Genetic variation in the HLA region is associated with susceptibility to herpes zoster

Herpes zoster, commonly referred to as shingles, is caused by the varicella zoster virus (VZV). VZV initially manifests as chicken pox, most commonly in childhood, can remain asymptomatically latent in nerve tissues for many years and often re-emerges as shingles. Although reactivation may be related to immune suppression, aging and female sex, most inter-individual variability in re-emergence risk has not been explained to date. We performed a genome-wide association analyses in 22 981 participants (2280 shingles cases) from the electronic Medical Records and Genomics Network. Using Cox survival and logistic regression, we identified a genomic region in the combined and European ancestry groups that has an age of onset effect reaching genome-wide significance (P>1.0 × 10⁻⁸). This region tags the non-coding gene HCP5 (HLA Complex P5) in the major histocompatibility complex. This gene is an endogenous retrovirus and likely influences viral activity through regulatory functions. Variants in this genetic region are known to be associated with delay in development of AIDS in people infected by HIV. Our study provides further suggestion that this region may have a critical role in viral suppression and could potentially harbor a clinically actionable variant for the shingles vaccine.

A rigorous algorithm to detect and clean inaccurate adult height records within EHR systems

BACKGROUND

Height is a critical variable for many biomedical analyses because it is an important component of Body Mass Index (BMI). Transforming EHR height measures into meaningful research-ready values is challenging and there is limited information available on methods for "cleaning" these data.

OBJECTIVES

We sought to develop an algorithm to clean adult height data extracted from EHR using only height values and associated ages.

RESULTS

The algorithm we developed is sensitive to normal decreases in adult height associated with aging, is implemented using an open-source software tool and is thus easily modifiable, and is freely available. We checked the performance of our algorithm using data from the Northwestern biobank and a replication sample from the Marshfield Clinic biobank obtained through our participation in the eMERGE consortium. The algorithm identified 1262 erroneous values from a total of 33937 records in the Northwestern sample. Replacing erroneous height values with those identified as correct by the algorithm resulted in meaningful changes in height and BMI records; median change in recorded height after cleaning was 7.6 cm and median change in BMI was 2.9 kg/m(2). Comparison of cleaned EHR height values to observer measured values showed that 94.5% (95% C.I 93.8-% - 95.2%) of cleaned values were within 3.5 cm of observer measured values.

CONCLUSIONS

Our freely available height algorithm cleans EHR height data with only height and age inputs. Use of this algorithm will benefit groups trying to perform research with height and BMI data extracted from EHR.

Presence of Borrelia burgdorferi sensu lato antibodies in the serum of patients with abdominal aortic aneurysms

Infectious agents are likely to play a role in the pathogenesis of chronic inflammatory diseases, including abdominal aortic aneurysms (AAAs). The goal of this study was to determine if Borrelia burgdorferi sensu lato (sl), a microorganism responsible for Lyme disease, is involved in the etiology of AAAs. The presence of serum antibodies against B. burgdorferi sl was measured with enzyme-linked immunosorbent assay (ELISA) and confirmed by Western blotting in 96 AAA and 108 peripheral artery disease (PAD) patients. Polymerase chain reaction (PCR) was used for the detection of Borrelia-specific DNA in the aneurysm wall. Among AAA patients 34% and among PAD patients 16% were seropositive for B. burgdorferi sl antibodies (Fisher's exact test, p = 0.003; odds ratio [OR] 2.79; 95% confidence interval [CI] 1.37-5.85). In the German general population, 3-17% are seropositive for Borrelia antibodies. No Borrelia DNA was detected in the aneurysm wall. Our findings suggest a relationship between AAAs and B. burgdorferi sl. We hypothesize that the underlying mechanism for B. burgdorferi sl in AAA formation is similar to that by the spirochete Treponema pallidum; alternatively, AAAs could develop due to induced autoimmunity via molecular mimicry due to similarities between some of the B. burgdorferi sl proteins and aortic proteins.

Expression of type I procollagen genes

All of the type I collagen in connective tissue is the product of one structural gene for the pro alpha 1(I) chain and another for the pro alpha 2(I) chain of type I procollagen. An intriguing question therefore is how the expression of the two genes differs in mineralizing and non-mineralizing tissues. One approach that our laboratory has pursued to answer this and related questions is to develop a new system whereby one can examine the self-assembly of collagen fibrils de novo by controlled enzymic cleavage of procollagen to collagen under physiological conditions. The system has made it possible for the first time to define thermodynamic parameters for the self-assembly process. We are now using the system to define the normal kinetics for fibril formation. The results should make it possible to study the effects of other components of extracellular matrix on fibril assembly, including the effects of bone-specific components that initiate mineralization. A second approach has been to define mutations in type I procollagen genes that cause increased brittleness of bone. Over a dozen mutations in type I procollagen genes have been found in probands with osteogenesis imperfecta. One of the surprises has been that at least 25% of the probands with lethal variants of osteogenesis imperfecta have mutations in type I procollagen genes. Another surprise has been the observation that a number of the mutations are tissue specific in terms of their phenotypic manifestations even though the same abnormal pro alpha chains are being synthesized in a variety of tissues.

