IL4Rα and ADAM33 as genetic markers in asthma exacerbations and type-2 inflammatory endotype

BACKGROUND

Genetic markers of susceptibility to asthma exacerbations in adults remain unclear.

OBJECTIVE

To identify genetic markers of asthma exacerbations, particularly in patients with type-2 inflammatory endotype.

METHODS

In this observational study of patients enrolled in the Kinki Hokuriku Airway disease Conference multicenter study, frequency of exacerbations requiring systemic corticosteroids during 2 years after enrolment and associated risk factors was determined. For genetic marker analysis, interleukin-4 receptor α (IL4RA) rs8832 and a disintegrin and metalloprotease 33 (ADAM33) S_2 (rs528557), T_1 (rs2280091), T_2 (rs2280090), and V_4 (rs2787094) variants were included. Elevated serum periostin levels at enrolment (≥95 ng/mL, defined as type-2 inflammatory endotype) were considered in the analysis.

RESULTS

Among 217 patients who were successfully followed up for 2 years after enrolment, 60 patients showed at least one asthma exacerbation during the 2 years. Airflow limitation (%FEV₁ <80%) and recent exacerbations but not genetic variants were identified as risk markers of exacerbations. A total of 27 patients showed type-2 inflammatory endotype (serum periostin ≥95 ng/mL at enrolment) and subsequent exacerbations; risk factors in these patients were airflow limitation (odds ratio, 6.51; 95% confidence interval (CI): 2.37-18.6; P=.0003), GG genotype of IL4RA rs8832 (odds ratio, 4.01; 95% CI: 1.47-11.0; P=.007), and A allele of ADAM33 T_2 (odds ratio, 2.81; 95% CI: 1.05-7.67; P=.04) by multivariate analysis. In addition, GG genotype of IL4RA rs8832 was associated with type-2 endotype, whereas A allele of ADAM33 T_2 was associated with mixed type of eosinophilic/type-2 and neutrophilic inflammations.

CONCLUSIONS AND CLINICAL RELEVANCE

IL4RA and ADAM33 variants may be risk markers of asthma exacerbations in type-2 inflammatory endotype. Precise endotyping may facilitate the identification of genetic risk markers of asthma exacerbations.

A rare variant in CYP27A1 and its association with atopic dermatitis with high serum total IgE

This study investigated rare variants associated with atopic dermatitis. We performed exome analyses on 37 patients who were diagnosed with atopic dermatitis by board-certified dermatologists and had total serum IgE levels greater than 1000 IU/ml. The exome analysis identified seven variants with <1% allele frequency in Asian (ASN) population of 1000 Genomes Project phase 1 data and >5% allele frequency in the atopic dermatitis exome samples. We then conducted a replication study using 469 atopic dermatitis patients with total serum IgE ≥1000 IU/ml and 935 Japanese controls to assess the presence of these 7 candidate variants. The replication study confirmed that CYP27A1 rs199691576 (A/G) was associated with atopic dermatitis with high serum IgE levels (P = 0.012, odds ratio = 2.1). CYP27A1 is involved in the metabolism of vitamin D3, which plays important roles in modulating immune function. Previous studies have reported polymorphisms in vitamin D pathway genes that are associated with allergy-related phenotypes. Our data confirm the importance of genes regulating the vitamin D pathway in the development of atopic dermatitis.

Novel scoring system and algorithm for classifying chronic rhinosinusitis: the JESREC Study

Background

Chronic rhinosinusitis (CRS) can be classified into CRS with nasal polyps (CRSwNP) and CRS without nasal polyps (CRSsNP). CRSwNP displays more intense eosinophilic infiltration and the presence of Th2 cytokines. Mucosal eosinophilia is associated with more severe symptoms and often requires multiple surgeries because of recurrence; however, even in eosinophilic CRS (ECRS), clinical course is variable. In this study, we wanted to set objective clinical criteria for the diagnosis of refractory CRS.

Methods

This was a retrospective study conducted by 15 institutions participating in the Japanese Epidemiological Survey of Refractory Eosinophilic Chronic Rhinosinusitis (JESREC). We evaluated patients with CRS treated with endoscopic sinus surgery (ESS), and risk of recurrence was estimated using Cox proportional hazard models. Multiple logistic regression models and receiver operating characteristics curves were constructed to create the diagnostic criterion for ECRS.

Results

We analyzed 1716 patients treated with ESS. To diagnose ECRS, the JESREC scoring system assessed unilateral or bilateral disease, the presence of nasal polyps, blood eosinophilia, and dominant shadow of ethmoid sinuses in computed tomography (CT) scans. The cutoff value of the score was 11 points (sensitivity: 83%, specificity: 66%). Blood eosinophilia (>5%), ethmoid sinus disease detected by CT scan, bronchial asthma, aspirin, and nonsteroidal anti‐inflammatory drugs intolerance were associated significantly with recurrence.

Conclusion

We subdivided CRSwNP in non‐ECRS, mild, moderate, and severe ECRS according to our algorithm. This classification was significantly correlated with prognosis. It is notable that this algorithm may give useful information to clinicians in the refractoriness of CRS before ESS or biopsy.

Genomewide association study identifies HAS2 as a novel susceptibility gene for adult asthma in a Japanese population

BACKGROUND

It is increasingly clear that asthma is not a single disease, but a disorder with vast heterogeneity in pathogenesis, severity, and treatment response. To date, 30 genomewide association studies (GWASs) of asthma have been performed, including by our group. However, most gene variants identified so far confer relatively small increments in risk and explain only a small proportion of familial clustering.

OBJECTIVE

To identify additional genetic determinants of susceptibility to asthma using a selected Japanese population with reduced tobacco smoking exposure.

