Smoking-Related DNA Methylation is Differentially Associated with Cadmium Concentration in Blood.

Tobacco smoking, a risk factor for several human diseases, can lead to alterations in DNA methylation. Smoking is a key source of cadmium exposure; however, there are limited studies examining DNA methylation alterations following smoking-related cadmium exposure. To identify such cadmium exposure-related DNA methylation, we performed genome-wide DNA methylation profiling using DNA samples from 50 smokers and 50 non-smokers. We found that a total of 136 CpG sites (including 70 unique genes) were significantly differentially methylated in smokers as compared to that in non-smokers. The CpG site cg05575921 in the AHRR gene was hypomethylated (Δ ß > - 0.2) in smokers, which was in accordance with previous studies. The rs951295 (within RNA gene LOC105370802) and cg00587941 sites were under-methylated by > 15% in smokers, whereas cg11314779 (within CELF6) and cg02126896 were over-methylated by ≥ 15%. We analyzed the association between blood cadmium concentration and DNA methylation level for 50 smokers and 50 non-smokers. DNA methylation rates of 307 CpG sites (including 207 unique genes) were significantly correlated to blood cadmium concentration (linear regression P value < 0.001). The four significant loci (cg05575921 and cg23576855 in AHRR, cg03636183 in F2RL3, and cg21566642) were under-methylated by > 10% in smokers compared to that in non-smokers. In conclusion, our study demonstrated that DNA methylation levels of rs951295, cg00587941, cg11314779, and cg02126896 sites may be new putative indicators of smoking status. Furthermore, we showed that these four loci may be differentially methylated by cadmium exposure due to smoking.

An epigenomic signature of postprandial hyperglycemia in peripheral blood leukocytes.

Postprandial hyperglycemia is known to be one of the earliest signs of abnormal glucose homeostasis associated with type 2 diabetes. This study aimed to assess clinical significance of a 1-h postprandial glucose level for the development of diabetes, and identify epigenetic biomarkers of postprandial hyperglycemia. We analyzed clinical data from the oral glucose tolerance tests for healthy subjects (n=4502). The ratio (Glu60/Glu0) of 1-h glucose levels to fasting glucose levels was significantly associated with an insulin sensitive index (QUICKI, quantitative insulin sensitivity check index) (ß=0.055, P=1.25E-04) as well as a risk of future pre-diabetic and diabetic conversion. Next, DNA methylation profile analyses of 24 matched pairs of the high and low Glu60/Glu0 ratio subjects showed that specific DNA methylation levels in the promoter region of an olfactory receptor gene (olfactory receptor gene family10 member A4, OR10A4) were associated with the Glu60/Glu0 ratios (ß=0.337, P=0.03). Moreover, acute oral glucose challenges decreased the DNA methylation levels of OR10A4 but not the global DNA methylation in peripheral leukocytes of healthy subjects (n=7), indicating that OR10A4 is a specific epigenomic target of postprandial hyperglycemia. This work suggests possible relevance of olfactory receptor genes to an earlier molecular biomarker of peripheral hyperglycemia and diabetic conversion.

Association of Serum Metabolites with Serum Indices and Preanalytical Factors of Biobanked Serum Samples.

Background: Serum indices (hemolysis, icterus, and lipemia; HIL) are known to impact clinical chemistry assay results. This study aimed to investigate the impact of HIL indices on serum metabolite profiles and the association of serum metabolite levels with pre-analytical factors of serum samples. Methods: A cohort of serum samples (n = 12,196) from the Korean Genome and Epidemiology Study (KoGES) was analyzed for HIL indices and the pre-analytical variables (SPRECs) which were generated in the process of serum collection. We further performed targeted metabolomics on a subset comprising hemolyzed (n = 60), icteric (n = 60), lipemic (n = 60) groups, and a common control group of non-HIL samples (n = 60) using the Absolute IDQ p180 kit. Results: We found 22 clinical chemistry analytes significantly associated with hemolysis, 25 with icterus, and 24 with lipemia (p < 0.0001). Serum metabolites (n = 27) were associated with all of hemolysis, icterus, and lipemia (p < 0.05). The PC ae C36 2 had exhibited a significant association with pre-analytical factors corresponding to the third (pre-centrifugation delay between processing) and sixth (post-centrifugation) elements of the SPREC. Conclusions: This study showed the association of the serum index and pre-analytical factors with serum metabolite profiles. In addition, the association of pre-analytical factors with serum metabolite concentrations would corroborate the utility of SPRECs for the quality control of biobanked serum samples.