The use of high-dimensional biology (genomics, transcriptomics, proteomics, and metabolomics) to understand the preterm parturition syndrome

High-dimensional biology (HDB) refers to the simultaneous study of the genetic variants (DNA variation), transcription (messenger RNA [mRNA]), peptides and proteins, and metabolites of an organ, tissue, or an organism in health and disease. The fundamental premise is that the evolutionary complexity of biological systems renders them difficult to comprehensively understand using only a reductionist approach. Such complexity can become tractable with the use of "omics" research. This term refers to the study of entities in aggregate. The current nomenclature of "omics" sciences includes genomics for DNA variants, transcriptomics for mRNA, proteomics for proteins, and metabolomics for intermediate products of metabolism. Another discipline relevant to medicine is pharmacogenomics. The two major advances that have made HDB possible are technological breakthroughs that allow simultaneous examination of thousands of genes, transcripts, and proteins, etc., with high-throughput techniques and analytical tools to extract information. What is conventionally considered hypothesis-driven research and discovery-driven research (through "omic" methodologies) are complementary and synergistic. Here we review data which have been derived from: 1) genomics to examine predisposing factors for preterm birth; 2) transcriptomics to determine changes in mRNA in reproductive tissues associated with preterm labour and preterm prelabour rupture of membranes; 3) proteomics to identify differentially expressed proteins in amniotic fluid of women with preterm labour; and 4) metabolomics to identify the metabolic footprints of women with preterm labour likely to deliver preterm and those who will deliver at term. The complementary nature of discovery science and HDB is emphasised.

Atteinte unguéale et infiltration sclérodermiforme du visage au cours d’une amylose systémique

INTRODUCTION

Mucocutaneous involvement in systemic amyloidosis occurs in 29 to 40 p. 100 of cases. Nail abnormalities are infrequent in AL amyloidosis. We report an original case of AL amyloidosis associated with cutaneous and integument alterations and scleroderma-like infiltration of the face.

CASE REPORT

A 73 year-old woman was hospitalized because of weight loss and asthenia. She had been treated 4 years earlier with chemotherapy for a IgG-type multiple myeloma with complete resolution of the underlying monoclonal gammapathy. Cutaneous examination showed nail dystrophy of all fingernails associated with scleroderma-like skin changes on the chin and lips. Histopathologic study of a chin biopsy confirmed the presence of amyloid deposits in the dermis. Laboratory data were normal, without signs of recurrence of multiple myeloma.

DISCUSSION

We report an original case of a patient who developed two unusual cutaneous manifestations associated with AL amyloidosis. Moreover, there was no correlation between the severity of the cutaneous lesions and the extent of the underlying hematological disease.

Web-site-based recruitment for research studies on abdominal aortic and intracranial aneurysms

Our current understanding on the pathogenesis of abdominal aortic and intracranial aneurysms is limited, but genetic and environmental factors as well as their interactions are likely to play important roles in the development and rupture of aneurysms. To identify genetic factors contributing to these diseases, we are carrying out genome-wide screening studies, which require a large number of patients and family members. Current methods of finding patients who qualify for genetic studies are, however, often costly and ineffective. To improve patient recruitment, a Web site was developed (cmmg.biosci.wayne.edu/ags). The site gives general information about our study, solicits participation into the study, and provides links to relevant medical and educational sites. During the time period of July, 1999, to December, 2000, the site received 5, 108 visits (13 visits/day). Approximately 20 research study applications are received each month. A total of 49% (57/117) of the individuals responding to the aortic aneurysm and 63% (84/134) responding to the intracranial aneurysm study report at least two affected blood relatives in the family and, therefore, qualify for our genetic studies. In conclusion, Web-based patient recruitment is successful and provides an improved success rate due to the fact that the responders are more motivated to participate in research studies.

Genomic organization of the human COL3A1 and COL5A2 genes: COL5A2 has evolved differently than the other minor fibrillar collagen genes

We report here on the complete structure of the human COL3A1 and COL5A2 genes. Collagens III and V, together with collagens I, II and XI make up the group of fibrillar collagens, all of which share a similar structure and function; however, despite the similar size of the major triple-helical domain, the number of exons coding for the domain differs between the genes for the major fibrillar collagens characterized so far (I, II, and III) and the minor ones (V and XI). The main triple-helical domain being encoded by 49-50 exons, including the junction exons, in the COL5A1, COL11A1 and COL11A2 genes, but by 43-44 exons in the genes for the major fibrillar collagens. Characterization of the genomic structure of the COL3A1 gene confirmed its association with the major fibrillar collagen genes, but surprisingly, the genomic organization of the COL5A2 gene was found to be similar to that of the COL3A1 gene. We also confirmed that the two genes are located in tail-to-tail orientation with an intergenic distance of approximately 22 kb. Phylogenetic analysis suggested that they have evolved from a common ancestor gene. Analysis of the genomic sequences identified a novel single nucleotide polymorphism and a novel dinucleotide repeat. These polymorphisms should be useful for linkage analysis of the Ehlers-Danlos syndrome and related disorders.

A study of novel polymorphisms in the upstream region of vasoactive intestinal peptide receptor type 2 gene in autism

We investigated the vasoactive intestinal peptide receptor type 2 (VIPR2) gene as a candidate gene for autism. We searched for mutations in the VIPR2 gene in autistic individuals, and 10 novel polymorphisms were identified. Three polymorphisms in the upstream region were studied in detail, and there was no significant difference in the frequencies between the autistic group (n = 14) and unrelated controls (n = 52). The distribution of the genotypes in two of the three polymorphisms differed somewhat between autistic subjects with gastrointestinal problems and those without. Moreover, there was a trend showing a correlation between the genotypes for the third polymorphism and the severity of stereotypical behavior as ranked by the Gilliam Autism Rating Scale. These preliminary results suggest that VIPR2 may have a role in gastrointestinal symptoms and stereotypical behaviors in autism, although a larger collection of samples suitable for transmission disequilibrium tests is necessary to validate the results.