METHODS

We performed a GWAS by genotyping a total of 480 098 single-nucleotide polymorphisms (SNPs) for a Japanese cohort consisting of 734 healthy controls and 240 patients with asthma who had smoked for no more than 10 pack-years. The SNP with the strongest association was genotyped in two other independent Japanese cohorts consisting of a total of 531 healthy controls and 418 patients with asthma who had smoked for no more than 10 pack-years. For the hyaluronan synthase 2 (HAS2) gene, we investigated SNP-gene associations using an expression quantitative trait loci (eQTL) database and also analysed its gene expression profiles in 13 different normal tissues.

RESULTS

In the discovery GWAS, a SNP located upstream of HAS2, rs7846389, showed the strongest statistical significance (P = 1.43 × 10(-7) ). In the two independent replication cohorts, rs7846389 was consistently associated with asthma (nominal P = 0.0152 and 0.0478 in the first and second replication cohorts, respectively). In the meta-analysis, association of rs7846389 with susceptibility to asthma reached the level of genomewide significance (P = 7.92 × 10(-9) ). This variant was strongly correlated with HAS2 mRNA expression. The strongest expression of the gene was detected in the lung.

CONCLUSIONS

Our study identified HAS2 as a novel candidate gene for susceptibility to adult asthma.

GLCCI1 variant accelerates pulmonary function decline in patients with asthma receiving inhaled corticosteroids

BACKGROUND

In steroid-naive patients with asthma, several gene variants are associated with a short-term response to inhaled corticosteroid (ICS) treatment; this has mostly been observed in Caucasians. However, not many studies have been conducted for other ethnicities. Here, we aimed to determine the relationship between the annual decline in forced expiratory flow volume in one second (FEV1 ) and the variant of the glucocorticoid-induced transcript 1 gene (GLCCI1) in Japanese patients with asthma receiving long-term ICS treatment, taking into account the effect of high serum periostin levels, a known association factor of pulmonary function decline and a marker of refractory eosinophilic/Th2 inflammation.

METHODS

In this study, 224 patients with asthma receiving ICS treatment for at least 4 years were enrolled. The effects of single-nucleotide polymorphisms (SNPs) in GLCCI1, stress-induced phosphoprotein 1 (STIP1), and T gene on the decline in FEV1 of 30 ml/year or greater were determined.

RESULTS

Besides the known contributing factors, that is, the most intensive treatment step, ex-smoking, and high serum periostin levels (≥95 ng/ml), the GG genotype of GLCCI1 rs37973, and not other SNPs, was independently associated with a decline in FEV1 of 30 ml/year or greater. When patients were stratified according to their serum periostin levels, the GG genotype of rs37973 was significantly associated with blood eosinophilia (≥250/μl) in the high serum periostin group.

CONCLUSIONS

A GLCCI1 variant is a risk factor of pulmonary function decline in Japanese patients with asthma receiving long-term ICS treatment. Thus, GLCCI1 may be associated with response to ICS across ethnicities.

Variants in the 17q21 asthma susceptibility locus are associated with allergic rhinitis in the Japanese population

BACKGROUND

Allergic rhinitis (AR) is a very common disorder peaking in the teenage years that is mediated by hypersensitivity responses to environmental allergens. Although it is well established that the ORMDL3 locus at chromosome 17q21 is associated with susceptibility to bronchial asthma, the genetic influences of the polymorphisms of the locus in allergic rhinitis are unclear.

OBJECTIVE

To examine whether the polymorphisms in the 17q21 asthma susceptibility locus are associated with allergic rhinitis in the Japanese population.

METHODS

We performed linkage disequilibrium (LD) mapping of the locus using the HapMap database and conducted an association study of the locus with a total of 15 tag SNPs in two independent populations. We further evaluated correlations of genotypes with changes in expression of genes at the region in lymphoblastoid cell lines in the Japanese population and assessed the expression levels of the genes in nasal epithelium and various human tissues.

RESULTS

We found a significant association between a total of five polymorphisms in the 17q21 asthma susceptibility locus, rs9303277, rs7216389, rs7224129, rs3744246, and rs4794820, and AR (minimum P(combined)  = 0.00074, rs4794820). The expression level of the ORMDL3 transcript was significantly correlated with the genotype of rs12150079, rs7216389, rs3744246, and rs4794820 with P < 0.01 (minimum P = 0.0058, rs7216389), and ORMDL3 mRNA was highly expressed in nasal epithelium.

CONCLUSION

Genetic variants in the 17q21 asthma susceptibility locus are significantly associated with AR in the Japanese population.

Associations between decay-accelerating factor polymorphisms and allergic respiratory diseases

BACKGROUND

Allergic diseases such as asthma and allergic rhinitis are major causes of morbidity in developed countries. The pathology underlying allergic respiratory diseases is considered to be IgE-mediated type I allergy characterized by mucosal inflammation that occurs in response to allergen exposure. They are common diseases involving a complex inheritance. Complement systems are known to play an important role in allergic diseases. Decay-accelerating factor (DAF) is important for the regulation of the complement system and is a good candidate for determining the susceptibility to allergic diseases.

OBJECTIVE

The present study aimed to investigate whether polymorphisms in the DAF gene are associated with allergic respiratory diseases in the Japanese population.

METHODS

We performed mutation screenings of DAF and conducted a tag single-nucleotide polymorphisms (SNP) association analysis for 684 unrelated adult individuals with seasonal allergic rhinitis (SAR) with Japanese ceder pollen, 188 mite-sensitive adults with asthma, and 346 unrelated non-allergic healthy controls.

RESULTS

DAF is located in the tight linkage disequilibrium (LD) block spanning 62 kb. The tag SNP analysis revealed that rs10746463 was significantly associated with SAR (P=0.00033) and mite-sensitive adult asthma (P=0.044). The rs2564978 and rs3841376 haplotypes, which are located in the promoter region of DAF, were in complete LD with rs10746463 (r2=1). Luciferase reporter assays with constructs containing the 5' flanking regions of DAF showed that the plasmid with rs2564978 C/rs3841376 deletion (the risk haplotype) had a statistically significantly lower transcriptional activity than that containing the rs2564978 T/rs3841376 insertion.

