable at the dermal-epidermal junction by immunofluorescence study. This finding suggests that post-transcriptional events account for the absence of alpha6(IV) in the Alport dermal-epidermal junction.

Differential expression of collagen IV isoforms in experimental glomerulosclerosis

Expansion of the glomerular mesangial matrix (MM), thickening of the glomerular basement membrane (GBM), and eventually the development of glomerulosclerosis are often seen in immunologically mediated kidney diseases. In addition to quantitative changes in the extracellular matrix (ECM), qualitative changes in ECM molecules may contribute to alterations in the composition of the glomerular matrix. The expression of collagen IV, alpha 1-5(IV) mRNA, and polypeptides was therefore investigated during the development of chronic graft-versus-host disease (GvHD) in mice, a model for lupus nephritis, and in chronic serum sickness (CSS) in rats, a model for membranous nephropathy. Immunohistochemical studies showed increased mesangial expression of alpha 1 and alpha 2 early in the disease, but only late in the GBM. In contrast, alpha 3 and alpha 4 increased in the GBM during disease, but not in the MM. The mRNA levels for all collagen IV chains were increased in isolated glomeruli before morphological alterations were detectable. The mRNA increase was earlier and more profound for alpha 3, alpha 4 and alpha 5 than for alpha 1 and alpha 2. Expression of alpha 3(IV) was greatest in GvHD, whereas expression of alpha 4 was greatest in CSS. As determined by in situ hybridization (ISH), alpha 1 mRNA was observed dispersed in the glomerulus, but alpha 3, alpha 4, and alpha 5 mRNAs were mainly located in cells at the periphery of the glomerular tuft. The changes in the relative abundance of collagen IV mRNA in disease states may perturb the collagen IV network, altering glomerular structure and function, and may thereby play a central role in the development of glomerulonephritis and glomerulosclerosis.

Ultrastructural immunocytochemistry of collagenous and non-collagenous proteins in fast-frozen, freeze-substituted, and low-temperature-embedded renal tissue in Alport syndrome

This paper describes the ultrastructural immunolocalization of the alpha 2 chain of collagen IV, laminin, and the amino terminal propeptide of collagen I (N-Pro I) in glomeruli of rapidly frozen, freeze-substituted, and low-temperature-embedded renal biopsy specimens from two cases of Alport disease and from normal kidneys. The alpha 2 chain of collagen IV is present in the whole thickness of the basement membrane in glomeruli of Alport patients, while it is limited to the subendothelial portion of the basement membrane of normal glomeruli. Laminin has the same distribution in both normal and Alport glomeruli, but is apparently more concentrated along the basement membrane of normal glomeruli. N-Pro I is localized in mesangial areas and in the basement membrane in Alport cases, while it is not detected in normal glomeruli. These data suggest complex rearrangements of major constituents of the glomerular basement membrane network and demonstrate early deposition of fibrillary collagen proteins in the matrix before the appearance of banded collagen fibres. This finding could be an indicator of early evolution towards glomerulosclerosis.

Structure of the human laminin alpha2-chain gene (LAMA2), which is affected in congenital muscular dystrophy

We have determined the structure and complete exon size pattern of the human laminin alpha2-chain gene (LAMA2), which has been shown to be affected in congenital muscular dystrophy (Helbling-Leclerc, A., Zhang, X., Topaloglu, H., Cruaud, C., Tesson, F., Weissenbach, J., Tomé, F. M. S., Schwartz, K., Fardeau, M., Tryggvason, K., and Guicheney, P. (1995) Nat. Genet. 11, 216-218). The gene is over 260, 000 base pairs and contains 64 exons. The sequence of all exon-intron borders was determined. Two of the exons, i.e. exons 43 and 52, are extremely small in size, 6 and 12 base pairs, respectively. Comparison of the exon pattern of the human LAMA2 gene with that of the Drosophila LAMA gene revealed that only 2 of 63 intron locations in the 5'-end of the human gene match the intron locations in the Drosophila gene, which contains 14 introns.