Crossing over is rarely associated with mitotic intragenic recombination in Schizosaccharomyces pombe

Chromosomal rearrangements can result from crossing over during ectopic homologous recombination between dispersed repetitive DNA. We have previously shown that meiotic ectopic recombination between artificially dispersed ade6 heteroalleles in the fission yeast Schizosaccharomyces pombe frequently results in chromosomal rearrangements. The same recombination substrates have been studied in mitotic recombination. Ectopic recombination rates in haploids were approximately 1-4 x 10(-6) recombinants per cell generation, similar to allelic recombination rates in diploids. In contrast, ectopic recombination rates in heterozygous diploids were 2.5-70 times lower than allelic recombination or ectopic recombination in haploids. These results suggest that diploid-specific factors inhibit ectopic recombination. Very few crossovers occurred in ade6 mitotic recombination, either allelic or ectopic. Allelic intragenic recombination was associated with 2% crossing over, and ectopic recombination between multiple different pairing partners showed 1-7% crossing over. These results contrast sharply with the 35-65% crossovers associated with meiotic ade6 recombination and suggest either differential control of resolution of recombination intermediates or alternative pathways of recombination in mitosis and meiosis.

Matrix glycosaminoglycans in the growth phase of fibroblasts: more of the story in wound healing

BACKGROUND

Understanding wound healing and ways to accelerate the healing process includes understanding the factors that influence the synthesis of granulation tissue, which fills the wound before epithelialization. An important phase of early wound healing involves secretion of glycosaminoglycans (GAGs) by fibroblasts which form a hydrophilic matrix suitable for remodeling during healing. The complexity of GAG structure and function in the extracellular matrix (ECM) remains poorly studied in wound healing. There is no established model for cutaneous wound healing due to variations in donor age, anatomic site, or stage of organ development. Rat embryo fibroblasts (REF) developed as a model to study malignant changes in fibroblasts were used as a model for fibroblasts in early wound healing because they lack the confounding variations based on age, site, and stage present in other fibroblasts used to study early wound healing. The purpose of this study was to identify and characterize the sulfated GAGs synthesized by REF-D.

MATERIALS AND METHODS

Rat embryo fibroblasts (REF-D) were cultured in serum-based medium and radiolabeled during their growth phase with (35)S to identify the GAG chains usually associated with proteoglycans (PGs). The sites of attachment (ECM-rich) were collected with detergent in sodium acetate buffer, pH 5.8, in the presence of protease inhibitors. Sulfated molecules were collected by ion-exchange chromatography and then assayed for GAGs. Nitrous acid deamination was used to determine heparan sulfate GAGs, and chondroitinase was used for chondroitin/dermatan sulfate GAGs. The proportion of individual GAGs was expressed with respect to sulfated molecules isolated. In addition, RNA was isolated from subconfluent REF-D, and core proteins for proteoglycans (decorin, biglycan, syndecan-2, and perlecan) were assayed by reverse transcription polymerase chain reaction.

RESULTS

There were two major configurations of GAGs: free GAG chains (79.7% of sulfated molecules) and GAGs attached to the core protein of a proteoglycan (15.6%). The free GAG chains were composed of chondroitin sulfate (79.1% +/- 3.5) and heparan sulfate (28.7% +/- 2.1). In the smaller group of PGs, both heparan sulfate (94.8% +/- 7.3) and chondroitin sulfate (88.9% +/- 3.2) chains were attached to a core protein. REF-D expressed mRNA for biglycan and decorin, which are chondroitin sulfate-containing PGs. In addition, REF-D expressed mRNA for syndecan-2 and perlecan, which are PGs that contain primarily heparan sulfate chains.

CONCLUSIONS

A majority of GAG chains synthesized by subconfluent REF-D are chondroitin sulfate. A smaller proportion of chondroitin sulfate chains associate with a core protein as part of a PG (e.g., biglycan, decorin, syndecan-2). Heparan sulfate chains are also present, with a small proportion associated with a core protein (e.g., the PGs syndecan-2, perlecan). The greater presence of free GAG chains forming weak interactions with surrounding molecules may assist fibroblasts that are moving and replicating during this phase. Therefore, REF-D are particularly well suited to study early wound healing by their expression of chondroitin sulfate chains and associated PGs without the influence of donor age, stage, or anatomic site.

Mutations in fibrillar collagens (types I, II, III, and XI), fibril-associated collagen (type IX), and network-forming collagen (type X) cause a spectrum of diseases of bone, cartilage, and blood vessels

This review summarizes the data on 278 different mutations found to date in the genes for types I, II, III, IX, X, and XI collagens from 317 apparently unrelated patients. A majority (217 mutations; 78% of the total) of the mutations are single-base and either change the codon of a critical amino acid (63%), or lead to abnormal RNA splicing (13%). Most of the amino acid substitutions are those of a bulkier amino acid for the obligatory glycine of the repeating-Gly-X-Y-sequence of the collagen triple helix (155; 56%). Altogether, 26 different mutations (9.4% of the mutations) occur in more than one unrelated individual. The 65 patients in whom the 26 mutations were characterized constitute almost one-fifth (20.5%) of the 317 patients analyzed. The mutations in types I, II, III, IX, X, and XI collagens cause a wide spectrum of diseases of bone, cartilage, and blood vessels, including osteogenesis imperfecta, a variety of chondrodysplasias, types IV and VII of the Ehlers-Danlos syndrome, and, rarely, some forms of osteoporosis, osteoarthritis, and familial aneurysms.

Two new recurrent nucleotide mutations in the COL1A1 gene in four patients with osteogenesis imperfecta: about one-fifth are recurrent

Previous observations on mutations causing osteogenesis imperfecta (OI) suggested that unrelated patients had private mutations. Here preliminary studies on two patients with type I OI indicated that some mutations in the COL1A1 gene for type I procollagen cannot be detected by analyses of cDNAs. Therefore, we developed a protocol whereby 43 exon and exon flanking sequences of the COL1A1 gene can be amplified by PCR and scanned for mutations by denaturing gradient gel electrophoresis. Two new recurrent nucleotide mutations in the gene were found in four apparently unrelated patients with OI. Analysis of previous publications indicated that up to one-fifth of the mutations causing OI are recurrent in the sense that they were identical in apparently unrelated probands. About 80% of these identical mutations were in CpG dinucleotide sequences.

