An association study of 13 SNPs from seven candidate genes with pediatric asthma and a preliminary study for genetic testing by multiple variants in Taiwanese population.

INTRODUCTION: Asthma is one of the most common chronic diseases in children. It is caused by complex interactions between various genetic factors and exposures to environmental allergens and irritants. Because of the heterogeneity of the disease and the genetic and cultural differences among different populations, a proper association study and genetic testing for asthma and susceptibility genes is difficult to perform. MATERIALS AND METHODS: We assessed 13 single-nucleotide polymorphisms (SNPs) in seven well-known asthma susceptibility genes and looked for association with pediatric asthma using 449 asthmatic subjects and 512 non-asthma subjects in Taiwanese population. RESULTS: CD14-159 C/T and MS4A2 Glu237Gly were identified to have difference in genotype/allele frequencies between the control group and asthma patients. Moreover, the genotype synergistic analysis showed that the co-contribution of two functional SNPs was riskier or more protective from asthma attack. Our study provided a genotype synergistic method for studying gene-gene interaction on polymorphism basis and genetic testing using multiple polymorphisms.

The polymorphisms of protein-tyrosine phosphatase receptor-type delta gene and its association with pediatric asthma in the Taiwanese population.

We previously reported an association between genetic differences of pediatric asthma subtypes and a short tandem repeat (STR) marker, D9S286. It has been known that the protein-tyrosine phosphatase receptor-type delta (PTPRD) gene is located downstream of D9S286 and that the physical distance between them is about 0.25 Mb. We selected and conducted genotyping on 76 single-nucleotide polymorphisms (SNPs) that encircle the genomic region of PTPRD in Taiwanese children with or without asthma. A total of 996 subjects were divided into testing group (674 subjects) and validation group (322 subjects). The results were further validated with the third subject group (611 subjects) recruited from different geographical regions. After Bonferroni correction, 3 out of 80 SNPs were found to be strongly significant (P < 0.05/76 = 0.000658) in the allele frequency test. This association was confirmed by validation groups. The results indicate that polymorphisms of PTPRD are strongly associated with pediatric bronchial asthma in the Taiwanese population.

Association of single nucleotide polymorphisms of MD-1 gene with pediatric and adult asthma in the Taiwanese population.

BACKGROUND AND PURPOSE: MD-1 (myeloid differentiation 1; also known as Ly86, lymphocyte antigen 86), interacting with radioprotective 105, plays an important role in the Toll-like receptor 4 signaling pathway. It has been suggested that MD-1 is involved in the development of inflammation and atopic diseases. The purpose of this study was to investigate the genetic association of single nucleotide polymorphisms (SNPs) of MD-1 and asthma in the Taiwanese population. METHODS: Genotyping 34 SNPs in the MD-1 gene region was performed in a case-control study involving 281 children with asthma and 237 controls. A further 309 children and adults were genotyped for the SNP rs7740529 only, for validation of an identified association. RESULTS: In intron 1, we identified an SNP, rs7740529, which is associated with asthma in Taiwanese children (p=0.0358). Inclusion of a further 309 subjects increased the significance of the association (p=0.0093), and also demonstrated that rs7740529 is associated with adult asthma. The TT genotype confers risk of both pediatric and adult asthma. CONCLUSION: These results suggest that MD-1 could be a susceptible gene for asthma in the Taiwanese population.

Prediction of complex traits based on the epistasis of multiple haplotypes.

Analysis of epistasis, or gene-gene interactions, is of particular importance for revealing the molecular mechanisms of complex human diseases. Multiple genes, each of which has a moderate effect, might interact and produce a complex phenotypic trait. In this paper, we present a novel method of epistasis analysis, utilizing multiple phase-resolved haplotypes residing in different genomic regions. Prediction models can then be derived from the epistasis to indicate the susceptibility of a person to a dichrotomous phenotypic trait. The simulation results showed that the prediction accuracy of this method is dependent on the penetrance rate of the underlying model. The computation cost, on the other hand, is dependent on the number of genomic regions involved for the complex phenotypic trait.

The high prevalence of the poor and ultrarapid metabolite alleles of CYP2D6, CYP2C9, CYP2C19, CYP3A4, and CYP3A5 in Taiwanese population.

