Structural analyses of the polymorphic area in type II collagen gene

Population haplotype analysis and evolutionary relations of the COL2A1 gene

We have determined the allele frequencies and pairwise linkage disequilibria of restriction fragment length polymorphisms (RFLPs) distributed over the entire COL2A1 gene (spanning 23.6 kb) in a population of unrelated Dutch Caucasians. Pairwise linkage disequilibrium analysis of RFLP sites between exon 5B and 51 indicated a high degree of partly positive (the rare alleles of both loci are associated) and partly negative (the rare allele is associated with the common allele) linkage disequilibrium. The high degree of linkage disequilibrium enabled the assignment of 13 out of 128 possible haplotypes with 7 RFLPs. An evolutionary tree of these haplotypes was derived using a minimum spanning tree approach, indicating at least two ancestral haplotypes. Our data indicate that disease related population studies involving the COL2A1 gene should include a minimum of 4 RFLPs (D9, A9, H33, P51) to obtain 98% of possible haplotypes occurring.

Conservation of the sizes of 53 introns and over 100 intronic sequences for the binding of common transcription factors in the human and mouse genes for type II procollagen (COL2A1)

Over 11,000 bp of previously undefined sequences of the human COL2A1 gene were defined. The results made it possible to compare the intron structures of a highly complex gene from man and mouse. Surprisingly, the sizes of the 53 introns of the two genes were highly conserved with a mean difference of 13%. After alignment of the sequences, 69% of the intron sequences were identical. The introns contained consensus sequences for the binding of over 100 different transcription factors that were conserved in the introns of the two genes. The first intron of the gene contained 80 conserved consensus sequences and the remaining 52 introns of the gene contained 106 conserved sequences for the binding of transcription factors. The 5'-end of intron 2 in both genes had a potential for forming a stem loop in RNA transcripts.

Type II collagen mutations in rare and common cartilage diseases

Cartilage diseases include a wide variety of clinical phenotypes from common osteoarthrosis to several different types of chondrodysplasias, i.e. 'disorders of cartilage', of which more than 100 different have been described. Patients frequently suffer from various symptoms affecting their joints and/or the growth of their long bones. The amount of hyaline cartilage at articular surfaces is often diminished and structurally abnormal. The surface of the cartilage may have an irregular appearance with defects extending into the subchondral bone. The major constituents of this hyaline cartilage are collagens and proteoglycans, the most abundant protein being type II collagen. It is a homotrimer of three identical alpha-chains, which are encoded by a single gene on human chromosome 12. The gene for type II collagen therefore became a likely candidate for some forms of chondrodysplasias and cartilage degeneration. Recently, both linkages and exclusions between this gene and various cartilage diseases have been reported and a growing number of mutations within the gene have also been identified.

Clinical correlations of osteoarthritis associated with a single-base mutation (arginine519 to cysteine) in type II procollagen gene. A newly defined pathogenesis

OBJECTIVE

To investigate the occurrence and clinical correlation of the arg519-to-cys mutation in the type II procollagen gene in patients with osteoarthritis (OA).

METHODS

Sixty-six subjects from 7 families with a strong family history of generalized OA and 13 patients with erosive OA were evaluated clinically and radiologically. Blood samples from 58 subjects in the familial OA group and from all 13 patients with erosive OA were obtained for DNA analysis. Exon 31 of COL2A1, which spans residue 519, was amplified by polymerase chain reaction.

RESULTS

The arg519-to-cys mutation was detected in 2 of the 7 families with generalized OA. In these 2 families, the mutation was present in the 2 probands and in 19 other clinically affected family members, as well as in 3 (so-far) clinically unaffected family members (ages 25, 14, and 11 years). It was absent in 18 clinically unaffected members tested. The mutation was associated with a distinctive pattern of early-onset, aggressive, generalized OA with a mild spinal chondrodysplasia. Inheritance was autosomal dominant. No mutation was found in any of the patients with erosive OA.

CONCLUSION

The arg519-to-cys mutation defines a new pathogenic factor in generalized OA with characteristic clinical and radiologic features. The demonstration of a mutation in 3 of 8 families with OA studied thus far suggests a significant incidence of genetically related clinical OA.

Early-onset osteoarthritis linked to the type II procollagen gene. Detailed clinical phenotype and further analyses of the gene

OBJECTIVE

To specify in detail the clinical phenotype in 2 Finnish families demonstrating linkage between the type II procollagen gene (COL2A1) and osteoarthritis (OA). We also reevaluated the linkage and screened the exon sequences of the COL2A1 gene for mutations.

METHODS

We used single-stranded conformation polymorphism and denaturing gradient-gel electrophoresis techniques for the analyses.

RESULTS

The patients' phenotype represented typical, but early-onset, OA. There was no clinical or radiographic evidence of chondrodysplasia. No mutation in the protein-coding regions of the COL2A1 gene could be identified. However, the linkage analysis with a new multiallelic marker resulted in a statistically more significant logarithm of odds (LOD) score than has been reported.