Genetic analysis of MMP3, MMP9, and PAI-1 in Finnish patients with abdominal aortic or intracranial aneurysms

MMP3, MMP9, and PAI-1 are present at increased levels in abdominal aortic aneurysms (AAAs). The promoters of these genes contain polymorphisms, with alleles that exhibit different transcriptional activities in vitro. Association studies were performed using these polymorphisms and DNA isolated from 47 AAA patients, 57 intracranial aneurysm (IA) patients, and 174 controls, all from Finland. PAI-1 and MMP9 genotypes did not associate with aneurysms. The frequency of the 5A MMP3 allele was somewhat higher in the AAA than that in the control group (P = 0.0609 after Bonferroni correction), whereas the MMP3 allele frequencies in the IA group did not differ from those of the controls (P = 0.9667). These findings suggest that the transcriptionally more active 5A MMP3 allele might be a genetic risk factor for AAA among Finns. They are in agreement with previous studies demonstrating higher level of MMP3 expression in AAA than in control tissues.

Founder mutations and the high prevalence of myotonia congenita in northern Finland

OBJECTIVE AND BACKGROUND

To find an explanation at the molecular level for the high prevalence of myotonia congenita in northern Finland and the exceptional pattern of inheritance of the disease in many families, and to study genotype-phenotype correlation in the patients.

METHODS

Forty-six patients with myotonia congenita and 16 unaffected relatives from 24 families were studied. All 23 exons and their flanking regions of the gene for the chloride channel protein (ClC-1) were sequenced from at least one patient from all families.

RESULTS

There were three different mutations of ClC-1 in the patients: one in exon 11, a T-to-G transversion that resulted in the substitution of cysteine for phenylalanine at amino acid position 413 (F413C); one in exon 15, a C-to-T transition that resulted in the substitution of valine for alanine at amino acid position 531 (A531V); and one in exon 23, a C-to-T transition that resulted in the substitution of a stop codon for an arginine codon at amino acid position 894 (R894X).

CONCLUSIONS

Molecular studies showed that even in families with apparent dominant inheritance, the actual mode of inheritance was autosomal recessive. This was explained not only by the observed consanguinity in some families but by an enrichment of three different mutations of the ClC-1 gene and a consequent high number of compound heterozygotes in the population. One of the mutations is unique to northern Finland. The conspicuous enrichment of the mutations is likely due to the founder effect and isolation by distance, as in other diseases in the Finnish heritage.

Analysis of coding sequences for tissue inhibitor of metalloproteinases 1 (TIMP1) and 2 (TIMP2) in patients with aneurysms

Aneurysms are characterized by dilation, i.e. expansion and thinning of all the arterial wall layers, which is accompanied by remodeling of the connective tissue. Genes involved in the regulation of tissue remodeling are therefore candidate genes. We analyzed TIMP1 and TIMP2 coding sequences in 12 individuals with abdominal aortic aneurysms (AAA), one individual with AAA and intracranial aneurysms (IA), four individuals with IA and two clinically unaffected individuals. We identified two nucleotide variants in both the TIMP1 and the TIMP2 coding sequences. All differences occurred in the third base positions of codons and were neutral polymorphisms. A significant difference was observed in the frequency of TIMP2 nt 573 polymorphism between 168 alleles from AAA patients and 102 control alleles.

Degradation of basement membrane by prostate tumor heparanase

BACKGROUND

The degradation of basement membrane (BM) by cancer is an important event that characterizes invasive biological behavior. A component of BM is heparan sulfate proteoglycan (HSPG). The glycanase(s) that degrade HSPG in BM are not yet isolated. We recently identified HSPG-degrading activity (PC-3M heparanase) in the conditioned media (CM) of malignant prostate carcinoma cells (PC-3M and LNCaP C4-2). Antibodies (Abs) to a recently isolated heparanase from human platelets (CTAP-III), cross-react with PC-3M heparanase although they differ in size; under reduced conditions PC-3M heparanase is 60 kDa whereas CTAP-III is 10 kDa by polyacrylamide gel electrophoresis. PC-3M heparanase therefore shares homology with CTAP-III. The purpose of this study was to test the inhibition of PC-3M heparanase by Abs specific to the N- and C-terminals of CTAP-III.

MATERIALS AND METHODS

CM from PC-3M and LNCaP C4-2 cells were tested for heparanase activity. Each reaction contained substrate as [3H]glucosamine-labeled HSPG (>50 kDa) from the BM of the EHS tumor, CM from PC-3M or LNCaP C4-2 cells, and inhibitor or buffer (negative control). Protease inhibitors were present throughout. After incubation for 3-20 h at 37 degreesC and pH 5.8, the reaction was stopped with 0.2% SDS. Each reaction mixture was centrifuged in an Ultrafree-MC 30,000 NMWL filter unit (Millipore) and radioactivity in the filtrate counted by scintillation counting. Results. For both cell lines, there was a linear relationship between the amount (microgram) of CM and degradation of HSPG. Degradation was inhibited by 54.1% (mean) using carrageenan lambda (10 microgram/ml), a nonspecific glycanase inhibitor (P < 0.05 by ANOVA). Ab to the N-terminus of CTAP-III (anti-Hep A) reduced degradation by 10-50% (mean 31.1%) and to the C-terminus (anti-Hep C) by 38.8-64.3% (mean 51.1%) (P < 0.003 by ANOVA).

CONCLUSIONS

The degradation of HSPG by malignant prostate cancer cell lines is inhibited by both a nonspecific glycanase inhibitor, and specific Abs to a homologous platelet heparanase. Based upon molecular weight, PC-3M heparanase is different from platelet heparanase and degrades BM.