Human transcriptome analysis of acute responses to glucose ingestion reveals the role of leukocytes in hyperglycemia-induced inflammation.

Glucose ingestion-induced hyperglycemia has been known to induce inflammation, which is related to the pathogenesis of diabetic complications. To examine acute gene expression responses to physiological oral glucose ingestion in human circulating leukocytes, we conducted a microarray study of human circulating leukocytes sampled before, 1 h after, and 2 h after glucose ingestion in community-based participants without previous histories of diabetes (n = 60). Ingestion of 75 g glucose successfully induced acute hyperglycemia (glucose concentration 91.6 ± 5.3 mg/dl for fasting and 180.7 ± 48.5 mg/dl for 1 h after glucose ingestion). Oral glucose ingestion significantly increased the expressions of 23 genes and decreased the expressions of 13 genes [false discovery rate (FDR) P value <0.05]. These genes are significantly involved in immunity by way of natural killer cell-mediated immunity, granulocyte-mediated immunity, and the cytokine-mediated signaling pathway (FDR P value <0.05). The present study demonstrated 36 genes that showed acute gene expression change in human leukocytes within 1 h after glucose ingestion, suggesting that leukocytes participate in the inflammatory process induced by acute hyperglycemia. We believe that these results will provide some basic insight into the role of leukocytes in hyperglycemia-induced inflammation and the pathogenesis of diabetic complications.

Molecular signatures in response to Isoliquiritigenin in lymphoblastoid cell lines.

Isoliquiritigenin (ISL) has been known to induce cell cycle arrest and apoptosis of various cancer cells. However, genetic factors regulating ISL effects remain unclear. The aim of this study was to identify the molecular signatures involved in ISL-induced cell death of EBV-transformed lymphoblastoid cell lines (LCLs) using microarray analyses. For gene expression and microRNA (miRNA) microarray experiments, each of 12 LCL strains was independently treated with ISL or DMSO as a vehicle control for a day prior to total RNA extraction. ISL treatment inhibited cell proliferation of LCLs in a dose-dependent manner. Microarray analysis showed that ISL-treated LCLs represented gene expression changes in cell cycle and p53 signaling pathway, having a potential as regulators in LCL survival and sensitivity to ISL-induced cytotoxicity. In addition, 36 miRNAs including five miRNAs with unknown functions were differentially expressed in ISL-treated LCLs. The integrative analysis of miRNA and gene expression profiles revealed 12 putative mRNA-miRNA functional pairs. Among them, miR-1207-5p and miR-575 were negatively correlated with p53 pathway- and cell cycle-associated genes, respectively. In conclusion, our study suggests that miRNAs play an important role in ISL-induced cytotoxicity in LCLs by targeting signaling pathways including p53 pathway and cell cycle.

Copy number variation at leptin receptor gene locus associated with metabolic traits and the risk of type 2 diabetes mellitus.

BACKGROUND: Recent efforts have been made to link complex human traits and disease susceptibility to DNA copy numbers. The leptin receptor (LEPR) has been implicated in obesity and diabetes. Mutations and genetic variations of LEPR gene have been discovered in rodents and humans. However, the association of DNA copy number variations at the LEPR gene locus with human complex diseases has not been reported. In an attempt to study DNA copy number variations associated with metabolic traits and type 2 diabetes mellitus (T2DM), we targeted the LEPR gene locus in DNA copy number analyses. RESULTS: We identified DNA copy number variations at the LEPR gene locus among a Korean population using genome-wide SNP chip data, and then quantified copy numbers of the E2 DNA sequence in the first two exons overlapped between LEPR and LEPROT genes by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method. Among the non-diabetic subjects (n = 1,067), lower E2 DNA copy numbers were associated with higher fasting glucose levels in men (p = 1.24 x 10(-7)) and women (p = 9.45 x 10(-5)), as well as higher total cholesterol levels in men (p = 9.96 x 10(-7)). In addition, the significant association between lower E2 DNA copy numbers and lower level of postprandial 2 hr insulin was evident only in non-diabetic women, whereas some obesity-related phenotypes and total cholesterol level exhibited significant associations only in non-diabetic men. Logistic regression analysis indicated that lower E2 DNA copy numbers were associated with T2DM (odds ratio, 1.92; 95% CI, 1.26-2.96; p < 0.003) in our nested case-control study. Interestingly, the E2 DNA copy number exhibited a negative correlation with LEPR gene expression, but a positive correlation with LEPROT gene expression. CONCLUSIONS: This work suggests that a structural variation at the LEPR gene locus is functionally associated with complex metabolic traits and the risk of T2DM.

