Exome resequencing combined with linkage analysis identifies novel PTH1R variants in primary failure of tooth eruption in Japanese

Massively parallel sequencing of target regions, exomes, and complete genomes has begun to increase the opportunities for identifying genetic variants underlying rare and common diseases dramatically. Here we applied exome resequencing to primary failure of tooth eruption (PFE) to identify the genetic causality of the disease. Two Japanese families having PFE were recruited and examined by genome-wide linkage study and subsequently exome analyses. Linkage analyses of these two families comprising eight affected individuals and two unaffected individuals revealed linkage signals at 10 loci with a maximum LOD score of 1.5. Four affected individuals in one family were pooled and further processed for exome analysis, followed by massive parallel sequencing. After three-step filtering including annotation and functional expectation, three variants were found to be candidates for PFE. Among the three variants, only a novel variant of parathyroid hormone 1 receptor gene (PTH1R), R383Q, was cosegregated in the first PFE family. Accordingly, we screened the gene for variants at all coding exons and the respective intron-exon boundaries in the second family and two sporadic individuals with PFE. We also identified a novel missense variant, P119L, cosegregating in the second family and missense variants P132L and R147C in the sporadic cases. These variants all were in the highly conserved region across zebrafish to chimpanzee and not observed in 192 unrelated controls, supporting the pathogenicity of the variants. The combination of linkage and exome analyses employed in this study provides a powerful strategy for identifying genes responsible for Mendelian disorders.

Particular human leukocyte antigen alleles are associated with biochemical traits in the Japanese population

We analyzed genetic associations among 7 biochemical traits (fasting plasma glucose, HbA1c, total cholesterol, low-density lipoprotein [LDL] cholesterol, high-density lipoprotein cholesterol, triglyceride, and uric acid) and 6 HLA loci using 1,616 individuals who visited the Health Evaluation and Promotion Center at Tokai University Hospital. Significant differences between the individuals carrying particular HLA alleles and those not carrying the alleles in certain biochemical traits were observed by Mann-Whitney U test. In female subjects, DPB1*03:01 was significantly associated with HbA1c (p = 0.0000665), and DRB1*14:03 was associated with total cholesterol concentration (p = 0.0015). In male subjects, C*14:02 demonstrated significant associations with fasting plasma glucose with p values of 0.0041. By contrast, Fisher's exact test indicated that female DRB1*14:03 was associated with a high concentration of total cholesterol (p = 000323, odds ratio [OR] = 4.32, 95% confidence interval [95% CI] = 1.83-10.36), whereas female DPB1*02:01 had a protective effect against a high concentration of LDL cholesterol (p =0.0043, OR = 0.41, 95% CI = 0.19-0.79). These associations have a statistical power of more than 0.8 and still retain significance after Bonferroni correction.

Germline copy number variations in BRCA1-associated ovarian cancer patients

We investigated characteristics of germline copy number variations (CNV) in BRCA1-associated ovarian cancer patients by comparing them to CNVs present in sporadic ovarian cancer patients. Germline CNVs in 51 BRCA1-associated, 33 sporadic ovarian cancer patients, and 47 healthy women were analyzed by both signal intensity and genotyping data using the Affymetrix Genome-Wide Human SNP Array 6.0. The total number of CNVs per genome was greater in the sporadic group (median 26, range 12-34) than in the BRCA1 group (median 21, range 11-35; post hoc P < 0.05) or normal group (median 20, range 7-32; post hoc P < 0.05). While the number of amplifications per genome was higher in the sporadic group (median 13, range 7-26) than in the BRCA1 group (median 8, range 3-23; post hoc P < 0.001), the number of deletions per genome was higher in the BRCA1 group (median 12, range 6-24) than in the sporadic group (median 9, range 3-17; post hoc P < 0.01). In addition, 31 previously unknown CNV regions were present specifically in the BRCA1 group. When we performed pathway analysis on the 241 overlapping genes mapped to these novel CNV regions, the 'purine metabolism' and '14-3-3-mediated signaling' pathways were over-represented (Fisher's exact test, P < 0.01). Our study shows that there are qualitative differences in genomic CNV profiles between BRCA1-associated and sporadic ovarian cancer patients. Further studies are necessary to clarify the significance of the genomic CNV profile unique to BRCA1-associated ovarian cancer patients.

