Deletion of 19 base pairs in intron 13 of the gene for the pro alpha 2(I) chain of type-I procollagen (COL1A2) causes exon skipping in a proband with type-I osteogenesis imperfecta

Detection of clinically relevant exonic copy-number changes by array CGH

Array comparative genomic hybridization (aCGH) is a powerful tool for the molecular elucidation and diagnosis of disorders resulting from genomic copy-number variation (CNV). However, intragenic deletions or duplications--those including genomic intervals of a size smaller than a gene--have remained beyond the detection limit of most clinical aCGH analyses. Increasing array probe number improves genomic resolution, although higher cost may limit implementation, and enhanced detection of benign CNV can confound clinical interpretation. We designed an array with exonic coverage of selected disease and candidate genes and used it clinically to identify losses or gains throughout the genome involving at least one exon and as small as several hundred base pairs in size. In some patients, the detected copy-number change occurs within a gene known to be causative of the observed clinical phenotype, demonstrating the ability of this array to detect clinically relevant CNVs with subkilobase resolution. In summary, we demonstrate the utility of a custom-designed, exon-targeted oligonucleotide array to detect intragenic copy-number changes in patients with various clinical phenotypes.

Relation of PvuII site polymorphism in the COL1A2 gene to the risk of fractures in prepubertal Finnish girls

Genetic susceptibility to fractures may be detectable in early childhood. We evaluated the associations between the polymorphic PvuII site of the COL1A2 gene and bone properties assessed by different modalities (dual-energy X-ray absorptiometry; peripheral quantitative computed tomography; gel coupling scanning quantitative ultrasonometry; ultrasound bone sonometry), bone turnover markers, and the occurrence of fractures in 244 prepubertal Finnish girls. Tanner stage and physical characteristics did not differ significantly among girls with different COL1A2 genotypes. The polymorphism was not significantly associated with different bone properties or any of the bone turnover markers when girls at Tanner stage I (prepuberty) and stage II (early puberty) were considered together, but there was a significant association with spine bone mineral content (BMC) and bone mineral density (BMD), as well as with speed of sound (SOS) (P < 0.05), when girls at Tanner stage I were considered separately, as a purpose to avoid the confounding effect that the pubertal growth spurt has on skeletal development. The distribution of fractures was different between the three genotype groups (P = 0.023). The P alleles were over-represented in girls who had been fractured at least once; 88% of them had at least one copy of the P allele (either PP or Pp). Girls with the PP genotype had 4.9 times higher relative risk for fractures than girls with the pp genotype (95% CI, 1.4 to 17.4; P = 0.015). No significant difference was found between fractured and nonfractured girls in anthropometric measurements, physical activity, or bone mass. However, BMD of the spine and SOS at the radius and tibia were significantly lower in the fractured girls. We conclude that the COL1A2 polymorphism is associated with nonosteoporotic fractures in prepubertal girls independently of bone density.

Hereditary skin diseases of anchoring fibrils

Remarkable progress has been made in the last few years in understanding the functions of the anchoring fibrils, polymers of collagen VII, that connect the epidermal basement membrane with the dermal connective tissue. Novel insights into the biology of these fibrils have been gained from studies on dystrophic epidermolysis bullosa (DEB), a group of inherited blistering disorders caused by abnormalities of the anchoring fibrils. Mutations in the COL7A1 gene encoding collagen VII have been disclosed in a number of DEB families, and the mutation analyses and studies on genotype-phenotype correlations in DEB have revealed an unusual complexity of the gene defects and their biological consequences. In analogy to heritable disorders of other collagen genes, predictable phenotypes of COL7A1 mutations causing premature termination codons (PTC) or dominant negative interference have been observed. However, collagen VII seems to be unique among collagens in that many mutations lead to minimal phenotypes, or to no phenotype at all. Furthermore, the mild DEB phenotypes can be severely modulated by a second mutation in individuals compound heterozygous for two different COL7A1 defects. Therefore, not only definition of mutations with diagnostic analyses, but also cell biological, protein chemical and suprastructural studies of the mutated molecules are required for understanding the pathomechanisms underlying DEB.