Fibulin-2 exhibits high degree of variability, but no structural changes concordant with abdominal aortic aneurysms

We used conformation sensitive gel electrophoresis and direct sequencing of PCR products to screen for mutations in the cDNA for fibulin-2, an extracellular matrix protein, from 11 patients with abdominal aortic aneurysms and two controls. When compared with the published reference sequence, a total of 14 single-base sequence variations were detected. Seven of the changes were neutral in that they did not result in an amino acid substitution. There were five missense changes at sites not conserved between human and mouse, and two missense changes at sites conserved between human and mouse. All but two of the sequence variants studied were also present in an additional set of 102 control alleles analyzed. One of these two changes was a missense mutation, but it did not segregate with abdominal aortic aneurysms in the family, whilst the other change was neutral. In conclusion, fibulin-2 has a large number of sequence variations in comparison with our previous analyses of type III collagen, and these variations will be useful in association studies. There was an excellent overall agreement between direct sequencing of PCR-products and conformation sensitive gel electrophoresis.

First-stage autosomal genome screen in extended pedigrees suggests genes predisposing to low bone mineral density on chromosomes 1p, 2p and 4q

Osteoporosis is characterized by low bone density, and osteopenia is responsible for 1.5 million fractures in the United States annually. In order to identify regions of the genome which are likely to contain genes predisposing to osteopenia, we genotyped 149 members of seven large pedigrees having recurrence of low bone mineral density (BMD) with 330 DNA markers spread throughout the autosomal genome. Linkage analysis for this quantitative trait was carried out using spine and hip BMD values by the classical lod-score method using a genetic model with parameters estimated from the seven families. In addition, non-parametric analysis was performed using the traditional Haseman-Elston approach in 74 independent sib pairs from the same pedigrees. The maximum lod score obtained by parametric analysis in all families combined was +2.08 (theta = 0.05) for the marker CD3D on chromosome 11q. All other combined lod scores from the parametric analysis were less than +1.90, the threshold for suggestive linkage. Non-parametric analysis suggested linkage of low BMD to chromosomes 1p36 (Zmax = +3.51 for D1S450) and 2p23-24 (Zmax = +2.07 for D2S149). Maximum multi-point lod scores for these regions were +2.29 and +2.25, respectively. A third region with associated lod scores above the threshold of suggestive linkage in both single-point and multi-point non-parametric analysis was on chromosome 4qter (Zmax = +2.95 for D4S1539 and Zmax = +2.48 for D4S1554). Our data suggest the existence of multiple genes involved in controlling spine and hip BMD, and indicate several candidate regions for further screening in this and other independent samples.

A recombinant homotrimer of type I procollagen that lacks the central two D-periods. The thermal stability of the triple helix is decreased by 2 to 4 degrees C

A D-period cassette system was developed that can be used to synthesize a variety of recombinant homotrimers of type I procollagen. A construct lacking the central two D-periods of pro alpha 1(I) chains was assembled and expressed as a recombinant protein in the mammalian cell line. The recombinant protein was purified to homogeneity and the thermal stability of the triple helix assayed by rapid protease digestion. The results indicated that deletion of the central 468 amino acids from the major triple helix lowered the thermal stability of the protein by 2 to 4 degrees C. The results therefore begin to define regions of the molecule that vary in their contributions to helical stability.

Synthesis and conformational properties of a recombinant C-propeptide of human type III procollagen

A cDNA was prepared that coded for the signal peptide of type III procollagen linked to the complete C-propeptide of the protein. The cDNA was then used to express the protein in a baculovirus recombinant system. Recombinant protein was recovered as a trimer from the medium of transfected cells in a yield of 1 to 2.5 mg per liter. Mapping of peptide fragments with and without reduction indicated that the protein contained the expected interchain disulfide bonds. Analysis by circular dichroism suggested that the conformation of the protein corresponded to the native conformation. Therefore, the protein should be appropriate for further tests of its biological function and analysis of structure by X-ray diffraction.

Familial intracranial aneurysms

BACKGROUND

We set out to determine the prevalence of incidental intracranial aneurysms in first-degree relatives aged 30 years or more of people with intracranial aneurysms, and to see if polycystic kidney disease contributes to the aggregation of familial intracranial aneurysms.

METHODS

91 families with two or more affected members had previously been identified from a 14 year series of 1150 intracranial aneurysm patients treated at the University Hospital of Kuopio, Finland. Magnetic resonance angiography was used as a preliminary screening method, followed by conventional four-vessel angiography to verify suspected aneurysms. Participants were also screened for polycystic kidneys by ultrasonography.

FINDINGS

Incidental aneurysms were detected in 40 individuals: 38 of 438 individuals from 85 families without polycystic kidney disease or other diagnosed heritable disorders, and two of 22 individuals from six families known to have polycystic kidney disease. The crude and age-adjusted prevalence of incidental intracranial aneurysms among screened first-degree relatives was 8.7 (SE 1.3)% (95% CI 6.2-11.7) and 9.1 (1.4)% (6.2-11.7), respectively, for the familial group and the crude prevalence for the polycystic kidney group was 9.1 (6.1)% (1.1-29.2).

INTERPRETATION

Our results demonstrate a high prevalence of incidental intracranial aneurysms among first-degree relatives aged 30 years or older of patients with the condition and indicate that the risk of having an aneurysm is about four times higher for a close relative than for someone from the general population. Also, polycystic kidney disease families are a small fraction of the familial intracranial aneurysm families.

Multiple defects in type III collagen synthesis are associated with the pathogenesis of abdominal aortic aneurysms

Confluent skin fibroblast cultures were prepared from 40 patients diagnosed with and surgically treated for an abdominal aortic aneurysm. An analysis of secreted type I and type III collagen in the media of these fibroblast preparations revealed reduced secretion of type III collagen from six patients. DNA sequence analysis of the entire coding domain of the pro alpha 1 (III) collagen mRNA in skin fibroblast RNA from these six patients revealed a C to T substitution at nucleotide 607 in one of the probands that would result in the replacement of a leucine residue with phenylalanine in the second position of the first tripeptide repeat in the triple-helical domain of type III collagen. Allele-specific hybridization analysis of genomic DNA from this proband and family members indicated that this non-glycine substitution probably contributed to the aneurysmal phenotype in this patient. No coding sequence mutations were found in the other five patients. It is clear from this study, therefore, that aberrant synthesis of type III collagen, as a consequence of both a coding sequence mutation and other factors contributing to reduced secretion of type III procollagen, will result in the development of an aortic aneurysm in a significant percentage of patients with this disease.