CONCLUSIONS

Our results suggest that DAF is one of the genes involved in conferring susceptibility to allergic respiratory diseases and show that decreased levels of DAF may be associated with the enhanced specific IgE responses occurring in allergic diseases in the Japanese population.

Association of serum interleukin-33 level and the interleukin-33 genetic variant with Japanese cedar pollinosis

BACKGROUND

IL-33, an IL-1-like cytokine, is a ligand for IL1RL1, which is an important effector molecule of type 2 T helper responses. Although IL-33/IL1RL1 interaction has been suggested to be important in induction of allergic airway inflammation, serum levels of IL-33 and the genetic influences of the polymorphisms of IL-33 in human allergic diseases are unclear.

OBJECTIVE

The aim of this study was to examine whether the serum IL-33 level and polymorphisms in IL-33 are associated with Japanese cedar (JC) pollinosis, the most common form of allergic rhinitis, and a major public health problem, in Japan.

METHODS

We performed linkage disequilibrium (LD) mapping of the gene using the HapMap database, and two selected tag single nucleotide polymorphisms were genotyped. We conducted an association study of IL-33 (JC pollinosis, n=170; normal controls, n=100) and measured the IL-33 levels in sera of the 270 subjects by ELISA.

RESULTS

Serum levels of IL-33 were significantly higher in patients with JC pollinosis (P=0.0018) than in controls. In genetic association analysis, we found a positive association between the polymorphism and JC pollinosis (P=0.048).

CONCLUSION

Our results support a role for IL-33 in the pathogenesis of JC pollinosis.

Functional analysis of a polymorphism in the promoter region of the IL-12/23p40 gene

BACKGROUND

Human IL-12B gene on chromosome 5q31 encodes the common p40 subunit of IL-12 and IL-23. IL-12 is known to play critical roles in the generation of T-helper type 1 (TH(1)) cells, whereas IL-23 is involved in maintenance and/or population expansion of TH(17) cells. Although several reports suggested an association between a polymorphism (-6415CTCTAA/GC) in IL-12B and asthma, the molecular mechanism how this polymorphism is involved in allergic inflammation is still unclear.

METHODS

The transcription activity was analysed by reporter assay. A transcription factor binding to -6415 polymorphic site was identified by electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) assay. The amount of cytokines produced from peripheral monocytes were determined by ELISA.

RESULTS

Reporter assay showed that the transcription activity of the GC allele was higher than that of the CTCTAA allele. A transcription factor Sp1 bound to the region including the GC allele with a higher affinity than that of the CTCTAA allele in EMSA. In vivo binding of Sp1 to IL-12B gene carrying -6415GC was confirmed by ChIP assay. Overexpression of Sp1 up-regulated transcription activity of promoter carrying GC allele sequence, whereas the CTCTAA promoter was not affected by Sp1. We examined the correlation between -6415CTCTA/GC polymorphism and production of cytokine IL-12/23p40, IL-12p70, and IL-23 on peripheral blood monocytes, and monocytes with the GC/GC allele exhibited significantly higher expression of IL-12p70 protein than those with the CTCTAA/CTCTAA allele (P=0.009).

CONCLUSIONS

The -6415 polymorphism is involved in cytokine production potential by affecting Sp1-mediated transcription activity.

Promoter polymorphisms in the IRF3 gene confer protection against systemic lupus erythematosus

In order to identify a novel candidate gene in systemic lupus erythematosus (SLE), we analysed a panel of six genes encoding molecules involved in the type I interferon (IFN) system. We first identified variants in the five genes related to type I IFN pathway by sequencing. Genotyping of a panel of eight selected single-nucleotide polymorphisms (SNPs) in six candidate genes ( TLR9, MYD88, IRF3, IRF7, IFNB1, IFNA17) was performed in 137 patients with SLE and matched with 152 healthy controls using polymerase chain reaction-restriction fragment length polymorphism analysis. In functional assay, quantitative real-time polymerase chain reaction was performed to assess constitutive IRF3 mRNA expression in peripheral blood mononuclear cells from healthy subjects with different IRF3 promoter haplotypes. Among eight SNPs genotyped, an IRF3 SNP at –925 was found to be associated with SLE after correction for multiple tests (corrected P = 0.016). Of total five IRF3 SNPs genotyped, the promoter IRF3 SNPs –925A/G and –776C/T showed the most significant association with SLE. With regard to –925A/G, the frequency of GG genotype was significantly decreased among SLE patients compared with the control group (1.5% vs. 9.9%; χ2 = 10.0, P = 0.0015, odds ratio 0.12, 95% confidence interval 0.027–0.554). Our experimental data indicated that constitutive IRF3 mRNA expression was significantly lower in cells carrying the minor G-T/G-T haplotype pair compared with those carrying the major A-C haplotype. In conclusion, we showed that the promoter SNPs of the IRF3 gene were significantly associated with resistance against SLE.

Transforming growth factor-beta(2) polymorphisms are associated with childhood atopic asthma

BACKGROUND

Transforming growth factor (TGF)-beta plays an important role in the regulation of airway inflammation and remodelling in asthma. Recent studies suggest that TGF-beta(2) is a predominant isoform expressed in severe asthma and it is also associated with airway remodelling.

OBJECTIVE

To determine whether the polymorphisms in TGF-beta(2) are associated with childhood atopic bronchial asthma in a Japanese population.

METHODS

We identified a total of eight polymorphisms and characterized the linkage disequilibrium (LD) mapping of the gene. Three variants in the promoter and 3'UTR were genotyped, and we conducted an association study of TGF-beta(2) (childhood atopic asthma n=297, normal controls n=555). An association analysis of these variants and an expression and functional analysis were performed.