Biology of anchoring fibrils: lessons from dystrophic epidermolysis bullosa

Anchoring fibrils are adhesive suprastructures that ensure the connection of the epidermal basement membrane with the dermal extracellular matrix. The fibrils represent polymers of collagen VII, the major structural fibril component, but may also contain other proteins. Remarkable progress has been made in the last few years in understanding the functions of skin basement membrane components including the anchoring fibrils. Novel insights into the biology of the anchoring fibrils have been gained from experimental studies on dystrophic epidermolysis bullosa (DEB), a group of inherited blistering disorders caused by mutations in the gene for collagen VII, COL7A1. Mutation analyses of DEB families have disclosed more than 100 COL7A1 gene defects so far, but the unusual complexity of the mutation constellations and their biological consequences are only beginning to emerge. In analogy to heritable disorders of other collagen genes, predictable phenotypes of COL7A1 mutations causing premature termination codons or dominant negative interference have been observed. However, collagen VII seems to represent a remarkable exception among collagens in that many mutations, including heterozygous glycine substitutions and deletions, lead to minimal phenotypes, or to no phenotype at all. In contrast to fibrillar collagens, structural abnormalities of collagen VII molecules in anchoring fibrils appear to be tolerated to a certain extent. However, the mild DEB phenotypes can be severely modulated by a second aberration in individuals compound heterozygous for two different COL7A1 mutations. Therefore, not only definition of mutation(s) but also cell biological, protein chemical and suprastructural studies of the mutated molecules yield novel insight into the molecular pathomechanisms underlying disease.

Deletions within COL7A1 exons distant from consensus splice sites alter splicing and produce shortened polypeptides in dominant dystrophic epidermolysis bullosa

We describe two familial cases of dominant dystrophic epidermolysis bullosa (DDEB) that are heterozygous for deletions in COL7A1 that alter splicing, despite intact consensus splice-site sequences. One patient shows a 28-bp genomic deletion (6081del28) in exon 73 associated with the activation of a cryptic donor splice site within this exon; the combination of both defects restores the phase and replaces the last 11 Gly-X-Y repeats of exon 73 by a noncollagenous sequence, Glu-Ser-Leu. The second patient demonstrates a 27-bp deletion in exon 87 (6847del27), causing in-frame skipping of this exon; consensus splice sites, putative branch sites, and introns flanking exons 73 and 87 showed a normal sequence. Keratinocytes from the probands synthesized normal and shortened type VII collagen polypeptides and showed intracellular accumulation of type VII procollagen molecules. This first report of genomic deletions in COL7A1 in DDEB suggests a role for exonic sequences in the control of splicing of COL7A1 pre-mRNA and provides evidence that shortened type VII collagen polypeptides can alter, in a dominant manner, anchoring-fibril formation and can cause DDEB of differing severity.

Incorporation of structurally defective type II collagen into cartilage matrix in kniest chondrodysplasia

Kniest dysplasia, a human chondrodysplasia that severely affects skeletal growth, is caused by mutations in the type II collagen gene, COL2A1. We report here on abnormal type II collagen in the cartilage from a lethal Kniest dysplasia case and identify a novel exon-skipping mutation. Screening of cyanogen bromide (CB) peptides from the cartilage samples by SDS-PAGE indicated an abnormality in peptide alpha1(II)CB11. Further peptide mapping and N-terminal sequence analysis showed a 15-amino-acid deletion encoded by exon 15 in about 25% of the alpha1(II) chains in the cartilage. The mutation responsible for exon skipping was found by sequencing amplified genomic DNA. The baby was heterozygous for a G to A transition at the first position of the splice donor of intron 15. Pepsin-solubilized type II collagen from the cartilage matrix contained both normal alpha1(II) and shortened chains expressed from the mutant allele. Trypsin cleaved the native molecules below 37 degrees C selectively at a site within the exon 15-encoded domain of the normal alpha1(II) chains. This is best explained by the coassembly of normal and truncated alpha1(II) chains into heterotrimers in which the triple helix is normally folded in both directions from the deletion site but the latter presents a region of local disruption. The findings support an emerging pattern of COL2A1 mutations that can cause Kniest dysplasia. Short deletions (single or partial exon) clustered in one region of the alpha1(II) chain are favored, resulting in abnormal heterotrimeric molecules that become a significant component of the cartilage extracellular matrix.