CONCLUSION

Familial OA with classic clinical and radiographic findings is tightly linked to the COL2A1 gene. Systematic screening of the 54 exons did not, however, reveal any mutations; this suggests that the mutation may lie in the promoter region or within the introns of this 35-kb gene.

Detection of sequence variants in the gene for human type II procollagen (COL2A1) by direct sequencing of polymerase chain reaction-amplified genomic DNA

The direct sequencing of the human type II procollagen (COL2A1) gene from polymerase chain reaction (PCR)-amplified genomic DNA is described. Thirty-two regions of the COL2A1 gene were asymmetrically amplified with intron primers which were specifically chosen to amplify a region spanning 500 to 800 bp of sequence encoding one or more exons and their accompanying intervening sequences. Primers for dideoxynucleotide sequencing of the PCR products were then designed to provide complete exon sequence information and to insure that intron:exon splice junction sequence data would be obtained. Amplification and sequencing reactions were performed on an automated workstation to facilitate the handling of multiple DNA templates. The procedure allowed efficient sequencing of over 25,000 bp of each allele of the COL2A1 gene per diploid genome. We used this method for the comparative analyses of COL2A1 sequences in DNA isolated from the blood of 42 unrelated individuals and we identified 21 neutral sequence variants in the gene. The sequence variations were confirmed by independent assays, including restriction enzyme digestion. The sequence variants described here will be important for identifying haplotypes of the type II procollagen gene that will be useful in defining a genetic etiology for diseases of cartilaginous tissues.

Completion of the intron-exon structure of the gene for human type II procollagen (COL2A1): variations in the nucleotide sequences of the alleles from three chromosomes

A new procedure for preparing cosmid libraries was used to isolate three alleles for the human gene for type II procollagen (COL2A1). Over 20,000 bp of one allele were completely sequenced and over 10,000 bp of the two other alleles were sequenced. The data located and defined 26 exons and introns of the gene not previously analyzed. The results completed the structure of the gene except for the newly discovered exon 2A that undergoes alternative splicing (Ryan et al., 1990, Trans. Ann. Meet. Orthop. Res. Soc. 15:65). As a result, it is the most completely known structure of a gene for a human fibrillar collagen. The results confirm the previous impression that exon sizes are highly conserved among the genes for the three major fibrillar collagens. Comparison of clones from the three alleles defined five neutral variations in coding sequences and seven variations in the intron that also are probably neutral variations. The normal sequences and the variations in sequences will be important for identifying different alleles and haplotypes of the gene and for the analysis of genetic mutations in the gene that cause diseases of cartilage such as chondrodysplasias and osteoarthritis.

Efficient procedure for preparing cosmid libraries from microgram quantities of genomic DNA fragments size fractionated by gel electrophoresis

A modified procedure for preparing cosmid libraries from genomic DNA is described. Genomic DNA was partially digested with a restriction endonuclease, and DNA fragments of appropriate size fractionated by agarose gel electrophoresis. A cosmid library was prepared, prescreened, and used to isolate gene inserts with previously published procedures. In one series of experiments, a modified cosmid vector containing stuffer fragments was used to prepare cosmid libraries containing partial SphI digests of 25 to 35 kb. From 10(5) to 10(7) clones were obtained per microgram of size-fractionated genomic DNA. From 10 to 100 hybridization-positive clones of a single copy gene (COL2A1) were obtained from plates that were positive in the prescreening step. Restriction mapping of over 20 clones and nucleotide sequencing of over 20,000 bp in each of two clones indicated that the inserts were faithful copies of the gene. In another experiment, a standard cosmid vector was used to prepare a cosmid library containing partial BamHI fragments of 30 to 45 kb. Genomic libraries can be prepared with 5 to 20 micrograms of genomic DNA and a large number of clones containing 25 to 45 kb fragments of a single copy gene can be isolated in about three weeks.

Single base mutation in the type II procollagen gene (COL2A1) as a cause of primary osteoarthritis associated with a mild chondrodysplasia

A cosmid clone was isolated that contained an allele for the type II procollagen gene previously shown to be coinherited with primary generalized osteoarthritis in a large family. Affected members of the family had evidence of a mild chondrodysplasia, but they developed progressive osteoarthritic changes in many joints that had no epiphyseal deformities. The clone contained 52 of the 54 exons of the gene. Nucleotide sequencing of greater than 20,000 base pairs from the clone demonstrated that all the coding sequences and all the intron-exon boundaries were normal except for a single base mutation that converted the codon for arginine at position 519 of the alpha 1(II) chain to a codon for cysteine, an amino acid not found in type II collagen from humans or a variety of other species. The mutation was found in all affected members of the family but not in unaffected members or in 57 unrelated individuals.