RESULTS

3'UTR 94862T >A was found to be significantly associated with the risk of childhood atopic asthma (P=0.00041). The -109-->ACAA ins promoter variant was also associated with the risk of childhood atopic asthma (P=0.0037). TGF-beta(2) expression was observed in both the normal and asthmatic bronchial epithelium, and both real-time PCR and an ELISA showed a significant basal and TGF-beta(1)-induced TGF-beta(2) expression in the bronchial epithelial cell line BEAS2B. Furthermore, the promoter variant -109-->ACAA ins increased the TGF-beta(2) promoter-reporter activity in BEAS2B cells.

CONCLUSIONS

Our data suggest that TGF-beta(2) may therefore be involved in the development of childhood atopic asthma by means of functional genetic polymorphism. The polymorphisms in TGF-beta(2) may become important information for asthma susceptibility in children.

Association between ADAM33 polymorphisms and adult asthma in the Japanese population

BACKGROUND

ADAM33, a member of the ADAM (a disintegrin and metalloprotease) family, is a putative asthma susceptibility gene recently identified by positional cloning. It is important to know whether the association exists in ethnically diverse populations.

OBJECTIVE

To assess whether genetic functional variants of ADAM33 relate to the susceptibility or some phenotypes in adult patients with bronchial asthma in a Japanese population.

METHODS

We searched for single nucleotide polymorphisms (SNPs) in ADAM33 by PCR-directed sequencing and identified 48 SNPs. Fourteen SNPs were selected with regard to the LD pattern, and genotyped by Taq-Man and PCR-RFLP methods. We conducted an association study of ADAM33 with 504 adult asthmatic patients and 651 controls, and haplotype analyses of related variants were performed.

RESULTS

Significant associations with asthma were found for the SNPs T1 (Met764Thr), T2 (Pro774Ser), S2 and V-3 (with the lowest P-value for T1, P = 0.0015; OR 0.63). We analysed the haplotype using these four polymorphisms, and found a positive association with haplotype CCTG (P = 0.0024).

CONCLUSION

Our results replicate associations reported recently in other ethnic populations, and suggest that the ADAM33 gene is involved in the development of asthma through genetic polymorphisms.

Association of the hCLCA1 gene with childhood and adult asthma

Asthma is caused by bronchial inflammation. This inflammation involves mucus overproduction and hypersecretion. Recently, a mouse model of asthma showed that gob-5 is involved in the pathogenesis of asthma. The gob-5 gene is involved in mucus secretion and its expression is upregulated upon antigen attack in sensitized mice. The observation suggests that human homologue of gob-5, hCLCA1 (human calcium-dependent chloride channel-1), may be involved in human disease. We screened for single-nucleotide polymorphisms (SNPs) in hCLCA1 in the Japanese population. We identified eight SNPs, and performed association studies using 384 child patients with asthma, 480 adult patients with asthma, and 672 controls. In haplotype analysis, we found a different haplotype distribution pattern between controls and childhood asthma (P<0.0001) and between controls and adult asthma (P=0.0031). We identified a high-risk haplotype (CATCAAGT haplotype; P=0.0014) and a low-risk haplotype (TGCCAAGT haplotype; P=0.00010) in cases of childhood asthma. In diplotype analysis, patients who had the CATCAAGT haplotype showed a higher risk for childhood asthma than those who did not (P=0.0011). Individuals who had the TGCCAAGT haplotype showed a lower risk for childhood asthma than those who did not (P<0.0001). Our data suggested that variation of the hCLCA1 gene affects patients' susceptibility for asthma.

Polymorphisms in ADAM33 are associated with allergic rhinitis due to Japanese cedar pollen

BACKGROUND

A recent report provided evidence that a disintegrin and metalloprotease domain 33 (ADAM33), a member of the ADAM family, is a novel susceptibility gene in asthma linked to bronchial hyper-responsiveness. However, there has been no investigation of the genetic role of ADAM33 variants in nasal allergy.

OBJECTIVE

The purpose of this study was to test the association between ADAM33 polymorphisms and Japanese cedar pollinosis (JCPsis), a most common seasonal allergic rhinitis in Japan.

METHODS

We conducted a case-control association study among a Japanese population, involving 95 adult individuals with JCPsis and 95 normal healthy controls. A total of 22 single-nucleotide polymorphisms (SNPs) in ADAM33 were genotyped using PCR-based molecular methods.

RESULTS

Six SNPs of ADAM33 gene, three in introns (7575G/A, 9073G/A and 12540C/T) and three in the coding region (10918G/C, 12433T/C and 12462C/T), were strongly associated with JCPsis (P = 0.0002-0.022 for absolute allele frequencies) and most of the SNPs were in linkage disequilibrium with each other. A higher frequency of the common alleles of these SNPs was noted for the subjects with JCPsis in comparison with healthy controls. We also identified a haplotype associated with the disease susceptibility. In addition, associations were found between ADAM33 polymorphisms and various cedar pollinosis phenotypes including clinical severity, eosinophil counts in nasal secretion and allergen-specific IgE levels in sera, but not total serum IgE levels.

CONCLUSION

These results indicate that polymorphisms in the ADAM33 gene are associated with susceptibility to allergic rhinitis due to Japanese cedar pollen, but the functional relationship still needs clarification.

A decade in HIV treatment: what is the state of the art and how did we arrive

Simultaneous developments in the understanding of human immunodeficiency virus (HIV) pathogenesis and the development of new sensitive assays to measure HIV RNA have contributed to new approaches in the management of HIV infection. This article reviews major scientific developments in the treatment of HIV disease and outlines current clinical guidelines for primary care providers. Because effective prescribing stems from understanding how medications achieve their clinical effect, the mechanisms of action of nucleoside reverse-transcriptor inhibitors (NRTIs), nonnucleoside reverse-transcriptor inhibitors (NNRTIs), and protease inhibitors (PIs) are covered. The evolution of therapy from NRTI monotherapy to PI- and/or NNRTI-containing combination therapy is traced.