Human genes for dental anomalies

The development of the tooth at gene level is beginning to be understood. This paper reviews current knowledge and the advances in research on human genes whose defect leads to dental anomalies. Amelogenesis imperfecta (AI) is a diverse group of hereditary disorders characterized by a variety of developmental enamel defects including hypoplasia and hypomineralization, some of which have been revealed to be associated with defective amelogenin genes. The human amelogenin genes on X and Y chromosomes have been cloned and investigated extensively. Although autosomally inherited forms of AI are more common than the X-linked forms, most studies on the genes causing AI have been performed on the genes of X-linked forms. Recently, the gene for the human tuftelin protein (an enamelin) has been cloned as a candidate gene for the autosomal forms of AI with another gene on chromosome 4 involved in some families. Dentinogenesis imperfecta (DI) may be associated with osteogenesis imperfecta (OI), which is an autosomal dominant bone disease. Most patients with OI have mutations in either the COLIA1 or COLIA2 genes, which encode the alpha 1(I) or alpha 2(I) subunits of type I collagen, the major organic component of bone and dentin. Gene defects causing isolated DI have not been identified. Recently, it was demonstrated that a missense mutation of MSXI, a human homeobox gene, causes autosomal dominant agenesis of second premolars and third molars. Data indicating an important function for MSXI, the mouse counterpart of the human MSXI gene, in mouse tooth development have been accumulating since 1991. Knockout mice lacking this gene exhibited multiple craniofacial anomalies including complete tooth agenesis. X-linked anhidrotic ectodermal dysplasia (EDA), characterized by abnormal hair, teeth, and sweat glands, was demonstrated to be caused by a mutation in a novel transmembrane protein gene that is expressed in epithelial cells and in other adult and fetal tissues. The predicted EDA protein may belong to a novel class of proteins with a role in epithelial-mesenchymal signaling. Several mutations have been reported in genes causing hypophosphatasia, which is characterized by defective mineralization of the skeletal and dental structures.

Multiexon deletions in the type I collagen COL1A2 gene in osteogenesis imperfecta type IB. Molecules containing the shortened alpha2(I) chains show differential incorporation into the bone and skin extracellular matrix

Osteogenesis imperfecta (OI) type IB is a rare subset of the mildest form of OI, clinically characterized by moderate bone fragility, blue sclera, and dentinogenesis imperfecta. Cultured skin fibroblasts from two unrelated individuals (OI-197 and OI-165) with the typical features of OI type IB produced shortened alpha2(I) chains. Reverse transcription-polymerase chain reaction of the alpha2(I)-cDNA revealed deletions in the triple helical domain of 5 exons (exons 7-11) in OI-197, and 8 exons (exons 10-17) in OI-165. This exon skipping was caused by genomic deletions in one allele of COL1A2 with the breakpoints located in introns 6 and 11 in OI-197, and introns 9 and 17 in OI-165. The secretion and deposition of the mutant collagen into the matrix was measured in vitro in cultures of skin fibroblasts and bone osteoblasts, grown in the presence of ascorbic acid to induce collagen matrix formation and maturation, as well as in collagen extracts from skin and bone. The secretion of mutant collagen was impaired and long term cultures of fibroblasts showed that the mutant collagen was not incorporated into the mature collagenous matrix produced in vitro by skin fibroblasts from both patients. Likewise, the shortened alpha2(I) chain was not demonstrable in skin extracts. In contrast, bone extracts from OI-197 showed the presence of the mutant collagen. This incorporation of the abnormal collagen into the mature matrix was also demonstrated in long term cultures of the patient's osteoblasts. The deposition of the mutant collagen by bone osteoblasts but not by skin fibroblasts demonstrates a tissue specificity in the incorporation of mutant collagen into the matrix which may explain the primary involvement of bone and not skin in these patients.

Splice site mutation causing deletion of exon 21 sequences from the pro alpha 2(I) chain of type I collagen in a patient with severe dentinogenesis imperfecta but very mild osteogenesis imperfecta

An eight-year-old boy was referred for dental assessment of dentinogenesis imperfecta, a full clinical examination also revealed joint hypermobility and some features of mild osteogenesis imperfecta although he had suffered few fractures. Analysis of the collagens produced by both gingival and skin fibroblast cultures showed the synthesis and intracellular retention of an abnormal alpha 2(I) chain that migrated faster than normal on SDS-PAGE. Cyanogen bromide peptide mapping of this intracellular protein indicated a probable deletion in the N-terminal peptide alpha 2CB4. The denaturation temperature of the mutant protein was only 36 degrees C, some 6 degrees C below normal. At 37 degrees C secretion of abnormal protein was not detectable but a lower temperature (30 degrees C) some was secreted into the medium. RT-PCR amplification of mRNA coding for alpha 2CB4 revealed a heterozygous deletion of the 108 bp exon 21 of COL1A2. Sequencing of PCR amplified genomic DNA identified a G --> A transition in the moderately conserved + 5 position of the IVS 21 5' consensus splice site causing the skipping of exon 21. Hybridization with allele-specific oligonucleotides showed no other family member had this base change. Since the cDNA deletion was associated with the (-) allele of a Pvu II polymorphism in exon 25 of COL1A2 we could demonstrate that the mutant pre-mRNA was alternatively spliced yielding both full length and deleted transcripts. Family genotype analysis indicated the mutation had originated in the paternal alpha 2(I) gene.