Lack of association of RAD51 genetic variations with hepatitis B virus clearance and occurrence of hepatocellular carcinoma in a Korean population

The RecA homolog, E. coli (S. cerevisiae) (RAD51) may modulate hepatitis B virus (HBV) infection by maintaining genome integrity and mediating homologous DNA repairs. In this study, 16 sequence variations were detected by resequencing all exons, the exon-intron boundary, and promoter regions of the human RAD51 gene in DNA samples of 24 unrelated individuals. To investigate the association of common variations in the RAD51 locus with HBV infection and hepatocellular carcinoma (HCC) occurrence, six common polymorphisms were genotyped in a total of 1,103 Korean HBV cohort, composed of 433 spontaneously recovered patients as controls and 670 chronic carriers of HBV, who were stratified further into 327 cirrhosis/chronic hepatitis patients and 343 patients with HCC infected with HBV. Logistic analyses revealed no significant association of RAD51 polymorphisms and haplotypes with HBV clearance and HCC occurrence (P > 0.05). Furthermore, with age of infection as an important factor in disease progression to HCC, results from the Cox proportional hazards analysis showed no significant associations between any of the tested RAD51 variants and the age of onset of HCC (P > 0.05), suggesting that genetic polymorphisms of RAD51 may not play an important role in clearance of HBV and disease progression to HCC. Although studies in other populations are needed to confirm these findings, this preliminary data may contribute to the current knowledge on the pathogenesis of hepatitis.

Possible role of EMID2 on nasal polyps pathogenesis in Korean asthma patients

BACKGROUND

Since subepithelial fibrosis and protruded extracellular matrix are among the histological characteristics of polyps, the emilin/multimerin domain-containing protein 2 (EMID2) gene is speculated to be involved in the presence of nasal polyps in asthma and aspirin-hypersensitive patients.

METHODS

To investigate the association between EMID2 and nasal polyposis, 49 single-nucleotide polymorphisms (SNPs) were genotyped in 467 asthmatics of Korean ancestry who were stratified further into 114 aspirin exacerbated respiratory disease (AERD) and 353 aspirin-tolerant asthma (ATA) subgroups. From pairwise comparison of the genotyped polymorphisms, 14 major haplotypes (frequency > 0.05) were inferred and selected for association analysis. Differences in the frequency distribution of EMID2 variations between polyp-positive cases and polyp-negative controls were determined using logistic analyses.

RESULTS

Initially, 13 EMID2 variants were significantly associated with the presence of nasal polyps in the overall asthma group (P = 0.0008-0.05, OR = 0.54-1.32 using various modes of genetic inheritance). Although association signals from 12 variants disappeared after multiple testing corrections, the relationship between EMID2_BL1_ht2 and nasal polyposis remained significant via a codominant mechanism (P corr = 0.03). On the other hand, the nominal associations observed between the genetic variants tested for the presence of nasal polyps in AERD (P = 0.003-0.05, OR = 0.25-1.82) and ATA (P = 0.01-0.04, OR = 0.46-10.96) subgroups disappeared after multiple comparisons, suggesting lack of associations.

CONCLUSIONS

These preliminary findings suggest that EMID2_BL1_ht2 may be a susceptibility marker of inflammation of the nasal passages among Korean asthma patients.

Association of variations in TPH1 and HTR2B with gestational weight gain and measures of obesity

Serotonin is involved in appetite regulation and energy homeostasis. Recently, it has been reported that 5-hydroxytryptamine receptor 2B (Htr2b) and tryptophan hydroxylase 1 (Tph1) play major role in β-cell proliferation in mouse during pregnancy. We investigated the genetic association of HTR2B and TPH1 with risk of gestational diabetes mellitus (GDM) and measures of obesity, in 869 Korean GDM women and carefully selected 632 nondiabetic control subjects. Six single-nucleotide polymorphisms (SNPs) in HTR2B and ten SNPs in TPH1 were selected for genotyping according to their tagging status. Genetic variants in HTR2B and TPH1 were not associated with the risk of GDM. In GDM women, SNPs of TPH1 were significantly associated with weight gain during pregnancy. In nondiabetic controls, SNPs of TPH1 were associated with waist circumference and BMI. We also found that a variant of TPH1 (rs623580) was associated with BMI in a genome-wide association study comprised of 8,842 subjects. Although genetic variants in HTR2B and TPH1 were not associated with risk of GDM, we found significant association of these variants with measures of obesity. However, further replication studies in a different population are required to confirm our findings.