Gene expression profiles of human small airway epithelial cells treated with low doses of 14- and 16-membered macrolides

Although long-term treatment with low doses of 14-membered macrolides is widely applied in management of patients with chronic inflammatory diseases, e.g., diffuse panbronchiolitis, chronic bronchitis, or chronic lung damage in newborns, the physiological mechanisms underlying the action of macrolides in these conditions are unclear. To clarify the pathological basis of these diseases and also to aid in the design of novel drugs to treat them, we chose to investigate the molecular target(s) of macrolides. Our experiments involved long-term culture of human small airway epithelial cells (hSAEC) in media containing 14-membered macrolides erythromycin (EM) or clarithromycin (CAM), or a 16-membered macrolide, josamycin (JM), which lacks clinical anti-inflammatory effects. We then analyzed gene expression profiles in the treated cells using a cDNA microarray consisting of 18,432 genes. We identified nine genes whose expression was significantly altered during 22 days of culture with EM, and seven that were altered by CAM in that time. Four of those genes revealed similar behavior in cells treated with either of the 14-membered macrolides, but not JM. The products of these four genes may be candidates for mediating the ability of 14-membered macrolides to suppress chronic inflammation.

Loci on murine chromosomes 7 and 13 that modify the phenotype of the NOA mouse, an animal model of atopic dermatitis

The NOA (Naruto Research Institute Otsuka Atrichia) mouse is an animal model of allergic or atopic dermatitis, a condition characterized by ulcerative skin lesions with accumulation of mast cells and increased serum IgE. We reported earlier that a major gene responsible for dermatitis in the NOA mouse lay in the middle of chromosome 14, and that the incidence of disease clearly differed according to parental strain; the mode of inheritance was autosomal recessive with incomplete penetrance. In the study reported here, we searched for genes that might modify the NOA phenotype, and we identified two candidate loci that appeared to contain genes capable of modifying atopic or allergic dermatitis, one in the middle of chromosome 7 (chi2 = 14.66; P = 0.00013 for D7Mit62) and the other in the telomeric region of chromosome 13 (chi2 = 15.352; P = 0.000089 for D13Mit147). These loci correspond to regions of synteny in human chromosomes where linkages to asthma, atopy, or related phenotypes, such as serum IgE levels, have been documented.

Amino-acid substitutions in the IKAP gene product significantly increase risk for bronchial asthma in children

The complex etiology of bronchial asthma (BA), one of the most common inflammatory diseases throughout the world, involves a combination of various genetic and environmental factors. A number of investigators have undertaken linkage and association studies to shed light on the genetic background of BA, but the genetic aspects of this disease are still poorly understood. In the course of a project to screen the entire human genome for single nucleotide polymorphisms (SNPs) that might represent useful markers for large-scale association analyses of common diseases and pharmacogenetic traits, we identified six SNPs within the gene encoding I-kappaB-associated protein (IKAP), a regulator of the NF-kappaB signal pathway. Most of these SNPs were in linkage disequilibrium with each other. We observed a strong allelic association between BA in childhood and two of the SNP sites, T3214A (Cys1072Ser) and C3473T (Pro1158Leu); P = 0.000004 for T3214A and P = 0.0009 for C3473T. T3214A was also associated with BA in adult patients (P = 0.000002), but C3473T was not (P = 0.056). To confirm the above results, we compared estimated frequencies of haplotypes of the six SNPs between BA patients and controls. We found a strong association between BA in childhood and a specific haplotype, TGAAAT, that involved two amino-acid substitutions (819T, 2295G, 2446A, 2490A, 3214A, and 3473T; P = 0.00004, odds ratio, 2.94; 95% confidence interval [CI], 2.48-3.4). On the other hand, haplotype TACGTC, which differed from the TGAAAT haplotype in the last five nucleotides, was inversely correlated with the BA phenotype (P = 0.002; odds ratio, 9.83; 95% CI, 8.35-11.31). These results indicated that specific variants of the IKAP gene, or a variant in linkage disequilibrium with the TGAAAT haplotype, might be associated with mechanisms responsible for early-onset BA.

Genomic structure of a novel human gene (XYLB) on chromosome 3p22-->p21.3 encoding a xylulokinase-like protein

We isolated a novel human cDNA of 1963 nucleotides that included an open reading frame encoding a protein of 528 amino acids. Homology analysis indicated that the predicted gene product, XYLB, bore 22% identity to the xylulokinase of Haemophilus influenzae that plays an important role in energy metabolism. The gene consists of 18 exons and spans about 28 kb of genomic DNA on chromosome 3p21.3.

Molecular cloning, mapping, and characterization of two novel human genes, ORCTL3 and ORCTL4, bearing homology to organic-cation transporters

Through a large-scale sequencing of genomic DNA at 3p22-->p21.3, we have isolated two human genes (ORCTL3 alias OCTL1 and ORCTL4 alias OCTL2) encoding novel members of the family of organic-cation transporter molecules. The predicted proteins revealed the highest similarities to recently- isolated organic-cation transporter proteins, rat OCT-1r, rat NLT and mouse NKT. The transcripts of both genes were expressed ubiquitously in various human tissues, but some tissue-specific transcripts were also observed in kidney, testis, or skeletal muscle. The two genes are clustered within a 52-kb region of genomic DNA and ORCTL4 lies about 27 kb telomeric to ORCTL3 in the genomic DNA sequence in a tail-to-head orientation.

