The Duffy antigen receptor for chemokines regulates asthma pathophysiology.

BACKGROUND: The Duffy antigen receptor for chemokines (DARC) is an atypical receptor that regulates pro-inflammatory cytokines. However, the role of DARC in asthma pathophysiology is unknown. OBJECTIVE: To determine the role of DARC in allergic airways disease in mice, and the association between DARC single nucleotide polymorphisms (SNPs) and clinical outcomes in patients with asthma. METHODS: Mice with targeted disruption of the Darc gene (Darc∆E2 ) or WT mice were challenged over 3 weeks with house dust mite (HDM) antigen. Allergic airways disease was assessed 24 hours and 7 days following the final challenge. Additionally, associations between DARC SNPs and clinical outcomes were analysed in a cohort of poorly controlled asthmatics. RESULTS: Total airway inflammation following HDM did not differ between Darc∆E2 and WT mice. At 24 hours, Darc∆E2 mice had increased airway hyperresponsiveness; however, at 7 days airway hyperresponsiveness had completely resolved in Darc∆E2 but persisted in WT mice. In poorly controlled asthmatics, DARC SNPs were associated with worse asthma control at randomization and subsequent increased risk of healthcare utilization (odds ratio 3.13(1.37-7.27), P=.0062). CONCLUSIONS AND CLINICAL RELEVANCE: Our animal model and human patient data suggest a novel role for DARC in the temporal regulation in asthma pathophysiology and symptoms.

Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus).

Dramatic changes in the North American landscape over the last 12 000 years have shaped the genomes of the small mammals, such as the white-footed mouse (Peromyscus leucopus), which currently inhabit the region. However, very recent interactions of populations with each other and the environment are expected to leave the most pronounced signature on rapidly evolving nuclear microsatellite loci. We analyzed landscape characteristics and microsatellite markers of P. leucopus populations along a transect from southern Ohio to northern Michigan, in order to evaluate hypotheses about the spatial distribution of genetic heterogeneity. Genetic diversity increased to the north and was best approximated by a single-variable model based on habitat availability within a 0.5-km radius of trapping sites. Interpopulation differentiation measured by clustering analysis was highly variable and not significantly related to latitude or habitat availability. Interpopulation differentiation measured as FST values and chord distance was correlated with the proportion of habitat intervening, but was best explained by agricultural distance and by latitude. The observed gradients in diversity and interpopulation differentiation were consistent with recent habitat availability being the major constraint on effective population size in this system, and contradicted the predictions of both the postglacial expansion and core-periphery hypotheses.

Organization, structure and evolution of the CYP2 gene cluster on human chromosome 19.

The cytochrome P450 superfamily of mixed-function oxygenases has been extensively studied due to its many critical metabolic roles, and also because it is a fascinating example of gene family evolution. The cluster of genes on human chromosome 19 from the CYP2A, 2B, and 2F subfamilies has been previously described as having a complex organization and many pseudogenes. We describe the discovery of genes from three more CYP2 subfamilies inside the cluster, and assemble a complete map of the region. We comprehensively review the organization, structure, and expression of genes from all six subfamilies. A general hypothesis for the evolution of this complex gene cluster is also presented.

Complex beta-satellite repeat structures and the expansion of the zinc finger gene cluster in 19p12.

We investigated the organization, architecture, and evolution of the largest cluster ( approximately 4 Mb) of Krüppel-associated box zinc finger (KRAB-ZNF) genes located in cytogenetic band interval 19p12. A highly integrated physical map ( approximately 700 kb) of overlapping cosmid and BAC clones was developed between genetic STS markers D19S454 and D19S269. Using ZNF91 exon-specific probes to interrogate a detailed EcoRI restriction map of the region, ZNF genes were found to be distributed in a head-to-tail fashion throughout the region with an average density of one ZNF duplicon every 150-180 kb of genomic distance. Sequence analysis of 208,967 bp of this region indicated the presence of two putative ZNF genes: one consisting of a novel member of this gene family (ZNF208) expressed ubiquitously in all tissues examined and the other representing a nonprocessed pseudogene (ZNF209), located 450 kb proximal to ZNF208. Large blocks of ( approximately 25-kb) inverted beta-satellite repeats with a remarkably symmetrical higher order repeat structure were found to bracket the functional ZNF gene. Hybridization analysis using the beta-satellite repeat as a probe indicates that beta-satellite interspersion between ZNF gene cassettes is a general property for 1.5 Mb of the ZNF gene cluster in 19p12. Both molecular clock data as well as a retroposon-mapping molecular fossil approach indicate that this ZNF cluster arose early during primate evolution (approximately 50 million years ago). We propose an evolutionary model in which heteromorphic pericentromeric repeat structures such as the beta satellites have been coopted to accommodate rapid expansion of a large gene family over a short period of evolutionary time. [The sequence data described in this paper have been submitted to GenBank under accession nos. AC003973 and AC004004.]