A possible association between ZNRD1 and aspirin-induced airway bronchoconstriction in a Korean population

BACKGROUND

The etiology of aspirin-exacerbated respiratory disease (AERD) has been attributed to the combination of environmental and genetic risk factors. Although widely investigated in various diseases associated with immune dysfunction, the human zinc ribbon domain containing 1 (ZNRD1) gene is thought to play a role in the pathogenesis of AERD by altering the mechanisms involved in disease development.

METHODS

We selected 6 single-nucleotide polymorphisms (SNPs) for genotyping from the International HapMap database in order to analyze the association between polymorphisms in ZNRD1 and AERD in a Korean asthma cohort. Genotyping was carried out using the TaqMan assay, and differences in genotype frequency distributions were analyzed using logistic regression models.

RESULTS

Nominal associations were found between ZNRD1 rs1150740 and risk ofAERD via codominant and dominant genetic inheritance (P=.03; odds ratio, 1.14 [1.14-10.16]). The same polymorphism was found to be significantly associated with a decrease in forced expiratory volume in the first second of expiration, an important diagnostic marker of AERD, even after multiple testing corrections (P=.006, P(corr)=.03 in codominant and dominant models).

CONCLUSIONS

These preliminary findings suggest a possible relationship between ZNRD1 and aspirin-induced respiratory dysfunctions in a Korean population and provide essential information on the etiology of AERD.

First Report of Leaf Spot Caused by Ascochyta marginata on Aralia elata in Korea

Aralia elata (Miq.) Seem., known as Japanese angelica tree, is a deciduous shrub belonging to the Araliaceae, which is native to East Asia. The young shoots have long been used in various dishes in East Asia. Commercial cultivation of this shrub, especially in polytunnels, is expanding in Korea. Several diseases including Sclerotinia rot have been known to be present on this plant (1,2). In early September 2007, leaf spot symptoms were first observed on several trees in Hongcheon, Korea. Microscopic observations revealed that the leaf spots were associated with an Ascochyta sp. Further surveys of the Ascochyta leaf spot showed the occurrence of the disease in approximately 5 to 10% of the trees in the 3 ha of commercial fields surveyed in Chuncheon, Gapyeong, Inje, and Jinju, Korea. Initial symptoms on leaves were circular to irregular, brown to dark brown, becoming zonate, and finally fading to grayish brown in the center with a yellow halo. Representative samples were deposited in the herbarium of Korea University. Conidiomata on leaf lesions were pycnidial, amphigenous, but mostly epiphyllous, immersed or semi-immersed in host tissue, light brown to olive brown, and 60 to 200 μm in diameter. Ostioles were papillate, 20 to 35 μm wide, and surrounded by a ring of darker cells. Conidia were hyaline, smooth, cylindrical to clavate, straight to mildly curved, slightly constricted at the septa, medianly one-septate, sometimes aseptate, 8 to 16 × 2.5 to 3.5 μm, and contained small oil drops. These morphological characteristics were consistent with the previous reports of Ascochyta marginata J.J. Davis (3,4). A monoconidial isolate was cultured on potato dextrose agar (PDA) plates and accessioned in the Korea Agricultural Culture Collection (Accession KACC43082). The conidia were readily formed on PDA. Inoculum for the pathogenicity tests was prepared by harvesting conidia from 30-day-old cultures of KACC43082 and a conidial suspension (approximately 2 × 10⁶ conidia/ml) was sprayed onto leaves of three healthy seedlings. Three noninoculated seedlings served as controls. Inoculated and noninoculated plants were covered with plastic bags for 48 h in a glasshouse. After 7 days, typical leaf spot symptoms started to develop on the leaves of the inoculated plants. The fungus, A. marginata, was reisolated from those lesions, confirming Koch's postulates. No symptoms were observed on control plants. Previously, the disease was reported in Japan (4) and China (3). To our knowledge, this is the first report of A. marginata on Japanese angelica trees in Korea. According to our field observations in Korea, the Ascochyta leaf spot mostly occurred on plants growing in a humid environment, especially during the rainy season. The seedlings as well as the trees growing in sunny, well-ventilated plots were nearly free from this disease. Therefore, the growing conditions seemed to be the most important factor for the development and severity of the disease. References: (1) C. K. Lee et al. Plant Pathol. J. 26:426, 2010. (2) S. H. Lee et al. Diseases of Japanese Angelica Tree and Their Control. Research Report 08-10. Korea Forest Research Institute. Seoul, Korea, 2008. (3) J. Sun et al. Acta Mycol. Sin. 14:107, 1995. (4) M. Yoshikawa and T. Yokoyama. Mycoscience 36:67, 1995.