Genetic linkage of familial granulomatous inflammatory arthritis, skin rash, and uveitis to chromosome 16

Blau syndrome (MIM 186580), first described in a large, three-generation kindred, is an autosomal, dominantly inherited disease characterized by multiorgan, tissue-specific inflammation. Its clinical phenotype includes granulomatous arthritis, skin rash, and uveitis and probably represents a subtype of a group of clinical entities referred to as "familial granulomatosis." It is the sole human model with recognizably Mendelian inheritance for a variety of multisystem inflammatory diseases affecting a significant percentage of the population. A genomewide search for the Blau susceptibility locus was undertaken after karyotypic analysis revealed no abnormalities. Sixty-two of the 74-member pedigree were genotyped with dinucleotide-repeat markers. Linkage analysis was performed under a dominant model of inheritance with reduced penetrance. The marker D16S298 gave a maximum LOD score of 3.75 at theta = .04, with two-point analysis. LOD scores for flanking markers were consistent and placed the Blau susceptibility locus within the 16p12-q21 interval.

Familial abdominal aortic aneurysms: screening of 71 families

OBJECTIVE

To find out the local prevalence of familial abdominal aortic aneurysms.

DESIGN

Retrospective open study.

SETTING

University hospital, Finland.

SUBJECTS

71 families of patients operated on for abdominal aortic aneurysm.

INTERVENTIONS

Ultrasound screening, personal interviews and study of population registers, death certificates and hospital records.

MAIN OUTCOME MEASURES

The diagnosis of asymptomatic abdominal aortic aneurysms.

RESULTS

148 of the 291 patients operated on replied to our letter (51%). The ultrasound examination was carried out on 123 siblings and detected abdominal aortic aneurysm in one sister (1/78 about 1%) and four brothers (4/45 about 9%). By the other methods data were obtained on 77 siblings (54 men and 23 women) of whom two sisters and six brothers were found to have abdominal aortic aneurysms. When the figures for the 71 families were combined, 10% of the brothers (10/99) and 3% of the sisters (3/101) had abdominal aortic aneurysms. These siblings were from 11 different families and so the prevalence of families with at least two affected persons was 16% (11/71). The index patient in 65 families was male and the prevalence of risk families (with two or more cases of aneurysm) in this group was 15% (10/65). The index case was a woman in six families giving a prevalence of 33% (2/6) (p = 0.2 between the groups).

CONCLUSION

The screening of families of patients with abdominal aortic aneurysms should be restricted to the brothers of these patients.

Expression of mRNAs for lysyl oxidase and type III procollagen in cultured fibroblasts from patients with the Menkes and occipital horn syndromes as determined by quantitative polymerase chain reaction

The Menkes syndrome and the occipital horn syndrome are two X-linked recessively inherited disorders characterized by abnormalities in copper metabolism. These abnormalities are associated with a reduction in the activity of lysyl oxidase (EC 1.4.3.13), an extracellular copper enzyme that initiates the crosslinking of collagens and elastin. We report here that the amount of lysyl oxidase mRNA, as studied by Northern blotting, and the number of lysyl oxidase mRNA molecules per picogram of RNA, as determined by a quantitative PCR method, were decreased in three cultured skin fibroblast lines from patients with the Menkes syndrome and two from patients with the occipital horn syndrome compared with four control cell lines. The decreased lysyl oxidase activity found in these disorders thus appears to be a least in part due to a pretranslational mechanism. No decrease was found in the number of the beta-actin mRNA molecules in the Menkes cell lines, but rather a slight increase, whereas a decrease was found in these molecules in the occipital horn cell lines. An additional abnormality found in the Menkes cell lines was a significant increase in the number of mRNA molecules for type III procollagen in two of the three cell lines investigated. The present and previous data indicate that the Menkes syndrome may involve several abnormalities in the expression of genes for connective tissue proteins.

Substitution of arginine for glycine at position 154 of the alpha 1 chain of type I collagen in a variant of osteogenesis imperfecta: comparison to previous cases with the same mutation

A substitution of arginine for glycine at amino acid position 154 of the alpha 1(I) collagen chain was found in a father and his three children. The phenotype of the patients includes manifestations of types I and III/IV osteogenesis imperfecta, but appears to be milder than that of the previously described two unrelated patients that had the identical mutation in the alpha 1(I) collagen chain. The variability in the phenotype raises the possibility of epistatic loci or environmental effects on expression of the disorder.

Direct sequencing of PCR products derived from cDNAs for the pro alpha 1 and pro alpha 2 chains of type I procollagen as a screening method to detect mutations in patients with osteogenesis imperfecta

More than 150 mutations in the genes for type I procollagen have been found in unrelated patients with osteogenesis imperfecta (OI), but mutations have been difficult to define in many patients with the mildest forms of the disease. Here, we have used robotically automated sequencing of the cDNAs for type I procollagen to screen for mutations in 12 patients suspected of having nonlethal OI (types I, III, and IV). Single base mutations that changed codons for obligate glycine residues were found in seven of the patients. Altogether, we analyzed 4,379 bp of sequences of both alleles of the pro alpha 1 (I) collagen (8,758 bp of allelic sequences) and 4,200 bp of sequences of both alleles of the pro alpha 2(I) collagen (8,400 bp of allelic) from each patient.