Coagulation parameters of ABO group-specific cryosupernatant.

Patients with thrombotic thrombocytopenic purpura that is refractory to conventional fresh frozen plasma (FFP) exchange therapy are sometimes switched to cryosupernatant as the replacement fluid, although its hemostatic properties are not well defined. We performed several key coagulation assays on three pools of four units from each of three ABO groups of cryosupernatant and FFP. Fibrinogen, factor VIII activity, and von Willebrand factor antigen (vWF:Ag) levels were all significantly lower in cryosupernatant compared with FFP, although at levels usually not considered clinically significant. We confirmed that group O FFP contained significantly less factor VIII activity and vWF:Ag compared with groups AB and B. In contrast to FFP, group AB cryosupernatant contained lower levels of fibrinogen, factor V activity, factor VIII activity, and vWF:Ag than groups O or B. Group AB cryosupernatant, with the lowest levels of vWF:Ag and universal ABO compatibility, may be the product of choice for refractory thrombotic thrombocytopenic purpura.

Familial hemiplegic migraine and episodic ataxia type-2 are caused by mutations in the Ca2+ channel gene CACNL1A4.

Genes for familial hemiplegic migraine (FHM) and episodic ataxia type-2 (EA-2) have been mapped to chromosome 19p13. We characterized a brain-specific P/Q-type Ca2+ channel alpha1-subunit gene, CACNL1A4, covering 300 kb with 47 exons. Sequencing of all exons and their surroundings revealed polymorphic variations, including a (CA)n-repeat (D19S1150), a (CAG)n-repeat in the 3'-UTR, and different types of deleterious mutations in FHM and EA-2. In FHM, we found four different missense mutations in conserved functional domains. One mutation has occurred on two different haplotypes in unrelated FHM families. In EA-2, we found two mutations disrupting the reading frame. Thus, FHM and EA-2 can be considered as allelic channelopathies. A similar etiology may be involved in common types of migraine.

Factor V R506Q gene mutation analysis by PCR-RFLP: optimization, comparison with functional testing for resistance to activated protein C, and establishment of cell line controls.

Resistance to activated protein C (APC) has been recently identified as a highly prevalent risk factor for the development of venous thrombosis. In the majority of cases, APC resistance correlates with the presence of a single point mutation in the factor V gene (FV R506Q). The mutation is present in 3% to 5% of the general population and in up to 50% of patients with a personal and family history of venous thrombosis. In the current study, the authors have optimized and implemented for clinical diagnosis a method for detection of FV R506Q using the polymerase chain reaction coupled with restriction fragment length polymorphism analysis (PCR-RFLP). Forty-one healthy adults and 139 patients referred for hypercoagulability testing were genotyped and their APC resistance ratios determined using commercially available reagents (COATEST APC Resistance Kit). Comparative analysis indicated that if functional APC resistance was defined as per manufacturer's guidelines, a significant number of individuals with a normal factor V genotype were categorized as APC resistant and conversely, a significant number of individuals heterozygous for FV R506Q were categorized as non-APC resistant. These results indicate that comparative functional and genotypic analyses in the individual clinical laboratory setting are critical for establishing normal ranges and cut-off values for functional APC resistance due to FV R506Q. To facilitate molecular evaluation of APC resistance, Epstein-Barr virus (EBV) immortalized B-lymphocyte cell lines were established from individuals heterozygous and homozygous for FV R506Q.

The location of MZF-1 at the telomere of human chromosome 19q makes it vulnerable to degeneration in aging cells.

A zinc-finger gene encoding a transcription factor that regulates hematopoiesis, MZF-1, is located at the extreme end of the q arm of human chromosome 19. Several lines of evidence indicate that MZF-1 lies less than 20 kb from the subtelomeric repeat region of 19q. Telomeres are known to degenerate as cells age; disruption of MZF-1 due to telomeric degeneration may play a role in the increased incidence of leukemia in the elderly.