Genetic variations in KIFC1 and the risk of aspirin exacerbated respiratory disease in a Korean population: an association analysis

Modest effects of genes in various pathways are significant in the etiology of complex human diseases, including aspirin exacerbated respiratory disease (AERD). By functioning as a relevant component of respiratory processes, the human kinesin family member C1 (KIFC1) is hypothesized to play a role in AERD pathogenesis. A case-control analysis was carried out by comparing the genotype distribution of six KIFC1 single-nucleotide polymorphisms between 93 AERD cases and 96 aspirin-tolerant asthma controls in a Korean population. After controlling for confounds, logistic and regression models via various modes of genetic inheritance facilitated the association analysis. Initial results revealed significant association at 0.05 level of significance between several KIFC1 variations and AERD (P = 0.01-0.05, OR = 1.81-1.90) as well as fall rate of forced expiratory volume in the 1st second, an important diagnostic marker of airways constriction (P = 0.04-0.05). However, the signals were not deemed significant after multiple testing corrections (P (corr) > 0.05). Although the results do not support a major role of KIFC1 in AERD pathogenesis in a Korean asthma cohort, further replication and validation studies are required to clarify the current findings.

Effect of diffuse panbronchiolitis critical region 1 polymorphisms on the risk of aspirin-exacerbated respiratory disease in Korean asthmatics

BACKGROUND

The functional role of the human diffuse panbronchiolitis critical region 1 (DPCR1) gene, located in the major histocompatibility complex class I, has not been widely investigated. However, this gene is a well known genetic marker for diffuse panbronchiolitis, a disease affecting human respiratory bronchioles. In this study we explored the association between polymorphisms in DPCR1 and aspirin-exacerbated respiratory disease (AERD), an asthma phenotype.

METHODS

Genotyping of 6 polymorphisms was carried out in a total of 189 Korean asthmatic patients stratified into 93 AERD cases and 96 aspirin tolerant asthma controls. Subjects who exhibited significant decrease of FEV(1) by aspirin provocation were identified as AERD subjects. Logistic and regression analyses were performed to investigate the association between DPCR1 polymorphisms and the risk of AERD as well as FEV(1) decline.

RESULTS

Initial analysis revealed significant association of rs2517449 with AERD, with a P value of .03 via a recessive model; however, the association signal disappeared after multiple testing corrections. In addition, rs2517449 and rs2240804 also showed association signals with decline of FEV(1) after aspirin provocation (P = .007 and .03, respectively, in a recessive model). After testing for multiple comparisons, only the association signal from rs2517449 was retained (P(corr) = .04), while other polymorphisms showed no associations with the risk of AERD and FEV(1) decline.

CONCLUSIONS

Our results show that polymorphisms in DPCR1 are not associated with the risk of AERD.

First Report of Powdery Mildew Caused by Golovinomyces biocellatus on Monarda didyma in Korea