Association studies of 33 single nucleotide polymorphisms (SNPs) in 29 candidate genes for bronchial asthma: positive association a T924C polymorphism in the thromboxane A2 receptor gene

Although intensive studies have attempted to elucidate the genetic background of bronchial asthma (BA), one of the most common of the chronic inflammatory diseases in human populations, genetic factors associated with its pathogenesis are still not well understood. We surveyed 29 possible candidate genes for this disease for single nucleotide polymorphisms (SNPs), the most frequent type of genetic variation, in genomic DNAs from Japanese BA patients. We identified 33 SNPs, only four of which had been reported previously, among 14 of those genes. We also performed association studies using 585 BA patients and 343 normal controls for these SNPs. Of the 33 SNPs tested, 32 revealed no positive association with BA, but a T924C polymorphism in the thromboxane A2 receptor gene showed significant association (chi2=4.71, P=0.030), especially with respect to adult patients (chi2=6.20, P=0.013). Our results suggest that variants of the TBXA2R gene or some nearby gene(s) may play an important role in the pathogenesis of adult BA.

Mapping of a gene responsible for dermatitis in NOA (Naruto Research Institute Otsuka Atrichia) mice, an animal model of allergic dermatitis

The NOA (Naruto Research Institute Otsuka Atrichia) mouse is an animal model of allergic or atopic dermatitis, a condition characterized by ulcerative skin lesions with accumulation of mast cells and increased serum IgE. These features of the murine disease closely resemble human atopy and atopic disorders. We performed linkage analysis in NOA back-cross progeny, as a step toward identifying and isolating a gene responsible for the NOA phenotype. We crossed NOA mice with five other murine strains (C57BL/6J, IQI, C3H/HeJ, DBA/2J, and BALB/cByJ) and then bred back-cross animals. Using microsatellite markers, we scanned the entire genomes of 559 N2 offspring from the five parental strains. Linkage analysis revealed a significant association between ulcerative skin lesions and markers on murine chromosome 14. Statistical analysis indicated that the critical region was assigned to the vicinity of D14Mit236 and D14Mit160.

Significantly elevated expression of PF4 (platelet factor 4) and eotaxin in the NOA mouse, a model for atopic dermatitis

The NOA (Naruto Research Institute Otsuka Atrichia) mouse, an animal model of allergic or atopic dermatitis, exhibits ulcerative skin lesions associated with accumulation of mast cells and eosinophils, a significantly increased level of serum IgE, and scratching behavior. To investigate genetic contributors to the pathological process of dermatitis in this murine model, we looked for genes that were expressed differently in spleens of NOA mice compared with controls, by means of a differential display method. We cloned and characterized one gene that revealed a significantly higher expression in the NOA mouse than in control strains. Its cDNA consisted of 570 nucleotides, including 315 nucleotides of open reading frame encoding 105 amino acids. The deduced amino acid sequence identified this gene as the murine homologue of rat and human platelet factor (PF) 4s (89% identity and 64% identity in 105 amino acids, respectively). PF4 is a heparin-binding protein that is released from alpha-granules of activated platelets and belongs to the family of chemokine molecules that contain a CXC motif. Our results suggested that increased expression of PF4 may play an important role in the etiology of allergic dermatitis.

[pncA gene mutations in clinical isolates of tubercle bacillus by polymerase chain reaction-direct sequencing method: in relationship to pyrazinamide resistance]

We screened clinical isolates of tubercle bacillus for mutations in the pncA gene, which encodes pyrazinamidase (PZase), by polymerase chain reaction (PCR)-direct sequencing method. Sixty-eight strains of tubercle bacillus were isolated from 32 patients with pulmonary tuberculosis. The patients were treated with antituberculous agents including pyrazinamide (PZA) for 2 months. Thirty-two of the 68 strains were isolated from sputum samples collected from the patients before treatment; 29 strains and 7 strains were collected after 1 month and 2 months of treatment, respectively. The pncA genes in these strains, were assessed for mutations by direct sequencing of PCR products using an automated sequencer. Similarly, we examined two clinical isolates (ka567 and minami22) of tubercle bacillus, determined to be deficient in PZase activity by the Wayne method. A PZA-sensitive strain (H37Rv, ATCC27294), and a PZA-resistant strain (H37Rv-PZA-R, ATCC35828) were used as negative and positive controls for mutations in the pncA gene, respectively. None of the 68 strains demonstrated any mutations in the pncA gene; however, the 2 PZase-deficient strains had missense mutations in the pncA gene resulting in an amino acid substitution from His82 to Arg in clone ka567, and from Ala171 to Val in clone minami22.

Molecular cloning of a candidate tumor suppressor gene, DLC1, from chromosome 3p21.3

The short arm of chromosome 3 is thought to contain multiple tumor suppressor genes, because one copy of this chromosomal arm frequently is missing in carcinomas that have arisen in a variety of tissues. We have isolated a novel gene encoding a 1755-amino acid polypeptide, through large-scale sequencing of genomic DNA at 3p21.3. Mutational analysis of this gene by reverse transcription-PCR revealed the lack of functional transcripts and an increase of nonfunctional RNA transcripts in a significant proportion (33%) of cancer cell lines and primary cancers (4 of 14 esophageal cancer cell lines, 2 of 2 renal cancer cell lines, 11 of 30 primary non-small cell lung cancers, and 3 of 10 primary squamous cell carcinomas of the esophagus). However, no alterations of the gene itself were detected in any of the cancers examined. Introduction of the cDNA significantly suppressed the growth of four different cancer cell lines, two of which produced no normal transcript on their own. No such effect occurred when antisense cDNA, cDNA corresponding to an aberrant transcript, or the vector DNA alone were transfected. These data suggest that aberrant transcription of this gene, designated DLC1 (deleted in lung cancer 1), may be involved in carcinogenesis of the lung, esophagus, and kidney.

Isolation and characterization of a novel serine threonine kinase gene on chromosome 3p22-21.3

Through large-scale DNA sequencing of a genomic region on chromosome 3p22-p21.3, we isolated a novel gene encoding a 527-amino-acid protein. Its 18 exons spanned a genomic region of about 90 kilobases, and the 4536-nucleotide cDNA contained an open reading frame of 1581 base pairs. The gene was expressed in all 16 human tissues examined by Northern blotting. The amino acid sequence of the predicted protein was 39% identical to that of human SOK1 (Ste20/oxidant stress response kinase-1), a molecule that is activated by oxidative stress. In view of its significant similarity to SOK1, we suspect that the novel gene, which we named OSR1, is a member of the SOK family of kinases in terms of function.