The molecular mechanism underlying the "rare allele phenomenon" in a subspecific hybrid zone of the California field mouse, Peromyscus californicus.

Natural hybrid zones are known to have unusually high levels of novel or otherwise rare electrophoretic variants (the "rare allele phenomenon"). These variant alleles are most likely the result either of high levels of unique mutations in hybrids or of intragenic recombination between divergent alleles from the parental populations. This study uses DNA sequence comparisons to determine which process has produced a rare allele of the 6-phosphogluconate dehydrogenase (6-PGD) gene in a subspecific hybrid zone of the California field mouse (Peromyscus californicus). About 70% of the coding sequence of 6-PGD was cloned and sequenced from three alleles, including two widespread alleles and one rare allele unique to hybrid populations. Sequence comparisons among the three alleles reveal no patterns that would indicate that the variant was formed by intragenic recombination. Instead, the unique allele of 6-PGD studied seems to have developed by the accumulation of base substitutions, which supports the hypothesis of increased mutation rates in hybrids.

Organization and evolution of the cytochrome P450 CYP2A-2B-2F subfamily gene cluster on human chromosome 19.

Cytochrome P450 genes from the CYP2A, CYP2B, and CYP2F subfamilies form a tight cluster which we have localized on the detailed physical map of human chromosome 19. The corresponding three gene subfamilies are also clustered in the mouse genome, on the region of chromosome 7 known to be syntenic to human chromosome 19. One hundred eight cosmid clones from the human P450 region were assembled into a single contig of 350 kb, restriction mapped, and probed with cDNAs from the three gene subfamilies. A total of 11 genes were identified in humans, including five from the 2A subfamily, three from the 2B subfamily, and three from the 2F subfamily; at least six of the 11 are pseudogenes. The organization of the genes, with members of the three subfamilies intermixed, indicates that the evolution of this gene cluster has been complex. The modern gene arrangement in humans is probably the result of a series of tandem duplications, plus at least one inverted duplication. The identification of all genes and pseudogenes in this cluster also makes it possible to determine the origins of some previously known variant P450 transcripts.

A genetic polymorphism in coumarin 7-hydroxylation: sequence of the human CYP2A genes and identification of variant CYP2A6 alleles.

A group of human cytochrome P450 genes encompassing the CYP2A, CYP2B, and CYP2F subfamilies were cloned and assembled into a 350-kb contig localized on the long arm of chromosome 19. Three complete CYP2A genes--CYP2A6, CYP2A7, and CYP2A13--plus two pseudogenes truncated after exon 5, were identified and sequenced. A variant CYP2A6 allele that differed from the corresponding CYP2A6 and CYP2A7 cDNAs previously sequenced was found and was designated CYP2A6v2. Sequence differences in the CYP2A6v2 gene are restricted to regions encompassing exons 3, 6, and 8, which bear sequence relatedness with the corresponding exons of the CYP2A7 gene, located downstream and centromeric of CYP2A6v2, suggesting recent gene-conversion events. The sequencing of all the CYP2A genes allowed the design of a PCR diagnostic test for the normal CYP2A6 allele, the CYP2A6v2 allele, and a variant--designated CYP2A6v1--that encodes an enzyme with a single inactivating amino acid change. These variant alleles were found in individuals who were deficient in their ability to metabolize the CYP2A6 probe drug coumarin. The allelic frequencies of CYP2A6v1 and CYP2A6v2 differed significantly between Caucasian, Asian, and African-American populations. These studies establish the existence of a new cytochrome P450 genetic polymorphism.

High-resolution genetic and physical mapping of multiple epiphyseal dysplasia and pseudoachondroplasia mutations at chromosome 19p13.1-p12.