Bergamot (Monarda didyma L.), which is native to eastern North America, is an aromatic herb in the family Lamiaceae. It is widely planted in gardens and parks for ornamental purposes and also grown indoors as a fragrant houseplant in Korea. In October 2007, several dozen bergamots planted outdoors in Bonghwa, Korea were found to be heavily infected with a powdery mildew. Symptoms first appeared as thin, white colonies, which subsequently developed into abundant growth on both sides of the leaves. Severe infections often caused leaf distortions and premature senescence. The same symptoms have also been found in bergamot plots in Osan, Suwon, Incheon, and Seoul from 2007 to 2011. Voucher specimens were deposited at Korea University, Seoul, Korea. Hyphae were septate, branched, and 4 to 8 μm wide. Appressoria on the mycelium were nipple shaped. Conidiophores arose from the lateral part of the hyphae, measured 100 to 180 × 10 to 12 μm, were simple, and produced two to four immature conidia in chains, followed by two to three cells. Conidia were hyaline, ellipsoid to barrel shaped, measured 28 to 40 × 16 to 20 μm (length/width ratio = 1.4 to 2.2), lacked distinct fibrosin bodies, and produced germ tubes on the subterminal position, with reticulate wrinkling of the outer walls. No chasmothecia were observed. The structures described above were typical of the Oidium subgenus Reticuloidium anamorph of the genus Golovinomyces, and the fungus measurements were compatible with those of Golovinomyces biocellatus (Ehrenb.) V.P. Heluta as described previously (1,4). The only other powdery mildew known on Monarda spp. is Neoerysiphe galeopsidis (1), which is clearly distinguished by its lobed hyphal appressoria and fine striations on conidial surfaces. To confirm the tentative identification based on morphological characteristics, internal transcribed spacer (ITS) rDNA sequences from two representative isolates (KUS-F23070 and F23117) were obtained using primers ITS5 and P3 as described by Takamatsu et al. (3). The resulting sequences of 523 bp were deposited in GenBank (Accession Nos. JN228358 and JN228359). A GenBank BLAST search produced an exact match for the sequences of G. biocellatus on several plants belonging to the Lamiaceae, with a 100% sequence similarity. Pathogenicity was confirmed through inoculation by gently pressing diseased leaves onto leaves of five healthy potted bergamot plants. Five noninoculated plants served as controls. Plants were maintained in a greenhouse at 25 ± 2°C. Inoculated plants developed signs and symptoms after 6 days, whereas the control plants remained healthy. The fungus present on the inoculated plants was morphologically identical to that originally observed on diseased plants. The powdery mildew infections of bergamot plants associated with G. biocellatus have been known in Europe (2) and Japan (4). The current work confirmed the occurrence of G. biocellatus infecting M. didyma in Korea. References: (1) U. Braun. Beih. Nova Hedw. 89:1, 1987. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Mycology and Microbiology Laboratory. ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , July 12, 2011, (3) S. Takamatsu et al. Mycol. Res. 113:117, 2009. (4) S. Tanda. J. Agric. Sci. Tokyo Agric. Univ. 47:274, 1997.

First Report of Powdery Mildew Caused by Golovinomyces ambrosiae on Ambrosia trifida in Korea

Ambrosia trifida L., commonly known as giant ragweed, is native to North America and was introduced to Korea in the 1970s (3). It is now widely naturalized, and since 1999, has been designated as one of 11 'harmful nonindigenous plants' by the Korean Ministry of Environment because of its adverse effects on native plants. Various strategies to eradicate this noxious weed have been tried without any success (3). In September 2009, powdery mildew infections of giant ragweed were found for the first time in Dongducheon, Korea, and specimens were isolated and deposited in the Korea University Herbarium (KUS-F24683). White mycelial and conidial growth was present mostly on adaxial leaf surfaces with sparse growth on abaxial leaf sides. Severely infected leaves were malformed. Slight purplish discoloration occurred on the leaves contiguous with colony growth. Mycelial colonies were conspicuous, amphigenous, and epiphytic with indistinct to nipple-shaped appressoria. Conidiophores were 80 to 180 μm long and produced two to five immature conidia in chains. Conidia were ellipsoid or doliiform, 28 to 38 × 16 to 24 μm, and lacked distinct fibrosin bodies. Chasmothecia were amphigenous, scattered or partly clustered, dark brown, spherical, 95 to 130 μm in diameter, and contained 6 to 16 asci. Appendages were mycelioid, numbering 10 to 24 per chasmothecium, 0.5 to 2.5 times as long as the chasmothecial diameter, 1 to 4 septate, and were brown at the base and becoming paler toward the tip. Asci were short stalked, 50 to 75 × 32 to 42 μm and contained two spores. Ascospores were ellipsoid-ovoid with a dimension of 22 to 30 × 15 to 18 μm. On the basis of these morphological characteristics, this fungus was identified as Golovinomyces ambrosiae (Schwein.) U. Braun & R.T.A. Cook (= G. cichoracearum var. latisporus (U. Braun) U. Braun) (1). To confirm the identification, the complete internal transcribed spacer (ITS) region of rDNA from KUS-F24683 was amplified with the primers ITS5 and P3 and sequenced (4). The resulting sequence of 508 bp was deposited in GenBank (Accession No. JF907589) and was identical to the ITS sequences of G. ambropsiae on A. artemisiifolia var. elatior from Japan (AB077631) and Korea (JF919680) as well as on A. trifida from the United States (AF011292). Therefore, the sequence analysis verified the pathogen to be G. ambrosiae. To our knowledge, this is the first record of powdery mildew infections on giant ragweed outside of North America (2). Although the disease incidence is still low, the disease could be a limiting factor to suppress the expansion of this noxious weed in Korea. References: (1) U. Braun and R. T. A. Cook. Mycol. Res. 113:616, 2009. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , May 5, 2011. (3) S. M. Oh et al. Impacts of Invasive Alien Weeds and Control Strategies of Noxious Weeds in Korea. National Institute of Agricultural Science and Technology, Suwon, Korea, 2007. (4) S. Takamatsu et al. Mycol. Res. 111:117, 2009.