ANRIL is implicated in the regulation of nucleus and potential transcriptional target of E2F1

ANRIL, a large antisense non-coding RNA, is in the proximity of CDKN2A and overlapped with CDKN2B at human chromosome 9p21, and has been strongly implicated in the association with high risk genetic markers of coronary artery disease (CAD). Mice model harboring large deletion of posterior part of ANRIL and CAD high risk genetic markers resulted in substantial suppression of both CDKN2A and CDKN2B; however, the mechanistic insights of regulation and function of ANRIL have remain elusive. To date multiple splice variants of ANRIL have been reported and expression of specific splice variant of ANRIL has been shown to be tightly associated with 9p21 CAD high risk markers. Here we identified a new splice variant of ANRIL and introduced it into HeLa cells to uncover functional aspects of ANRIL towards cellular function. For this purpose, we monitored global mRNA expressional changes and conducted gene ontology enrichment. The majority of mRNAs was down-regulated by ANRIL overexpression. Among them, a subset of mRNAs particularly involved in the regulation of nucleus and establishment or maintenance of chromatin architecture was significantly enriched. Such a circumstance was manifested after 48 h of ANRIL overexpression but no significant changes were seen after 24 h of ANRIL overexpression. Next we analyzed the sequences containing the intergenic region between ANRIL and CDKN2A (p14ARF) by introducing the sequences upstream of luciferase reporter gene. Based on the luciferase activity, the sequences tested were shown to act as promoter for ANRIL and p14ARF. Moreover, as well p14ARF, ANRIL promoter was responsive to transcription factor E2F1 in HeLa and A549 cells. Taken together, our present results indicate that co-regulation of ANRIL and p14ARF could be coupled by their unique intergenic region potentially through E2F1. Judged from the suppressive effect of ANRIL on a subset of mRNAs involved in the nuclear function suggests that ANRIL might have silencing effect on a specific gene set that accounts for a wide array of gene expression.

IFN-γ and TNF-α synergistically induce microRNA-155 which regulates TAB2/IP-10 expression in human mesangial cells

BACKGROUND/AIMS

MicroRNAs are noncoding small RNA molecules that posttranscriptionally regulate gene expression. microRNA-155 (miR-155), one of the microRNAs, is involved in the control of various genes. However, the role of miR-155 in inflammatory responses in mesangial cells is not known. In the present study, we examined the expression of miR-155 in mesangial cells.

METHODS

The expression of miR-155 in cultured normal human mesangial cells treated with interferon-γ (IFN-γ) and/or tumor-necrosis factor-α (TNF-α) was examined. The cells were transfected with miR-155 mimic, siRNA against transforming growth factor-β-activated kinase-1 (TAK1)-binding protein 2 (TAB2) or siRNA against nuclear factor-κB (NF-κB).

RESULTS

IFN-γ and TNF-α synergistically induced the expression of miR-155. Transfection of cells with miR-155 mimic inhibited the expression of TAB2 and IFN-γ-inducible protein of 10 kDa (IP-10). The expression of IP-10 was suppressed by knockdown of TAB2. Induction of miR-155 was inhibited by RNA interference against TAB2 or NF-κB.

CONCLUSION

Combined stimulation with IFN-γ and TNF-α induces miR-155 via TAB2 and NF-κB. miR-155 negatively regulates TAB2, as a negative feedback system, to lower IP-10 expression. miR-155 may play a role in the regulation of inflammatory and immune reactions in the kidney.

Genetics of Moyamoya disease

Moyamoya disease (MMD) is a disease pattern consisting of bilateral stenosis of the intracranial internal carotid arteries (ICA) accompanied by a network of abnormal collateral vessels that bypass the stenosis. Once symptomatic, insufficient cerebral blood flow or rupture of the fragile collaterals may cause stroke or hemorrhage, resulting in severe neurological dysfunction or death. The etiology of MMD is still unknown, although few associations with other diseases and environmental factors have been described. Strong regional differences in epidemiological data, as well as known familial cases, turned the focus to genetics for the insight into the disease's pathogenesis. Thus far, several reports have suggested specific genetic loci and individual genes as predisposing to MMD, but none have demonstrated reproducible results in independent cohorts. Small sample sizes, as well as a likely multifactorial origin, seem to be the most challenging tasks in identifying the disease-causing mechanisms. Once identified, susceptibility genes may allow preventive screening and a possible development of novel therapeutic options.