Validity of the zygosity questionnaire and characteristics of zygosity-misdiagnosed twin pairs in the Healthy Twin Study of Korea.

Determining valid zygosity is a basic and important requirement in a twin study, because misdiagnosing zygosity leads to biased results. The Healthy Twin Study has collected data from adult like-sex twins and their families since 2005. In the study, a questionnaire to determine zygosity was developed comprising four questions; one concerning the degree of resemblance, and three concerning the degree of confusion by the resemblance. Among 2,761 individuals (624 twin pairs) of twin and their families, 406 pairs of twins (mean age 38.3, 63.5% women) with both questionnaire and genotype information were selected to examine the validity of the zygosity questionnaire using 16 short tandem repeat markers. We first determined individual zygosity including undetermined category, and then decided the zygosity of a twin pair using a decision tree. Sensitivity of questionnaire diagnosis was 98.8% for monozygotic (MZ) and 88.9% for dizygotic (DZ) twins, and positive predictive value was 97.2% for MZ and 95.0% for DZ. When we compared correctly and wrongly diagnosed twin pairs, misdiagnosed DZ twins (nine pairs) showed striking similarity in stature or obesity even exceeding that of true MZ twins. Our finding suggests that a parsimonious questionnaire method of diagnosing the zygosity will be useful, and adding physical or physiological measurements to a questionnaire of zygosity diagnosis will either confound the correct diagnosis or reduce the efficiency of the study compared with using questionnaire alone or with introducing genotyping.

[Comparison of Helicobacter pylori eradication rate in patients with non-ulcer dyspepsia and peptic ulcer diseases according to proton pump inhibitors].

BACKGROUND/AIMS: Conflicting results have been reported whether patients with non-ulcer dyspepsia (NUD) respond differently to Helicobacter pylori (H. pylori) eradication treatment compared with patients with peptic ulcer diseases (PUD). The aim of this study was to evaluate any difference in H. pylori eradication rates between patients with NUD and PUD according to each proton pump inhibitor (PPI). METHODS: From September, 2004 to April, 2007, we retrospectively reviewed 2,297 patients with NUD (1,050 patients) or PUD (1,247 patients) infected with H. pylori. All patients received a standard 1 week triple therapy comprising of one of the five PPIs (pantoprazole, esomeprazole, omeprazole, lansoprazole, rabeprazole), clarithromycin and amoxicillin. The follow-up H. pylori test was performed 4 weeks after the completion of therapy. RESULTS: There was no significant difference in the eradication rates between the two groups. In comparison of eradication rates according to PPI, omeprazole- based triple therapy group showed higher eradication rate than other groups in patients with NUD, but not in patients with PUD. CONCLUSIONS: This study failed to show any difference in H. pylori eradication rate between patients with NUD and PUD. There is no convincing evidence that the eradication rate may be affected by different PPI.

[Effectiveness of 10 day-sequential therapy for Helicobacter pylori eradication in Korea].