First Report of Powdery Mildew Caused by Golovinomyces cichoracearum on Zinnia elegans in Turkey

Powdery mildews are one of the most common diseases of plants growing in many nurseries, city parks, and home gardens in Turkey. Common zinnia (Zinnia elegans Jacq.) is widely cultivated in Turkey for ornamental purposes. In September 2010, zinnia plants grown in Hatay, Turkey were found to be heavily infected with a powdery mildew. Pathogen mycelia and sporulation were observed as circular to irregular, white patches on both sides of the leaves and on stems and flower petals. As the disease progressed, infected leaves turned yellow and died. Hyphae were straight to wavy and 4 to 7 μm wide. Conidiophores arose from the upper part of the hyphae, measured 120 to 190 × 10 to 13 μm, were simple, and produced two to six immature conidia in chains with a sinuate edge, followed by two to three straight cells. Conidia were hyaline, ellipsoid to barrel-shaped, measured 25 to 42 × 14 to 22 μm (length/width ratio = 1.3 to 2.5), lacked distinct fibrosin bodies, and produced germ tubes on the perihilar position, with reticulate wrinkling of the outer walls. No chasmothecia were observed. The structures described above were typical of the Oidium subgenus Reticuloidium, anamorph of the genus Golovinomyces, and the fungus measurements were compatible with those of G. cichoracearum (DC.) V.P. Heluta described previously (1,3). To confirm the tentative identification based on morphological characteristics, molecular analysis of internal transcribed spacer (ITS) rDNA sequences from a representative material (MKU-ZK311077, duplicate KUS-F25655) was conducted. The complete ITS regions of rDNA were amplified using primers ITS5 and P3 as described by S. Takamatsu (4) and sequenced. The resulting sequence of 508 bp from MKU-ZK311077 was deposited in GenBank (Accession No. JN051414). A GenBank BLAST search using the current data revealed an exact match for several sequences of G. cichoracearum, including Australian and Korean powdery mildews on zinnia plants, with a 100% sequence similarity. Pathogenicity was confirmed through inoculation by gently pressing diseased leaves onto leaves of three healthy, potted zinnia plants. Three noninoculated plants served as controls. Plants were maintained in a greenhouse at 25°C. Inoculated plants developed signs and symptoms after 10 days, whereas the control plants remained healthy. The fungus present on the inoculated plants was morphologically identical to that originally observed on diseased plants. The powdery mildew infections of Z. elegans associated with G. cichoracearum are nearly circumglobal, including Europe, North America, South America, Africa, Oceania, and Western Asian localities like India, Nepal, Jordan, and Israel (1,2). The current work confirmed the occurrence of G. cichoracearum infecting Z. elegans in Turkey using detailed morphological and molecular analysis. References: (1) U. Braun. Beih. Nova Hedw. 89:1, 1987. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , May 24, 2011. (3) M. J. Park et al. Plant Pathol. J. 27:85, 2011. (4) S. Takamatsu et al. Mycol. Res. 113:117, 2009.

Lack of association of the RTN4R genetic variations with risk of schizophrenia and SPEM abnormality in a Korean population

This study examined the association of the reticulon 4 receptor (RTN4R) gene with schizophrenia and smooth pursuit eye movement (SPEM) abnormality in a Korean population. Although we failed to provide convincing evidence that RTN4R is associated with schizophrenia development and SPEM impairment, our findings may be useful for further genetic studies.

TGFBR3 polymorphisms and its haplotypes associated with chronic hepatitis B virus infection and age of hepatocellular carcinoma occurrence

OBJECTIVE

Hepatocellular carcinoma (HCC) is one of the most common cancers and is mainly caused by viral infections including hepatitis B virus (HBV). Recently, the decreased expression level of the transforming growth factor, beta receptor III (TGFBR3) gene, has been implicated in HCC and other human cancers. This study investigated whether TGFBR3 polymorphisms might be associated with HBV clearance and HCC occurrence.

METHODS

This study identified 27 single nucleotide polymorphisms (SNPs) in the exon, promoter, and exon-intron boundary regions of TGFBR3 by resequencing in 24 individuals. Then, 9 SNPs in the promoter and exons of the gene were genotyped from 1,065 Koreans composed of 637 chronic carriers (CC) and 428 spontaneously recovered (SR) subjects.