Genome-wide association analysis of copy number variations in subarachnoid aneurysmal hemorrhage

Subarachnoid aneurysmal hemorrhage (SAH) due to cerebral aneurysm rupture is a very serious disease resulting in high mortality rate. It has been known that genetic factors are involved in the risk of SAH. A recent breakthrough in genomic variation called copy number variation (CNV) has been revealed to be involved in risks of human diseases. In this study, we hypothesized that CNVs can predict the risk of SAH. We used the Illumina HumanHap300 BeadChip (317 503 markers) to genotype 497 individuals in a Japanese population. Furthermore, individual CNVs were identified using signal and allelic intensities. The genetic effect of CNV on the risk of SAH was evaluated using multivariate logistic regression controlling for age and gender in 187 common CNV regions (frequency >1%). From a total of 4574 individual CNVs identified in this study (9.7 CNVs per individual), we were able to discover 1644 unique CNV regions containing 1232 genes. The identified variations were validated using visual examination of the genoplot image, overlapping analysis with the Database of Genomic Variants (73.2%), CNVpartition (72.4%) and quantitative PCR. Interestingly, two CNV regions, chr4:153210505-153212191 (deletion, 4q31.3, P=0.0005, P(corr) (corrected P-value)=0.04) and chr10:6265006-6267388 (duplication, 10p15.1, P=0.0006, P(corr)=0.05), were significantly associated with the risk of SAH after multiple testing corrections. Our results suggest that the newly identified CNV regions may contribute to SAH disease susceptibility.

Differential Effects of Chromosome 9p21 Variation on Subphenotypes of Intracranial Aneurysm

Background and Purpose— Recently, a genome-wide association study identified associations between single nucleotide polymorphisms on chromosome 9p21 and risk of harboring intracranial aneurysm (IA). Aneurysm characteristics or subphenotypes of IAs, such as history of subarachnoid hemorrhage, presence of multiple IAs and location of IAs, are clinically important. We investigated whether the association between 9p21 variation and risk of IA varied among these subphenotypes.

Methods— We conducted a case-control study of 981 cases and 699 controls in Japanese. Four single nucleotide polymorphisms tagging the 9p21 risk locus were genotyped. The OR and 95% CI were estimated using logistic regression analyses.

Results— Among the 4 single nucleotide polymorphisms, rs1333040 showed the strongest evidence of association with IA ( P =1.5×10 −6 ; per allele OR, 1.43; 95% CI, 1.24–1.66). None of the patient characteristics (gender, age, smoking, and hypertension) was a significant confounder or effect modifier of the association. Subgroup analyses of IA subphenotypes showed that among the most common sites of IAs, the association was strongest for IAs of the posterior communicating artery (OR, 1.69; 95% CI, 1.26–2.26) and not significant for IAs in the anterior communicating artery (OR, 1.22; 95% CI, 0.96–1.57). When dichotomizing IA sites, the association was stronger for IAs of the posterior circulation–posterior communicating artery group (OR, 1.73; 95% CI, 1.32–2.26) vs the anterior circulation group (OR, 1.28; 95% CI, 1.07–1.53). Heterogeneity in these ORs was significant ( P =0.032). The associations did not vary when stratifying by history of subarachnoid hemorrhage (OR, 1.42; 95% CI, 1.18–1.71 for ruptured IA; OR, 1.27; 95% CI, 1.00–1.62 for unruptured IA) or by multiplicity of IA (OR, 1.57; 95% CI, 1.21–2.03 for multiple IAs; OR, 1.36; 95% CI, 1.15–1.61 for single IA).

Conclusions— Our results suggest that genetic influence on formation may vary between IA subphenotypes.