Multiple epiphyseal dysplasia (MED) and pseudoachondroplasia (PSACH) are autosomal dominant chondrodysplasias that have similar phenotypes at both clinical and cytological levels. With the recent mapping of PSACH and one form of MED (EDM1) to the pericentromeric region of chromosome 19, it is likely that the disease mutations are allelic. D19S212 and D19S215, genetic markers flanking the EDM1/PSACH locus, have been localized in a chromosome 19 physical map consisting of cosmid contigs ordered by high-resolution FISH. These two markers define an interval of approximately 3.1 Mb at the 19p13.1-p12 boundary. With as many as five informative crossovers within the D19S212-D19S215 interval in one family with EDM1 and one family with a mild form of PSACH, recombination mapping at greater resolution was undertaken. From cosmid contigs physically mapped within the D19S212-D19S215 interval, four new dinucleotide repeat polymorphisms have been identified. Analysis of recombinant haplotypes in the two families has narrowed the possible location of the EDM1/PSACH gene to an interval of approximately 600 kb.

Pseudoachondroplasia and multiple epiphyseal dysplasia due to mutations in the cartilage oligomeric matrix protein gene.

Pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (MED) are dominantly inherited chondrodysplasias characterized by short stature and early-onset osteoarthrosis. The disease genes in families with PSACH and MED have been localized to an 800 kilobase interval on the short arm of chromosome 19. Recently the gene for cartilage oligomeric matrix protein (COMP) was localized to chromosome 19p13.1. In three patients with these diseases, we identified COMP mutations in a region of the gene that encodes a Ca++ binding motif. Our data demonstrate that PSACH and some forms of MED are allelic and suggest an essential role for Ca++ binding in COMP structure and function.

Organization of the multiple polymorphic sites of the D19S11 locus within a 650-kb cosmid contig.

The D19S11 locus has been previously described as consisting of a complex set of six nonallelic polymorphic sites detected with a combination of four restriction enzymes and three probes that were subcloned from a single cosmid. These probes also hybridized to additional nonvariant fragments on Southern blots of human genomic DNA. In the course of establishing a contig map of human chromosome 19, a set of cosmids that were positive for at least one of the probes defining this locus was identified. These cosmids, along with additional cosmids, were assembled using a combination of strategies, including fluorescence in situ hybridization studies using G1 interphase nuclei and sperm pronuclei as chromatin targets, into a single overlapping set of cosmids that spans approximately 650 kb. Cosmids that are positive for the MEL gene probe are localized at the centromeric end of the spanning path, with some cosmids being positive for both the MEL gene probe and one of the D19S11 probes. The EcoRI fragments with homology to the various probes have been identified; some cosmids have homology to all three D19S11 probes. The positions for five of the six polymorphic sites were localized within a 40-kb region, with four sites within 15 kb.

Unusual patterns of susceptibility to degradation of DNA isolated from tissues in Peromyscus californicus.

Isolation of intact, high molecular weight genomic DNA from the livers of 2 subspecies of Peromyscus californicus without excessive degradation was typically unattainable, whereas highly intact DNA from livers of other Peromyscus (field mice) species is invariably obtained using the same isolation methods. Additionally, highly intact DNA was obtained from splenic tissues of adult P. californicus and hepatic tissue of juvenile animals, indicating that the phenomenon is tissue-specific and age-related.

Effect of intravenous midazolam on esophageal motility testing in normal human volunteers.

This study evaluates midazolam's immediate pharmacological impact on esophageal motility. Stationary esophageal motility in normal male volunteers was evaluated to obtain a baseline study. Immediately after the baseline study, each subject received midazolam 0.02 micrograms/kg intravenously, and underwent repeat manometry 5 min later. Midazolam produced a variety of motility changes. There was a decrease in upper esophageal sphincter resting pressures (p < 0.05). Median pressures increased in the esophageal body at 3 cm below the upper esophageal sphincter (p < 0.05). Lower esophageal sphincter residual pressure increased, and the percentage of relaxation decreased (p < 0.05). The most striking change was the induction of tracings consistent with nonspecific esophageal motility disorders (p < 0.01). On the basis of these results, we conclude that esophageal motility testing should not follow procedures in which midazolam is used, until the duration of its effects on the esophagus is known.

Hematogenous spinal leptomeningeal metastasis: a unique CT enhancement pattern.

A distinct CT enhancement pattern of leptomeningeal metastasis from a systemic malignancy is described, corresponding to the pathologic and myelographic patterns of this entity. The uniform total subarachnoid enhancement, simulating intrathecal contrast, heralded sheetlike tumor proliferation along the surface of the spinal cord in an asymptomatic patient. Since the majority of hypervascular intraspinal abnormalities show focal enhancement with intravenous contrast, recognition of this pattern may provide unique clinical information.