RESULTS

Two SNPs, rs1805113 (Phe676Phe) in exon 13 and rs1805117 in 3'-UTR (p = 0.009 and p = 0.008, respectively) were significantly associated with HBV clearance. In addition, Cox relative hazards analyses revealed that haplotype BL2_ht2 showed a significant association with the age of HCC occurrence among chronic HBV patients (relative hazard = 1.38; p = 0.007).

CONCLUSION

Our findings suggest that TGFBR3 polymorphisms and its haplotypes might be associated with HBV clearance and age of HCC occurrence.

Association analysis of thromboxane A synthase 1 gene polymorphisms with aspirin intolerance in asthmatic patients

AIM

Thromboxane A synthase (TBXAS1) converts prostaglandin H to thromboxane A, a potent constrictor of smooth respiratory muscle. Thus, functional alterations of the TBXAS1 gene may contribute to aspirin-intolerant asthma (AIA).

MATERIALS & METHODS

We investigated the relationship between SNPs in the TBXAS1 gene and AIA. Asthmatics (n = 470) were categorized into AIA (20% or greater decreases in forced expiratory volume in 1 s [FEV(1)], or 15% to 19% decreases in FEV(1) with naso-ocular or cutaneous reactions) and aspirin-tolerant asthma (ATA). A total of 101 SNPs were genotyped. mRNA expression of the TBXAS1 gene by peripheral blood mononuclear cells and plasma thromboxane B2 (TXB2) concentrations were measured by reverse transcriptase (RT)-PCR and ELISA.

RESULTS

Logistic regression analysis showed that the rare allele frequency of rs6962291 in intron 9 was significantly lower in the AIA group (n = 115) than in the ATA group (n = 270) (p(corr) = 0.04). The linear regression analysis revealed a strong association of rs6962291 with the aspirin challenge-induced FEV(1) fall (p = 0.003). RT-PCR revealed an exon-12-deleted splice variant. We measured TBXAS1 mRNA levels in peripheral blood mononuclear cells. The mRNA levels of the full-length wild-type and splice variant were significantly higher in the TT homozygotes than in the AA homozygotes of rs6962291 (1.00 ± 0.18 vs 0.57 ± 0.03 and 1.00 ± 0.18 vs 0.21 ± 0.05, p = 0.047 and 0.001, respectively). The plasma TXB2 level was significantly lower in rs6962291 AA carriers than in rs6962291 TT (p = 0.016) carriers.

CONCLUSION

The rare allele of rs6962291 may play a protective role against aspirin hypersensitivity via a lower catalytic activity of the TBXAS1 gene, attributed to the increase of a nonfunctioning isoform of TBXAS1.

Lack of association between CD58 genetic variations and aspirin-exacerbated respiratory disease in a Korean population

BACKGROUND

Exacerbation of asthma symptoms due to aspirin ingestion may lead to life-threatening lung failure. The adhesion molecule CD58 gene may play a crucial role in aspirin-exacerbated respiratory disease (AERD) pathogenesis by mediating the biological functions of asthma-inducing mechanisms including T helper cells, proinflammatory cytokines, and natural killer T cells.

OBJECTIVE

This study aimed to investigate the association of CD58 variations with aspirin-induced bronchospasm in Korean asthma patients.

METHODS

Seven single-nucleotide polymorphisms were selected for genotyping based on previously reported polymorphisms in the International HapMap database. Genotyping was carried out using TaqMan assay and 2 major haplotypes were obtained in 163 AERD cases and 429 aspirin-tolerant asthma controls. Frequency distributions of CD58 variations were analyzed using logistic and regression models.

RESULTS

Results showed that none of the analyzed CD58 single-nucleotide polymorphisms and haplotypes was significantly associated with AERD development and fall rate of FEV(1) by aspirin provocation, an important diagnostic marker of aspirin hypersensitivity.

CONCLUSIONS

This preliminary study suggests that CD58 does not affect AERD susceptibility in a Korean population, and may provide a new direction for future disease etiology.

Genetic effect of single-nucleotide polymorphisms in the PPARGC1B gene on airway hyperreactivity in asthmatic patients

BACKGROUND

Peroxisome proliferator-activated receptor gamma coactivator 1 beta (PPARGC1B) is a co-activator for intracellular receptors such as the estrogen receptor, PPAR, and glucocorticoid receptor, which are involved in asthma development.

OBJECTIVES

Genetic association of single-nucleotide polymorphisms (SNPs) in the PPARGC1B gene with the risk of asthma and airway hyperreactivity (AHR) was investigated, as well as the functional effects of these SNPs on PPARGC1B gene and protein expression.