Retinoic acid-inducible gene-I (RIG-I) is induced by IFN-{gamma} in human mesangial cells in culture: possible involvement of RIG-I in the inflammation in lupus nephritis

Interferon-gamma is a potent Th1-type cytokine and a key molecule in the pathogenesis of autoimmune diseases including lupus nephritis. Retinoic acid-inducible gene-I is a putative RNA helicase that plays an important role in immune and inflammatory reactions. We previously demonstrated the increased expression of the retinoic acid-inducible gene-I protein in the kidney tissue of patients with lupus nephritis, and the presence of a significant amount of retinoic acid-inducible gene-I mRNA in the urinary sediment of patients with this inflammatory renal disease. In the present study, interferon-gamma was found to induce the expression of retinoic acid-inducible gene-I in human mesangial cells in culture. Knockdown of retinoic acid-inducible gene-I inhibited the interferon-gamma-induced upregulation of interferon regulatory factor 7, a transcriptional factor involved in immune and inflammatory reactions. These findings suggest that retinoic acid-inducible gene-I produced by mesangial cells may be involved in the pathogenesis of lupus nephritis.

Association of the Jun dimerization protein 2 gene with intracranial aneurysms in Japanese and Korean cohorts as compared to a Dutch cohort

In a previous study a linkage region for association to IA patients was found on chromosome 14q22. In this study, we report the findings of a positional candidate gene, Jun dimerization Protein 2 (JDP2), and single nucleotide polymorphisms (SNP) of that gene that are associated with intracranial aneurysms in different ethnic populations. We screened the linkage region around chromosome 14q22 and narrowed it down to JDP2. We then genotyped case and control groups of three different ethnic populations: 403 Japanese intracranial aneurysm (IA) cases and 412 controls, 181 Korean IA cases and 181 controls, 379 Dutch cases and 642 Dutch controls. Genotyping was performed using polymerase chain reaction and direct sequencing technology. The allele distribution of three SNPs (two intronic: rs741846; P=0.0041 and rs175646; P=0.0014, and one in the untranslated region: rs8215; P=0.019) and their genotype distribution showed significant association in the Japanese IA patients. The allelic and genotypic frequency of one intronic SNP (rs175646; P=0.0135 and P=0.0137, respectively) and the genotypic frequency for the SNP in the UTR region (rs8215; P=0.049) was also significantly different between cases and controls of the Korean cohort. There was no difference in allelic or genotypic frequencies in the Dutch population. These SNPs in JDP2 are associated with intracranial aneurysms, suggesting that variation in or near JDP2 play a role in susceptibility to IAs in East Asian populations.

Abstract 2162: Gene expression profile for predicting survival in ovarian cancer across two independent datasets

Advanced-stage ovarian cancer patients are generally treated with platinum/taxane-based chemotherapy after primary debulking surgery. However, there is a wide range of outcomes for individual patients. Therefore, the clinicopathological factors alone are insufficient for predicting prognosis. To identify a progression-free survival (PFS) related profile for predicting survival, advanced-stage serous ovarian cancer tissues from 110 patients who underwent primary surgery and platinum/taxane-based chemotherapy were profiled using oligonucleotide microarrays. We first selected 88 PFS-related genes by a univariate Cox model (p &lt; 0.01). To avoid overfitting our dataset, we then adjusted regression coefficients of the genes by ridge regression Cox model using 10-fold cross-validation. The prognostic index for each patient based on the 88-gene expression profile with the estimated coefficients was significantly correlated with PFS time as a continuous variable. In multivariate analysis, the prognostic index was independently associated with PFS time compared to other clinical factors [hazard ratio (HR), 4.84; 95% confidence interval (CI), 3.50-6.55; p &lt; 0.001]. This prognostic ability was validated using an external validation dataset (n = 87) and proven by multivariate analysis (HR, 1.25; 95% CI, 1.08-1.45; p = 0.0032). The correlation between the prognostic index and overall survival time was confirmed in the two independent datasets. Furthermore, biological characterization of 88 PFS-related genes mainly highlighted several oncogenic signaling pathways. This PFS-related profile is the first step toward clinical practice for optimizing clinical management for advanced-stage serous ovarian cancer patients.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2162.