Characterization of a 1200-kb genomic segment of chromosome 3p22-p21.3

We previously determined the nucleotide sequence and characterized the 685-kb proximal half of CEPH YAC936c1, which corresponds to a portion of human chromosome 3p21.3. In the study reported here, we characterized the remaining 515-kb of this YAC clone corresponding to the telomeric half of its human insert. The newly sequenced region contained a total of ten genes including six reported previously: phospholipase C delta 1 (PLCD1), human activin receptor type IIB (hActR-IIB), organic cation transporter-like 1 (OCTL1), organic cation transporter-like 2 (OCTL2), oxidative stress response 1 (OSR1), and human xylulokinase-like protein (XYLB). The remaining four genes present in the telomeric region included two known genes, MyD88 and ACAA, and two novel genes. One (designated ENGL) of the novel sequences was found to encode an amino-acid sequence homologous to the family of DNA/RNA endonucleases, especially endonuclease G. The other gene F56 revealed no significant homology to any known genes. These results disclosed complete physical and transcriptional maps of the 1200-kb region of 3p present in YAC 936c1.

Genomic organization and mapping of the human activin receptor type IIB (hActR-IIB) gene

Activins, members of a family of proteins that includes transforming growth factor-beta (TGF-beta), are gonadal polypeptide hormones that stimulate secretion of follicle-stimulating hormone (FSH). During large-scale sequencing analysis of a 1.2-Mb fragment of human genomic DNA on 3p22-p21.3, we found the gene encoding activin receptor type IIB (hActR-IIB). Comparison of its reported cDNA sequence with this genomic sequence showed that the hActR-IIB gene consists of 11 exons and spans about 30 kb of genomic DNA.

Sequence analysis of a 685-kb genomic region on chromosome 3p22-p21.3 that is homozygously deleted in a lung carcinoma cell line

Frequent chromosomal aberrations and/or losses of heterozygosity involving the short arm of chromosome 3 in carcinomas of the lung, kidney and other tissues imply that multiple putative tumor suppressor genes may be present on this chromosomal arm. To search for one of these genes, we determined DNA sequences in the genomic region at 3p22-21.3 where we had previously detected a homozygous deletion in a lung cancer cell line. The DNA sequence results of an about 685-kb region indicated that the size of the homozygously deleted segment was 638,489 bp, in which we identified only four genes including the integrin alpha RLC and the trans-Golgi p230 genes, both reported previously. The predicted amino acid sequences of one of the two novel genes showed high homology to villin, a human cytoskeleton protein; those of the other gene, termed HYA22, revealed significant homology to YA22, a hypothetical protein predicted from DNA sequences of Schizosaccharomyces pombe. The computer programs HEXON or GRAIL were able to predict three-fourths of the exons; the smallest exon predicted by either program was 46 base pairs. Repetitive sequences contained in the genomic region included 151 copies of the Alu sequence (1 copy/every 4.5 kb), 19 copies of the L1 sequence (1 copy/every 36 kb), and 10 copies of the THE sequence.

Characterization of an 800 kb region at 3p22-p21.3 that was homozygously deleted in a lung cancer cell line

We have characterized a homozygous deletion at 3p22-p21.3 found in a lung cancer cell line ACC-LC-5. Three yeast artificial chromosomes (YACs) were isolated from a YAC library by hybridization with two cosmid probes (cCI3-1994 and cCI3-1999) representing loci that were homozygously deleted in five lung cancer cell lines. Cloning both ends of the region deleted in the cell line ACC-LC-5 revealed the deletion was an interstitial deletion within the chromosomal arm. A cosmid contig map covering the entire region corresponding to the homozygous deletion was constructed by means of Southern hybridizations. From these results and analyses by pulsed-field gel electrophoresis, this interstitial deletion on chromosome 3p22-21.3 in this cell line was estimated to be nearly 800 kb long and is smallest among five cell lines containing the homozygous deletion. The cosmid clones representing this region will contribute important new resources for isolating the putative tumor suppressor gene(s) on chromosome 3p22-21.3.

Aberrant upregulation of a novel integrin alpha subunit gene at 3p21.3 in small cell lung cancer

Our recent identification of homozygous deletions at 3p21.3 in lung cancer has provided further support for the presence of a tumor suppressor gene in this chromosomal region. As a part of our efforts for positional cloning of a tumor suppressor gene at 3p21.3, we have characterized a transcriptional unit within this region using genomic fragments with interspecies conservation. The identified gene was found to encode a novel integrin alpha subunit, termed alpha RLC, which is closely related to alpha 4 in structure but clearly different from alpha 4 in its expression pattern in the physiological and pathological setting of the lung. This finding and the exact localization of the gene suggest that it is a good candidate for a tumor suppressor gene in lung cancer, but our extensive search covering one third of the gene did not reveal any somatic mutations within the coding region. Interestingly, however, alpha RLC was abundantly expressed in fetal lung and lung cancers, particularly small cell lung cancers (SCLC). Its aberrant upregulation in the SCLC samples, both cell lines and primary tumors, which might have been caused by a yet unidentified mutations or by deletions of other gene, and its homology to alpha 4, which is thought to play a role in metastasis, suggest that altered alpha RLC expression may contribute to the acquisition of malignant phenotypes of this type of lung cancer.