Quantitative polymerase chain reaction of lysyl oxidase mRNA in malignantly transformed human cell lines demonstrates that their low lysyl oxidase activity is due to low quantities of its mRNA and low levels of transcription of the respective gene

Lysyl oxidase (EC 1.4.3.13), an extracellular copper amino oxidase, initiates the cross-linking of collagens and elastin by catalyzing oxidative deamination of the epsilon-amino group in certain lysine and hydroxylysine residues. We developed here a polymerase chain reaction (PCR) method for the quantification of lysyl oxidase mRNA in which a synthetic RNA is used as an internal standard for coamplification with the targeted mRNA. The amount of lysyl oxidase mRNA when studied by Northern blot analysis and the number of lysyl oxidase mRNA molecules when determined by the quantitative PCR method were found to be markedly low in various malignantly transformed cell lines relative to control cell lines, quantitative PCR indicating values of about 2-10% of those in the controls. No difference was found in the number of beta-actin mRNA molecules between the transformed cells and the controls. Nuclear runoff experiments indicated that most if not all of the decrease in the number of lysyl oxidase mRNA molecules can be explained by diminished transcription of the respective gene.

Ehlers-Danlos syndrome type IV: a single base substitution of the last nucleotide of exon 34 in COL3A1 leads to exon skipping

The Ehlers-Danlos syndrome has been classified into nine phenotypic presentations. Type IV is a variant of particular importance because people affected with this genodermatosis are at great risk of spontaneous hemorrhage from vascular rupture or bowel perforation. Recent molecular advances have identified mutations in the gene for type III procollagen as responsible for Ehlers-Danlos syndrome type IV. We report a case of a 14-year-old male with a typical presentation of the type IV variant who was found to have markedly dilated fibroblast cisternae and varying collagen fibril diameter on ultrastructural study. A novel genetic defect was noted by polymerase chain reaction and DNA sequencing of genetic material isolated from skin fibroblast cultures. Analysis of the gene for type III procollagen revealed a single base mutation in the last nucleotide of exon 34. The mutation led to abnormal RNA splicing and skipping of exon 34 on the mRNA level.

Special features of familial intracranial aneurysms: report of 215 familial aneurysms

FAMILIAL INTRACRANIAL ANEURYSMS (FIAs) were compared with nonfamilial aneurysms (non-FIAs); the study group from east Finland included 167 family members from 85 families with FIAs. In every family, there has been two or more proven cases of subarachnoid hemorrhages among first-degree family members. Two-hundred and fifteen FIAs were found. The patients with FIAs were younger, and their aneurysms were smaller. Half of the FIAs were on the middle cerebral artery (n = 106 of 215), preferentially on the right side. Nearly one-third of the ruptured FIAs were smaller than 6 mm, and more than 80% of the aneurysms were under 14 mm in diameter. There were no significant differences between the frequency of aneurysms at mirror sites in FIA and non-FIA groups. Among siblings with FIAs, the frequency of pairs with age at onset within 10 years of each other was more than twice that expected from randomly selected pairs in the non-FIA group.

DNA-based diagnostics in the study of heritable and acquired disorders

Recent advances in molecular biology techniques have made DNA diagnostics a reality. A major advance was the development of the polymerase chain reaction, which allows the direct analysis of a region of a known gene from minute quantities of template DNA. The DNA can even be isolated from such sources as saliva, hair roots, microscope slides, paraffin-embedded tissue, and clinical swabs, in addition to blood and biopsy material. Another major improvement is the development of automated procedures suitable for robotic stations. Together these improvements make DNA analysis an important part of diagnostic procedures in studying the etiology of diseases.

Aberrant splicing of the type III procollagen mRNA leads to intracellular degradation of the protein in a patient with Ehlers-Danlos type IV

Ehlers-Danlos syndrome type IV (EDS IV) is an autosomal dominant disorder characterized by fragile skin, blood vessels, and internal organs and associated with decreased production, secretion, or thermal stability of type III procollagen. Mutations in the gene for type III procollagen have been identified in patients exhibiting decreased secretion or thermal stability of the protein, but no defect has been elucidated to explain the decreased production of type III procollagen in some patients with EDS IV. We report on a patient with a moderate case of EDS IV who produced decreased amounts of type III procollagen despite normal levels of translatable type III procollagen mRNA. S1 nuclease analysis of the type III procollagen mRNA indicated a defect in the region encoding exon 27. Sequence analysis of cDNA clones and genomic fragments generated by polymerase chain reaction amplification revealed that sequences encoded by exon 27 were absent from 3 out of 5 cDNA clones and that a G at the +5 position of the splice donor site in intron 27 was changed to an A in one allele of the patient's type III procollagen gene. Using a cDNA-genomic DNA hybrid probe in S1 nuclease analysis, fragments consistent with mRNA species containing and lacking exon 27 were detected in a 1:1 ratio. Pulse label and chase experiments in the presence or absence of brefeldin A indicated that most of the type III procollagen molecules synthesized by the patient's fibroblasts were not secreted into the medium but were degraded in the endoplasmic reticulum-Golgi compartment by a nonlysosomal mechanism.

Robotic automation of dideoxyribonucleotide sequencing reactions

We developed a robot to carry out standard Sanger dideoxyribonucleotide sequencing reactions efficiently and with minimal human intervention. A commercial robot was adapted to our design and specifications, and we programmed it to perform up to 240 sequencing reactions in a single unattended run of 7 h. The robot configuration can be easily altered to allow 480 reactions to be performed in an unattended run of 14 h. The special features of our robot include cooled reagent reservoirs and cooled chambers for storage of DNA templates and completed reactions as well as reproducible aspiration of small volumes by using a sensing algorithm. The robot has successfully performed over 3500 DNA reactions in about 30 separate runs in our DNA core facility.