Genome-wide association study of intracranial aneurysm identifies three new risk loci

Saccular intracranial aneurysms (IAs) are balloon-like dilations of the intracranial arterial wall; their hemorrhage commonly results in severe neurologic impairment and death. We report a second genome-wide association study with discovery and replication cohorts from Europe and Japan comprising 5,891 cases and 14,181 controls with ∼832,000 genotyped and imputed SNPs across discovery cohorts. We identified three new loci showing strong evidence for association with IA in the combined data set, including intervals near RBBP8 on 18q11.2 (OR=1.22, P=1.1×10^-12), STARD13/KL on 13q13.1 (OR=1.20, P=2.5×10^-9) and a gene-rich region on 10q24.32 (OR=1.29, P=1.2×10^-9). We also confirmed prior associations near SOX17 (8q11.23-q12.1; OR=1.28, P=1.3×10^-12) and CDKN2A/B (9p21.3; OR=1.31, P=1.5×10^-22). It is noteworthy that several putative risk genes play a role in cell-cycle progression, potentially affecting proliferation and senescence of progenitor cell populations that are responsible for vascular formation and repair.

Positional effects of polymorphisms in probe-target sequences on genoplot images of oligonucleotide microarrays

Single nucleotide polymorphisms (SNPs) present in probe-target sequences (SPTS) have been shown to be associated with abnormal genoplot images. We explored the effects of SPTS positions on genoplot images using a data set from a genome-wide association study typed on an Illumina Human Hap300 platform. We screened the physical genomic positions of 308,330 autosomal probes to identify SPTS candidates deposited in dbSNP. The genoplot images across 293 individuals were inspected further in SNPs bearing an SPTS candidate. We identified 35,185 SNPs bearing a single SPTS candidate, including 264 SNPs showing abnormal genoplot images. The frequencies of SPTS at distances within 10 bases from the target SNP were significantly higher in the 264 SNPs showing abnormal genoplot images, than in the remaining 34,921 SNPs (49.62 vs 12.87%; Fisher exact test; P = 2.2 x 10(-16)). Of these 264 SNPs, we randomly selected 20 SNPs and resequenced them in 97 individuals. An SPTS within 10 bases of the target SNP was confirmed in all 20 SNPs, except for one SNP with a small deletion (7 bases) in the probe-target sequence. Taken together, these results suggest an association of a proximal SPTS with an abnormal genoplot image, which could result in spurious genotype detections, highlighting the importance of minimizing systematic errors in microarray experiments.

Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets

Background

Advanced-stage ovarian cancer patients are generally treated with platinum/taxane-based chemotherapy after primary debulking surgery. However, there is a wide range of outcomes for individual patients. Therefore, the clinicopathological factors alone are insufficient for predicting prognosis. Our aim is to identify a progression-free survival (PFS)-related molecular profile for predicting survival of patients with advanced-stage serous ovarian cancer.

Methodology/Principal Findings

Advanced-stage serous ovarian cancer tissues from 110 Japanese patients who underwent primary surgery and platinum/taxane-based chemotherapy were profiled using oligonucleotide microarrays. We selected 88 PFS-related genes by a univariate Cox model (p<0.01) and generated the prognostic index based on 88 PFS-related genes after adjustment of regression coefficients of the respective genes by ridge regression Cox model using 10-fold cross-validation. The prognostic index was independently associated with PFS time compared to other clinical factors in multivariate analysis [hazard ratio (HR), 3.72; 95% confidence interval (CI), 2.66–5.43; p<0.0001]. In an external dataset, multivariate analysis revealed that this prognostic index was significantly correlated with PFS time (HR, 1.54; 95% CI, 1.20–1.98; p = 0.0008). Furthermore, the correlation between the prognostic index and overall survival time was confirmed in the two independent external datasets (log rank test, p = 0.0010 and 0.0008).

Conclusions/Significance

The prognostic ability of our index based on the 88-gene expression profile in ridge regression Cox hazard model was shown to be independent of other clinical factors in predicting cancer prognosis across two distinct datasets. Further study will be necessary to improve predictive accuracy of the prognostic index toward clinical application for evaluation of the risk of recurrence in patients with advanced-stage serous ovarian cancer.

De novo mutations of voltage-gated sodium channel alphaII gene SCN2A in intractable epilepsies

BACKGROUND

Mutations of voltage-gated sodium channel alpha(II) gene, SCN2A, have been described in a wide spectrum of epilepsies. While inherited SCN2A mutations have been identified in multiple mild epilepsy cases, a de novo SCN2A-R102X mutation, which we previously reported in a patient with sporadic intractable childhood localization-related epilepsy, remains unique. To validate the involvement of de novo SCN2A mutations in the etiology of intractable epilepsies, we sought to identify additional instances.