BACKGROUND/AIMS: Antibiotic resistance and poor compliance are the main causes of Helicobacter pylori (H. pylori) eradication failure. Proton pump inhibitor (PPI)-based triple therapy is the most preferred regimen in clinical practice. However, a critical fall in the H. pylori eradication rate has been observed in the recent years. A novel 10 day-sequential therapy consists of five days of dual therapy followed by five days of triple therapy regimen has recently been described. We aimed to evaluate whether 10 day-sequential therapy eradicated H. pylori infection better than the PPI-based triple therapy in Korea. METHODS: 158 patients with proven H. pylori infection were randomized to receive either 10 day-sequential therapy (20 mg of omeprazole, 1.0 g of amoxicillin, each administered twice daily for the first 5 days, followed by 20 mg of omeprazole, 500 mg of clarithromycin, 500 mg of metronidazole, each administered twice daily for the remaining 5 days) or PPI-based triple therapy (20 mg of omeprazole, 1.0 g of amoxicillin, 500 mg of clarithromycin, each administered twice daily for 1 week). Outcome of eradication therapy was assessed 8 weeks after the cessation of treatment. RESULTS: Eradication rates of 10 day-sequential therapy and PPI-based triple therapy were 77.9% (60/77) and 71.6% (58/81) by intention to treat analysis, respectively (p=0.361). By per protocol analysis, eradication rates of 10 day-sequential therapy and triple therapy were 85.7% (60/70) and 76.6% (58/76), respectively (p=0.150). There were no significant differences in adverse event rates and treatment compliance between two groups. CONCLUSIONS: The 10 day-sequential therapy regimen failed to achieve significantly higher eradication rates than PPI-based triple therapy.

Instability at Short Tandem Repeats in Lymphoblastoid Cell Lines.

OBJECTIVES: Epstein Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) are a useful biological resource, however, genomic variations can happen during the generation and immortalization processes of LCLs. The purpose of this study was to identify genomic variations in LCL DNA compared with matched blood DNA using short tandem repeats (STRs) analysis. METHODS: We analyzed 15 STRs with blood DNA and their matched LCL DNA samples from 6645 unrelated healthy individuals. RESULTS: Mutations (such as repeat variations and triallelic patterns) of 15 STR loci were detected in 612 LCL DNAs (9.2% of total) without mutations in their matched blood DNA. The repeat variations of 15 STRs were detected in 526 LCL DNAs (mutation rate = 0.0792) and triallelic patterns were identified in 123 (mutation rate = 0.0185). Among 15 STRs, the most common repeat variations (n = 214, mutation rate = 0.0322) and triallelic patterns (n = 17, mutation rate = 0.0026) were found at FGA locus. CONCLUSION: Our study shows that mutations in STRs can occur during generation and immortalization of LCLs.

Opening of the national biobank of Korea as the infrastructure of future biomedical science in Korea.

On April 26, 2012, the Korea National Institute of Health officially held the opening ceremony of newly dedicated biobank building, 'NationalBiobank of Korea'. The stocked biospecimens and related information have been distributed for medical and public health researches. The Korea Biobank Project, which was initiated in 2008, constructed the Korea Biobank Network consisting of the National Biobank of Korea (NBK) with 17 regional biobanks in Korea. As of December 2011, a total of 525,416 biospecimens with related information have been secured: 325,952 biospecimens from the general population obtained through cohort studies and 199,464 biospecimens of patients from regional biobanks. A large scale genomic study, Korea Association Resource (KARE) and many researches utilized the biospecimens secured through Korea Genome Epidemiology Study (KoGES) and Korea Biobank Project (KBP). Construction of 'National Biobank of Korea', a dedicated biobank building at Osong means that NBK can manage and check quality of the biospecimens with promising distribution of 26 million vials of biospecimen, which provide the infrastructure for the development of health technology in Korea. The NBK and the National Library of Medicine (to be constructed in 2014) will play a central role in future biomedical research in Korea.

National Biobank of Korea: Quality control Programs of Collected-human Biospecimens.

Personalized medicine is emerging as a main paradigm for risk prediction, pre-diagnosis, and effective prevention and treatment of disease. A large number of human biospecimens and their clinical data are essential resources for the success of personalized medicine as well as other biomedical research. The National Biobank of Korea (NBK) has collected well-annotated and high quality human biospecimens, and distributes them to the Korean biomedical scientists, through the Korea Biobank Project (KBP). The ultimate goal of NBK activities is to promote biomedical research and public health. As of December- 2011, the NBK has collected various human biospecimens from 525,416 participants including 325,952 Korean populations and 199,464 patients. The purpose of this paper is to introduce the KBP and quality control programs for collection of human biospecimens with high quality of NBK.

Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.