METHODS

Direct sequencing of DNA from 24 Korean was performed to identify PPARGC1B SNPs. Genotyping was done in 264 controls and 949 asthmatics using single-base extension methods. PPARGC1B mRNA levels were measured using real-time PCR methodology. Luciferase and electrophoretic mobility shift assays (EMSA) were performed to functionally analyse PPARGC1B SNPs on promoter.

RESULTS

Eighteen SNPs and one insertion/deletion polymorphism were identified, and seven SNPs were genotyped. No significant difference existed in the distribution of SNPs and haplotypes between the asthmatics and controls. However, the allele frequency of -427C>T and +102525G>A;R265Q showed a significant association with log-transformed PC(20) methacholine values in the asthmatics (P=0.005-0.0004). Real-time PCR demonstrated higher PPARGC1B mRNA levels in asthmatics having -427CC allele than in those having -427TT or CT alleles (P=0.048). The ratio of the mRNA expression for each PPARGC1B exon4-mRNA compared with the wild type was similar in peripheral blood mononuclear cells carrying the +102525G>A allele. Luciferase reporter assays revealed that -427C allele caused higher promoter activity than -427T allele. EMSA demonstrated that -427C allele exhibited stronger binding activity to a nuclear protein in 293T cells than did the -427T allele.

CONCLUSIONS AND CLINICAL RELEVANCE

Polymorphisms of -427C>T on the promoter and those of +102525G>A on exon 5 of the PPARGC1B gene may affect the development of AHR through the modulation of PPARGC1B gene products. The PPARGC1B genotypes may serve as genetic markers for AHR.

Association of FANCC polymorphisms with FEV1 decline in aspirin exacerbated respiratory disease

Aspirin exacerbated respiratory disease (AERD) is a clinical condition characterized by severe decline in forced expiratory volume in one second (FEV1) following the ingestion of non-steroidal anti-inflammatory drugs (NSAIDs), including aspirin. The exacerbated inflammatory response in Fancc-deficient mice has been reported to be associated with hemopoietic responses that are also related to AERD pathogenesis. To investigate associations of FANCC polymorphisms with AERD and related phenotypes, this study genotyped 25 common single nucleotide polymorphisms (SNPs) in a total of 592 Korean asthmatics including 163 AERD and 429 aspirin-tolerant asthma (ATA) subjects. Logistic analysis revealed that genetic polymorphisms of the FANCC gene might not be directly related to AERD development and nasal polyposis (P > 0.05). However, the FEV1 decline by aspirin provocation showed significant associations with FANCC polymorphisms (P = 0.006-0.04) and a haplotype (unique to rs4647416G > A, P = 0.01 under co-dominant, P = 0.006 under recessive model). In silico analysis showed that the "A" allele of rs4647376C > A, which was more prevalent in AERD than in ATA, could act as a potential branch point (BP) site for alternative splicing (BP score = 4.16). Although replications in independent cohorts and further functional evaluations are still needed, our preliminary findings suggest that FANCC polymorphisms might be associated with the obstructive symptoms in allergic diseases.

Melatonin receptor 1 B polymorphisms associated with the risk of gestational diabetes mellitus

Backgrounds

Two SNPs in melatonin receptor 1B gene, rs10830963 and rs1387153 showed significant associations with fasting plasma glucose levels and the risk of Type 2 Diabetes Mellitus (T2DM) in previous studies. Since T2DM and gestational diabetes mellitus (GDM) share similar characteristics, we suspected that the two genetic polymorphisms in MTNR1B may be associated with GDM, and conducted association studies between the polymorphisms and the disease. Furthermore, we also examined genetic effects of the two polymorphisms with various diabetes-related phenotypes.

Methods

A total of 1,918 subjects (928 GDM patients and 990 controls) were used for the study. Two MTNR1B polymorphisms were genotyped using TaqMan assay. The allele distributions of SNPs were evaluated by x² models calculating odds ratios (ORs), 95% confidence intervals (CIs), and corresponding P values. Multiple regressions were used for association analyses of GDM-related traits. Finally, conditional analyses were also performed.

Results

We found significant associations between the two genetic variants and GDM, rs10830963, with a corrected P value of 0.0001, and rs1387153, with the corrected P value of 0.0008. In addition, we also found that the two SNPs were associated with various phenotypes such as homeostasis model assessment of beta-cell function and fasting glucose levels. Further conditional analyses results suggested that rs10830963 might be more likely functional in case/control analysis, although not clear in GDM-related phenotype analyses.