METHODS

We performed mutational analyses on SCN2A in 116 patients with severe myoclonic epilepsy in infancy, infantile spasms, and other types of intractable childhood partial and generalized epilepsies and did whole-cell patch-clamp recordings on Na(v)1.2 channels containing identified mutations.

RESULTS

We discovered 2 additional de novo SCN2A mutations. One mutation, SCN2A-E1211K, was identified in a patient with sporadic infantile spasms. SCN2A-E1211K produced channels with altered electrophysiologic properties compatible with both augmented (an approximately 18-mV hyperpolarizing shift in the voltage dependence of activation) and reduced (an approximately 22-mV hyperpolarizing shift in the voltage dependence of steady-state inactivation and a slowed recovery from inactivation) channel activities. The other de novo mutation, SCN2A-I1473M, was identified in a patient with sporadic neonatal epileptic encephalopathy. SCN2A-I1473M caused an approximately 14-mV hyperpolarizing shift in the voltage dependence of activation.

CONCLUSIONS

The identified de novo mutations SCN2A-E1211K, -I1473M, and -R102X indicate that SCN2A is an etiologic candidate underlying a variety of intractable childhood epilepsies. The phenotypic variations among patients might be due to the different electrophysiologic properties of mutant channels.

Gene expression profiling of advanced-stage serous ovarian cancers distinguishes novel subclasses and implicates ZEB2 in tumor progression and prognosis

To elucidate the mechanisms of rapid progression of serous ovarian cancer, gene expression profiles from 43 ovarian cancer tissues comprising eight early stage and 35 advanced stage tissues were carried out using oligonucleotide microarrays of 18,716 genes. By non-negative matrix factorization analysis using 178 genes, which were extracted as stage-specific genes, 35 advanced stage cases were classified into two subclasses with superior (n = 17) and poor (n = 18) outcome evaluated by progression-free survival (log rank test, P = 0.03). Of the 178 stage-specific genes, 112 genes were identified as showing different expression between the two subclasses. Of the 48 genes selected for biological function by gene ontology analysis or Ingenuity Pathway Analysis, five genes (ZEB2, CDH1, LTBP2, COL16A1, and ACTA2) were extracted as candidates for prognostic factors associated with progression-free survival. The relationship between high ZEB2 or low CDH1 expression and shorter progression-free survival was validated by real-time RT-PCR experiments of 37 independent advanced stage cancer samples. ZEB2 expression was negatively correlated with CDH1 expression in advanced stage samples, whereas ZEB2 knockdown in ovarian adenocarcinoma SKOV3 cells resulted in an increase in CDH1 expression. Multivariate analysis showed that high ZEB2 expression was independently associated with poor prognosis. Furthermore, the prognostic effect of E-cadherin encoded by CDH1 was verified using immunohistochemical analysis of an independent advanced stage cancer samples set (n = 74). These findings suggest that the expression of epithelial-mesenchymal transition-related genes such as ZEB2 and CDH1 may play important roles in the invasion process of advanced stage serous ovarian cancer.

Genome-wide association database developed in the Japanese Integrated Database Project

The establishment of high-throughput single-nucleotide polymorphism (SNP)-typing technologies has enabled astonishing progress to be made in genome-wide association studies (GWAS), and various novel genetic factors associated with complex diseases have been discovered. Our organization has created a public repository database (DB) to achieve a continuous and intensive management of GWAS data and to facilitate data sharing among researchers. In the GWAS DB, information on study design, quality control protocols, allele frequencies, genotype frequencies and statistical genetic analysis results are stored as publicly available data and can be accessed freely, whereas individual genotyping data and raw data are stored as restricted data and can only be accessed with authorization. All data are presented by a graphic viewer, which is designed to be user friendly for researchers who are not familiar with GWAS to accelerate disease-related studies. Furthermore, the DB allows users to compare various study results obtained by different institutions and on different platforms. The same data are also managed as a distributed annotation system to call up useful data from other DBs and to superimpose them on the GWAS data for help in interpretation. The DB is accessible at https://gwas.lifesciencedb.jp/.