Ordering of human chromosome 3p markers by radiation hybrid mapping

To construct a panel of radiation hybrids (RHs) for human chromosome 3p mapping, mouse microcell hybrid cells, A9(neo3/t)-5, containing a single copy of human chromosome 3p with pSV2neo plasmid DNA integrated at 3p21-p22 were irradiated and fused to mouse A9 cells. A panel of 96 RHs that retain several sizes and portions of human chromosome 3p segments was used to map 25 DNA markers for chromosome 3p. Eight of them, H28, H29, H32, H33, H35, H38, H48, and H64, were cloned from Alu-primed PCR products using A9(neo3/t)-5 cell DNA as a template. The most likely order of the 24 markers, except for H28, based on the statistical ordering method proposed by Falk, was cen-D3S4-D3S3-D3S30-H29-D3S13-D3S2-+ ++H48-D3F15S2-D3S32-D3S23-CCK-H35-H33- D3S11-D3S12-RARB-THRB(ERBA2-pBH302)- H64-H38-RAF1-D3S18-H32-D3S22-pter. The order and location of these markers were in good agreement with those previously determined by other mapping methods, suggesting that a panel of these 96 RHs is a valuable source for a rapid mapping of human chromosome 3p markers.

Isolation of diacylglyceryl-2-aminoethylphosphonate from bovine liver

Diacylglyceryl-2-aminoethylphosphonate was isolated from bovine liver by a combination of silicic acid column and silica gel thin-layer chromatographic techniques, and was identified from the results of elementary analysis, the infrared spectrum, chemical properties, and chromatographic behavior. This is the first isolation of a lipid-bound form of ciliatine in mammals.

A new bile acid conjugate, ciliatocholic acid, from bovine gall bladder bile

This study was carried out to investigate the occurrence of ciliatocholic acid in bovine gall bladder bile. Ciliatocholic acid was synthesized according to the method described by Bergstrôm and Norman for the synthesis of taurocholic acid. Elemental analysis, melting point, and the infrared spectrum of this substance were determined. An isolation procedure for ciliatocholic acid was established by stepwise elution with an HCl-ethanol solvent system using a Dowex-1 anion exchange resin column chromatographic technique. Ciliatocholic acid amounting to 158 mug (as ciliatine) per 100 ml of gall bladder bile was found in the fraction eluted with 0.01 N HCl in 50% ethanol. This coumpound was purified by preparative thin-layer chromatography and confirmed to be ciliatocholic acid from the hydrolytic stability, phosphorus determination, and chromatographic behavior. Thus, bovine gall bladder bile contains a small amount of ciliatocholic acid.

[2-Amino-ethylphosphonic acid transport in Pseudomonas aeruginosa]

2-Aminoethylphosphonic acid (ciliatine) can be used as a source of phosphorus or nitrogen by Pseudomonas aeruginosa. The conditions of its uptake have been investigated. The transport is inducible by ciliatine itself or by its homologue, 3-aminopropylphosphonate, but neither by other phosphonic compounds nor by carboxylic or sulfonic related derivatives. The induction was not suppressed by inorganic phosphate. The transport appears to be an active process, pH and temperature dependent: it requires energy and is dependent on new protein synthesis. The uptake follows Michaelis kinetics. The substrate specificity involved in ciliatine uptake favours the existence of two different transport systems: the first one, inducible by ciliatine, was very sensitive towards different aminophosphonic acids and was competitively inhibited by inorganic phosphate and methylphosphonate; the second transport system, inducible by 3-amino-propylphosphonate, appeared less sensitive towards alpha-aminophosphonic acids and was non competitively inhibited by phosphate and methylphosphonate. No interactions were observed with related aminocarboxylic acids or with taurine. Some molecular structural requirements for the binding of an effector on both permeases are discussed. The regulatory function of inorganic phosphate, the chief breakdown product of ciliatine, is also emphasized.

In vivo incorporation of cytidine-monophosphate-ciliatine into rat liver lipids

1. In vivo this investigation was carried out in order to compare the incorporation into rat lipids of free [1,2-minus 14C]-ciliatine and CMP-[1,2-minus 14C]-ciliatine which is the precursor in phosphonolipid biosynthesis. 2. The incorporation of the radioactivity from CMP-[1,2-minus 14C]-ciliatine took place more rapidly than that from free [1,2-minus 14C]-ciliatine in both liver and kidney. The amount of radioactivity from the CMP-[1,2-minus 14C]-ciliatine incorporated into total liver lipids was about 5 times higher than that incorporated into total liver lipids of rat two hrs after injecting free-[1,2-minus 14C]-ciliatine. 3. The amount of [1,2-minus 14C]-ciliatine incorporated into total liver lipids was 15 and 21 times higher than that incorporated into total kidney lipids of rat two and four hrs after injecting free [1,2-minus 14C]-ciliatine. 4. If the main pathway for the phosphonolipid biosynthesis is via CMP-ciliatine, the rate of phosphonolipid formation from CMP-ciliatine must therefore be higher than that from free-ciliatine. The results obtained here indicate therefore that the main pathway for phosphonolipid biosynthesis is a pathway involving CMP-ciliatine. 5. An unknow compound was detected in the water soluble fraction of the acid hydrolyzate of liver phosphonolipids. This material migrated with the N-trimethyl-derivative of ciliatine on the thin-layer chromatogram. The result shows that there is therefore a possibility of methylation of exogenous ciliatine to the phosphonate analogue of choline in the mammalian body.

The stimulatory effect of paracetamol and its derivatives on growth and the rat tibia test

Paracetamol (N-acetyl-p-aminophenol) given i.p. in doses of 3–20 mg./kg./24 hr. stimulated epiphysial cartilage growth in intact female rats. This stimulation was not a result of increased food intake. It may be mediated by the adrenal gland, since paracetamol stimulated cartilage growth in thyroidectomized but not in adrenalectomized rats. Of 12 paracetamol derivatives tested, most did not affect cartilage growth or were less active than paracetamol. A structure-activity relationship could be established. Our results suggest that the mechanism of the stimulatory effect of paracetamol on growth may be twofold: the drug probably stimulates somatotrophin (STH) production and/or potentiates STH action on growth.