Molecular basis of osteogenesis imperfecta and related disorders of bone

Recent work has demonstrated that more than 90% of patients with osteogenesis imperfecta (OI) have mutations in the gene for either the pro alpha 1 (I) chain or the gene for the pro alpha 2 (I) chain of type I procollagen. Three molecular mechanisms have explained the devastating effects of these mutations. In addition, the data provide several general conclusions about mutations in collagen genes. Studies in cell cultures with antisense oligonucleotides and studies in transgenic mice with an antisense gene raised the possibility that several strategies eventually may be developed to treat OI by converting severe forms of the disease to milder forms.

Sequencing of cDNA from 50 unrelated patients reveals that mutations in the triple-helical domain of type III procollagen are an infrequent cause of aortic aneurysms

Detailed DNA sequencing of the triple-helical domain of type III procollagen was carried out on cDNA prepared from 54 patients with aortic aneurysms. The 43 male and 11 female patients originated from 50 different families and five different nationalities. 43 patients had at least one additional blood relative who had aneurysms. Five overlapping asymmetric PCR products, covering all the coding sequences of the triple-helical domain of type III procollagen, were sequenced with 28 specific sequencing primers. Analysis of the sequencing gels revealed only two nucleotide changes that altered the structure of the protein. One was a substitution of threonine for proline at amino acid position 501 and its functional importance was not clearly established. The other was a substitution of arginine for an obligatory glycine at amino acid position 136. In 40 of the 54 patients, detection of a polymorphism in the mRNA established that both alleles were expressed. The results indicate that mutations in type III procollagen are the cause of only about 2% of aortic aneurysms.

Single base mutation that substitutes glutamic acid for glycine 1021 in the COL3A1 gene and causes Ehlers-Danlos syndrome type IV

The proposita described here was a 24-year-old woman with an acrogeric form of the Ehlers-Danlos syndrome including a massive dissecting aortic aneurysm. She was found to have a single-base mutation that substituted glutamic acid for glycine at amino acid position 1021 in the triple-helical domain of the type III procollagen. It is the most carboxy-terminal single-base mutation characterized to date in the COL3A1 gene. Analysis of medium and cell layer proteins from proposita's cultured skin fibroblasts showed that the mutant protein was poorly secreted, migrated more slowly on a polyacrylamide gel, and was partially unstable at +25 degrees C to brief digestion with trypsin.

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

Skin fibroblasts from a proband with mild osteogenesis imperfecta (type I) synthesized normal pro alpha 2(I) chains and shortened pro alpha 2(I) chains of type-I procollagen. The type-I collagen that contained the shortened alpha 2(I) chains was thermally unstable in that it was cleaved at 30 degrees C by a mixture of trypsin and chymotrypsin. The mutation generating the shortened pro alpha 2(I) chains was shown to be a deletion of 19 base pairs from +4 to +22 of intron 13 of the COL1A2 gene by sequencing of genomic DNA and allele-specific oligonucleotide hybridization. The same mutation was found in the proband's affected father. Probe-protection experiments with S1 nuclease demonstrated that about 88% of the RNA transcripts from the mutated allele were spliced by exon skipping from exon 12 to exon 14 and that about 12% of the RNA transcripts were normally spliced. There was no evidence for use of cryptic splice sites, even though two cryptic splice sites had more favorable statistical scores and delta G degree 37 values than the new site that was created by the mutation and that was used for splicing of 12% of the transcripts into a normal mRNA. Comparison of the results with observations on 17 previously reported mutations that produced in-frame deletions of amino acids from the triple-helical domain of type-I collagen indicated that deletions in the N-terminal half of the alpha 2(I) chain tended to produce milder phenotypes than similar deletions elsewhere in the alpha 1(I) or alpha 2(I) chains.

Efficient DNA sequencing on microtiter plates using dried reagents and Bst DNA polymerase

Sequenase, Taq DNA polymerase and Bst DNA polymerase were tested for sequencing of DNA on microtiter plates using dried down reagents. Several parameters were investigated to expedite the drying process while minimizing damage to the enzyme. Sequenase did not tolerate drying very well, and frequently generated sequences with weak signals and many sites of premature termination. With Taq DNA polymerase it was possible to obtain sequences of good quality. However, there was considerable variation of results between experiments and between batches of microtiter plates. Bst DNA polymerase generated sequences of excellent quality. It was stable for more than a week in dried-down state at -20 degrees C and at least overnight at room temperature. The method described here using Bst DNA polymerase is well suited for laboratory robots and workstations that typically employ 96-well microtiter plates.

Temperature sensitivity of aberrant RNA splicing with a mutation in the G+5 position of intron 37 of the gene for type III procollagen from a patient with Ehlers-Danlos syndrome type IV

A single-base mutation in intron 37 of the gene for type III procollagen (COL3A1) was found in a proband with the type IV variant of Ehlers-Danlos syndrome. Probe-protection experiments with S1 nuclease and RNA from fibroblasts incubated at 37 degrees C demonstrated that about 35% of the total mRNA or about 70% of the mRNA from mutated allele was spliced by exon skipping. The effects of the mutation were temperature-sensitive in that the amount of RNA from the mutated allele that was spliced by exon skipping was 87.1 +/- 7.7% at 31 degrees C, 70.1 +/- 6.5% at 37 degrees C, and 85.4 +/- 11.1% at 42 degrees C. The effects of temperature on aberrant RNA splicing were, therefore, the reverse of those reported for four previous mutants in collagen genes. The increase in abnormal RNA splicing when the temperature was raised from 31 degrees to 37 degrees C seen with previously reported mutants suggested that RNA-RNA hybridization of U1snRNA to the 5'-splice site in the substrate may be limiting in the processing of transcripts from the mutated alleles, since RNA-RNA hybridizations become less favorable at higher temperatures. The decrease in abnormal RNA splicing seen here when the temperature was raised from 31 degrees to 37 degrees C suggested that protein-RNA or protein-protein binding steps become rate limiting with the G+5 mutation in intron 37 of the COL3A1 gene.