Association of the growth hormone receptor gene polymorphisms with mandibular height in a Korean population

Growth hormone receptor gene (GHR) is one of the likely candidates for determining morphological traits, because GH is a key regulator of bone growth. The genetic association of GHR in exon 10 with mandibular ramus height has been found in different populations, Japanese and Chinese. On the other hand, two common isoforms of GHR, one full-length (fl-GHR) and the other lacking the extracellular domain encoded by exon 3 (d3-GHR), are associated with differences in responsiveness to GH. The purpose of this study involving 159 Korean subjects was to study the associations between a GHR polymorphism (d3/fl-GHR) that results in genomic deletion of exon 3 and craniofacial morphology, and to study the associations between GHR genotypes in exon 10 and craniofacial morphology. Moreover, the allelic frequencies in a multi-ethnic population (24 Han Chinese, 24 African-Americans, 24 European-Americans, and 24 Hispanics) in a GHR polymorphism (d3/fl-GHR) were compared in this study. The five craniofacial linear measurements (cranial base length, maxillary length, overall mandibular length, mandibular corpus length, and mandibular ramus height) obtained from lateral cephalograms were examined as craniofacial morphology. We found that the d3/fl-GHR polymorphism had no association for any measurements, and a statistically significant association (P=0.024) between the GHR polymorphisms P561T and C422F in exon 10 and mandibular ramus height. Neither SNPs besides P561T and C422F polymorphisms in exon 10 nor the measurements besides mandibular ramus height have statistically significances. Both derived alleles at P561T and C422F SNPs were highly associated with only one haplotype, haplotype-4 in Korean population. As quantitative haplotype association, the results showed a significant difference in mandibular ramus height between individuals having one haplotype-4 and others without haplotype-4 (P=0.028). Moreover, we found that the d3/fl-GHR polymorphism showed diverse frequency in different population. Regarding GHR genotypes in exon 10, the present study mostly reflected the results obtained for a Japanese population, although our current study does not replicate the correlation between the I526L polymorphism of GHR and mandibular ramus height as was reported in a previous study of Han Chinese. The results of the present study suggest that the GHR exon 10 SNPs, not d3/fl-GHR, contribute to changes in the mandibular ramus height of Koreans.

Gene-expression profiles in human nasal polyp tissues and identification of genetic susceptibility in aspirin-intolerant asthma

BACKGROUND

Aspirin-intolerant asthma (AIA) is a subtype of asthma induced by non-steroidal anti-inflammatory drugs and characterized by an aggressive mucosal inflammation of the lower airway (asthma) and the upper airways (rhinitis and nasal polyp). The lower airway lesion and the nasal polyp in AIA are postulated to have common pathogenic features involving aspirin sensitivity that would be reflected in the gene expression profile of AIA polyps.

OBJECTIVE

This study was conducted to clarify the pathogenesis of AIA using gene expression analysis in nasal polyps, and identify genetic susceptibilities underlying AIA in a case-control association study.

METHODS

Global gene expression of nasal polyps from nine AIA patients was examined using microarray technology in comparison with nasal polyps from five eosinophilic sinusitis (ES) patients, a related disease lacking aspirin sensitivity. Based on the AIA-specific gene expression profile of nasal polyp, candidate genes for AIA susceptibility were selected and screened by a case-control design of 219 AIA patients, 374 non-asthmatic control (CTR), and 282 aspirin-tolerant asthmatic (ATA) subjects.

RESULTS

One hundred and forty-three elevated and three decreased genes were identified as AIA-specific genes that were enriched in immune response according to Gene Ontology analysis. In addition, a k-means-based algorithm was applied to cluster the genes, and a subclass characteristic of AIA comprising 18 genes that were also enriched in immune response was identified. By examining the allelic associations of single nucleotide polymorphisms (SNPs) of AIA candidate genes relevant to an immune response with AIA, two SNPs, one each of INDO and IL1R2, showed significant associations with AIA (P=0.011 and 0.026 after Bonferroni's correction, respectively, in AIA vs. CTR). In AIA-ATA association analysis, modest associations of the two SNPs with AIA were observed.

CONCLUSION

These results indicate that INDO and IL1R2, which were identified from gene expression analyses of nasal polyps in AIA, represent susceptibility genes for AIA.