Conclusion

There have been studies that found associations between genetic variants of other genes and GDM, this is the first study that found significant associations between SNPs of MTNR1B and GDM. The genetic effects of two SNPs identified in this study would be helpful in understanding the insight of GDM and other diabetes-related disorders.

Association analysis of C6 genetic variations and aspirin hypersensitivity in Korean asthmatic patients

There has been increasing evidence that genetic mechanisms contribute to the development of aspirin-intolerant asthma (AIA), a life-threatening disease. The complement component (C6) is a constituent of a biochemical cascade that has been implicated in airway epithelial damage and nasal polyposis, and therefore, may be a risk factor for AIA. To investigate the association between C6 variations and AIA in a Korean asthma cohort, 27 SNPs were selected for genotyping based on previously reported polymorphisms in the HapMap database. Genotyping was carried out using TaqMan assay, and five major haplotypes were obtained in 163 AIA cases and 429 aspirin-tolerant asthma (ATA) controls subjects. Genotype frequency distributions of C6 polymorphisms and haplotypes were analyzed using logistic and regression models. Subsequent analyses revealed a lack of association between C6 genetic variations and AIA. From the initial analyses, marginal associations of rs10512766 (p = 0.04 in co-dominant model) and rs4957374 (p = 0.05 in dominant model) with AIA did not reach the threshold of significance after multiple testing corrections; thus this study failed to find convincing evidence that variations in C6 gene influence the risk of AIA in a Korean population. However, these preliminary results may contribute to the etiology of aspirin hypersensitivity in Korean asthmatic patients.

Association of the variants in AGT gene with modified drug response in Korean aspirin-intolerant asthma patients

The angiotensinogen (AGT) gene enhances the effect of several bronchoconstrictors and produces a peptide that is accumulated in the airways of asthma patients; events that may underpin the pathogenesis of aspirin-intolerant asthma (AIA). To carry out a case-control analysis between AGT and aspirin-induced bronchospasm following treatment with an anti-asthma drug, montelukast (MLK), 38 single nucleotide polymorphisms (SNPs) in AGT were genotyped in 56 AIA cohort. Genotyping was performed with TaqMan assay and haplotypes were inferred using PHASE algorithm ver. 2.0. Statistical analyses of each SNPs and haplotypes were performed using SAS version 9.1. Among 13 variants displaying significant signals, two SNPs (+2401C>G and +2476C>T) in the intronic region of AGT were significantly associated with modification of drug response even after correction for multiple testing (P=0.0009-0.002; P(corr)=0.02-0.03). Furthermore, the two variants also exhibited associations with MLK response rate (P=0.0003-0.0006; P(corr)=0.006-0.01). Although our results are preliminary and further replication in a larger-scale group of subjects should be warranted, these observations provide evidence that AGT variants might be one of genetic factors involved in the response of anti-asthma drugs in AIA patients.

ADH1B and ALDH2 polymorphisms and their associations with increased risk of squamous cell carcinoma of the head and neck in the Korean population

Alcohol consumption is a major risk factor for squamous cell carcinoma of the head and neck (SCCHN). Alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) are key enzymes in ethanol metabolism. The objective of this study was to investigate the relationships of ADH and ALDH single nucleotide polymorphisms (SNPs) with the risk of developing SCCHN in a Korean sample. We genotyped ADH1B +3170A>G (rs1229984) and ALDH2 +1951G>A (rs671) SNPs in 225 Korean SCCHN patients and 301 healthy controls by single base extension and TaqMan assay. The frequencies of the ADH1B +3170A>G (*2*2/*2*1/*1*1) genotypes were 48.0%/38.7%/13.3% in SCCHN patients, and 57.8%/37.2%/5.0% in controls, respectively. The odds ratio (OR) and 95% confidence interval of the ADH1B*1*1 genotype was 1.89 (1.23-2.92) relative to the *2*2 genotype. The frequencies of the ALDH2 +1951G>A (*1*1/*1*2/*2*2) genotypes were 67.6%/31.6%/0.9% in SCCHN patients, and 67.8%/29.6%/2.7% in controls, respectively. In subgroup analyses according to smoking and alcohol drinking status, the OR of the ADH1B*1*1 genotype was increased in the heavy drinker group [8.85 (1.095-40.0)] and in the heavy smoker group [4.7 (1.54-14.29)]. We conclude that the ADH1B*1*1 genotype is associated with an increased risk of SCCHN, especially in heavy drinkers and heavy smokers. This genotype could be a useful biomarker for identifying Koreans with a greater risk of SCCHN.