Amplification of specific mRNA from a single human renal glomerulus, with an approach to the separation of epithelial cell mRNA

A method has been developed by which single human glomeruli may be plucked from fresh renal biopsies under direct vision, followed by separation of mRNA using oligo-dT-linked paramagnetic beads. The mRNA was amplified by reverse transcription and polymerase chain reaction (RT-PCR). Primers for a variety of human and rat proteins have been developed. The quantity of the amplified cDNA was measured by an enzyme-linked immuno-sorbent assay (ELISA), where biotinylated forward strands of DNA were captured, probed with a fluorescein-conjugated DNA oligomer, and then assayed with an enzyme-linked anti-fluorescein antibody. The cDNA-linked beads are reported to be stable and can be reused with different primer sets, thus forming a "bank' of samples from cases with defined glomerular disorders, which can be used to address new questions as they arise. Using rat glomeruli, a method has been devised which permits at least partial separation of epithelial cell mRNA from mesangial and endothelial cell mRNA.

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.

Major COL4A5 gene rearrangements in patients with juvenile type Alport syndrome

Mutations in the COL4A5 gene, which encodes the a5 chain of type IV collagen, are found in a large fraction of patients with X-linked Alport syndrome. The recently discovered COL4A6, tightly linked and highly homologous to COL4A5, represents a second candidate gene for Alport syndrome. We analyzed 177 Italian Alport syndrome families by Southern blotting using cDNA probes from both COL4A5 and COL4A6. Nine unrelated families, accounting for 5% of the cases, were found to have a rearrangement in COL4A5. No rearrangements were found in COL4A6, with the exception of a deletion encompassing the 5' ends of both COL4A5 and COL4A6 genes in a patient with Alport syndrome and leiomyomatosis. COL4A5 rearrangements were all intragenic and included 1 duplication and 7 deletions. Polymerase chain reaction (PCR) analysis was carried out to characterize deletion and duplication boundaries and to predict the resulting protein abnormality. The two smallest deletions involved a single exon (exons 17 and 40, respectively), while the largest ones spanned exons 1 to 36. The clinical phenotype of patients in whom a rearrangement in COL4A5 was detected was severe, with progression to end-stage renal failure in juvenile age and hypoacusis occurring in most cases. These data have some important implications in the diagnosis of patients with Alport syndrome.

Isolation and structure of the COL4A6 gene encoding the human alpha 6(IV) collagen chain and comparison with other type IV collagen genes

The genes COL4A5 and COL4A6, coding for the basement membrane collagen chains, alpha 5(IV) and alpha 6(IV), respectively, are located head-to-head in close proximity on human chromosome Xq22, and COL4A6 is transcribed from two alternative promoters in a tissue-specific fashion (Sugimoto M., Oohashi T., and Ninomiya Y. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 11679-11683). Immunofluorescence studies using alpha chain-specific antibodies demonstrated that the two genes are expressed in a tissue-specific manner (Ninomiya, Y., Kagawa, M., Iyama, K., Naito, L., Kishiro, Y., Seyer, J. M., Sugimoto, M., Oohashi, T., and Sado, Y. (1995) J. Cell Biol. 130, 1219-1229). We report here for the first time the isolation and the structural organization of the human COL4A6 gene. The entire gene presumably exceeds 200 kilobase pairs and contains 46 exons. Exons 1' and 1 encode the two different 5'-UTRs and the two amino-terminal parts of of the signal peptide. The carboxyl part of the signal peptide and the 7 S domain are coded for by the following 6 different exons, 2-7, whereas the exons 7-42 encode the central COL 1 domain, which contains the Gly-X-Y repeats. The last three exons, 43-45, encode the carboxyl-terminal NC1 domain. Sizes of more than a half of the exons of the gene are the same as those of Col4a2 but quite different from those of COL4A5. Within the COL4A6 gene we found three CA repeat markers that can be used for allele detection. The detailed structure of the COL4A6 gene and the high heterozygosity microsatellite markers located within the gene will be useful for linkage analysis and familial diagnosis of diseases caused by mutations of this gene.

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.

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).