To identify the genetic bases for nine metabolic traits, we conducted a meta-analysis combining Korean genome-wide association results from the KARE project (n = 8,842) and the HEXA shared control study (n = 3,703). We verified the associations of the loci selected from the discovery meta-analysis in the replication stage (30,395 individuals from the BioBank Japan genome-wide association study and individuals comprising the Health2 and Shanghai Jiao Tong University Diabetes cohorts). We identified ten genome-wide significant signals newly associated with traits from an overall meta-analysis. The most compelling associations involved 12q24.11 (near MYL2) and 12q24.13 (in C12orf51) for high-density lipoprotein cholesterol, 2p21 (near SIX2-SIX3) for fasting plasma glucose, 19q13.33 (in RPS11) and 6q22.33 (in RSPO3) for renal traits, and 12q24.11 (near MYL2), 12q24.13 (in C12orf51 and near OAS1), 4q31.22 (in ZNF827) and 7q11.23 (near TBL2-BCL7B) for hepatic traits. These findings highlight previously unknown biological pathways for metabolic traits investigated in this study.

Bacterial Contamination of Blood DNA Samples is Associated with Donor's Health Condition.

Bacterial contamination often occurs in human blood DNA samples, possibly due to bacteremia or an inappropriate procedure during sample preparation. This study aimed at analyzing the clinical significance of bacterial DNA contamination in human blood DNA samples and to assess its influence on experimental data. DNA samples (N = 1359) were randomly selected from population-based cohort samples to determine bacterial DNA contamination by polymerase chain reaction and direct DNA sequencing. Bacterial DNA contaminated samples (N = 150) were then assessed for experimental quality of single nucleotide polymorphism (SNP) chip data, compared with uncontaminated DNA samples (N = 1209). DNA sequencing data showed that a major source of bacterial contaminants was derived from Alcaligenes species. The occurrence of bacterial DNA contaminations was significantly associated with some clinical variables including a postprandial glucose level at 60 min, % body fat, and waist-to-hip ratio. It was also found that there was no difference of SNP call rates between bacterial DNA contaminated samples and uncontaminated DNA samples. This study showed that bacterial DNA contamination in human blood samples was related to donor's health condition, suggesting that the occurrence of bacterial DNA contamination may provide useful health information of blood donors and a potential tool for human disease genomics.

The safety and efficacy of second-line single docetaxel (75 mg/m²) therapy in advanced non-small cell lung cancer patients who were previously treated with platinum-based chemotherapy.

PURPOSE: When used in the second-line setting, single-agent chemotherapy has produced response rates of more than 10% or median survival times greater than 4 months. We studied the safety and efficacy of using second-line single docetaxel (75 mg/m²) for advanced NSCLC patients who were previously treated with platinum-based chemotherapy in Korea. MATERIALS AND METHODS: Thirty-three patients with advanced NSCLC received chemotherapy from May 2002 to January 2005. We retrospectively reviewed the charts of these patients. The patients received 75 mg/m² of doxetaxel on day 1 and this was repeated at 3-week intervals. RESULTS: The median age was 63 years (range: 42~77 years); 16 patients had adenocarcinoma and 8 patients had squamous cell carcinoma. The median number of cycles was 4 (range: 1~7 cycles). Of the 33 patients, 6 patients had partial responses, 13 patients had stable disease and 14 patients had progressive disease. The response rate was 18.2%. The median overall survival was 11 months (range: 7~15 months), and the median progression free survival was 5 months (range: 3~7 months). The median response duration was 5 months (range: 4~9 months). A total of 137 cycles were evaluated for toxicity. We observed grade 3 or 4 neutropenia in 79 cycles (57.6%), grade 3 or 4 leukopenia in 46 cycles (33.6%), and grade 3 febrile neutropenia in 2 cycles (1.5%). The median nadir day was day 9 (range: day 5~19), and the median number of G-CSF injections was 2 (range: 0~6). The most common non-hematologic toxicities were myalgia/arthralgia and neurotoxicity, but any grade 3 or 4 non-hematologic toxicity was not observed. The major toxicity of this therapy was neutropenia. The absolute neutrophil count decreased relatively rapidly, but neutropenic fever or related infection was rare. There were no treatment-related deaths. CONCLUSION: These results revealed a satisfactory response rate (18.2%) with using docetaxel as the second-line chemotherapy for NSCLC. The second-line docetaxel was an active and well-tolerated regimen in patients with advanced NSCLC pretreated with platinum-based chemotherapy.