Genetic polymorphisms of drug metabolizing enzymes, such as cytochromes P450 (CYPs), play major roles in the variations of drug responsiveness in human. The aim of this study is to identify the high prevalence (minor allele frequencies >1%) of the abnormal metabolite alleles of CYP2C9, CYP2C19, CYP2D6, CYP3A4, and CYP3A5 in the Taiwanese population. The genotyping of the functional single nucleotide polymorphisms (SNPs) of CYPs were conducted by direct exon sequencing in 180 Taiwanese volunteers. Twenty-one unique SNPs including three newly identified SNPs were detected in the Taiwanese population. Six of the 21 SNPs in five genes showed frequencies more than 1%. The results indicated that it could be very useful and important in developing an inexpensive, convenient, and precise genotyping method for the high prevalence of CYPs metabolizing abnormal alleles in the Taiwanese population.

Suppression of primary breast, colon, gastric and bladder cancers cell growth in vitro by CKBM, a natural product.

CKBM is a product composed of natural ingredients and had been shown to possess certain anti-cancer effects in vitro and in vivo. The aim of the present study is to analyze the chemosensitivity in the treatment of primary colon, breast, gastric and bladder cancer cells by CKBM. A total of 77 patients with cancers of breast, colon, stomach or bladder were included in the present study. Primary cancer cells were isolated from the surgical removed tumors and treated with various dosages of CKBM for 5 days. ATP is then extracted and measured by luminescence assay. CKBM treatment inhibited primary colon, breast, gastric and bladder cancer growth dose-dependently. The IC values were smaller from tumor cells at early stages, when compared with the ones at later stages. The present study strongly indicated that CKBM exerted cytotoxic effect on primary cancer cells.

Cell Cycle Arrest by a Natural Product via G2/M Checkpoint.

CKBM is a natural product that exhibits a novel anti-tumor activity through the induction of cell cycle arrest and apoptosis. We have investigated its effects on cell cycle regulation using a gastric cancer cell line, AGS. The effects of CKBM on cell proliferation, cell cycle regulation and apoptosis were analyzed using BrdU (5-bromo-2'-deoxyuridine) cell proliferation assay and flow cytometric analysis, respectively. Specific cellular protein expressions were measured using Western blot analysis. Flow cytometric analysis indicated that CKBM induced G2/M cell cycle arrest and apoptosis, whereas differential protein expressions of p21, p53 and 14-3-3sigma (stratifin) using Western blot analysis were enhanced. The differential expressions of p21, p53 and 14-3-3sigma in AGS cancer cells after CKBM treatment may play critical roles in the G2/M cell cycle arrest that blocks cell proliferation and induces apoptosis.

Anti-tumorigenic and Pro-apoptotic effects of CKBM on gastric cancer growth in nude mice.

Natural botanical products can be integrated with western medicine to optimize the treatment outcome, increase immune function and minimize the side effects from western drug treatment. CKBM is a combination of herbs and yeasts formulated based on traditional Chinese medicinal principles. Previous study has demonstrated that CKBM is capable of improving immune responsiveness through the induction of cytokine mediators, such as TNF-alpha and IL-6. In this study, we aimed to investigate the effect of this immunomodulatory drug on gastric cancer growth using a human xenograft model. Gastric cancer tissues were implanted subcutaneously into athymic nude mice followed by a 14-day or 28-day of CKBM treatment. Results showed that higher doses of CKBM (0.4 or 0.8 ml/mouse/day) produced a dose-dependent inhibitory effect on gastric tumor growth after 28-day drug treatment. This was associated with a decrease of cellular proliferation by 30% with concomitant increase in apoptosis by 97% in gastric tumor cells when compared with the control group. In contrast, CKBM showed no effect on angiogenesis in gastric tumors. This study demonstrates the anti-tumorigenic action of CKBM on gastric cancer probably via inhibition of cell proliferation and induction of apoptosis, and provides future potential targets of this drug candidate on cancer therapy.

Identification and preliminary clinical evaluation of a 50.8-kDa serum marker for prostate cancer.

OBJECTIVES: To identify a 50.8-kDa biomarker to perform a preliminary clinical evaluation of its utility as an aid in the early detection of prostate cancer. METHODS: The 50.8-kDa protein, previously called NMP48, was partially purified from the serum of an individual with prostate cancer and identified by peptide mass fingerprinting of tryptic peptides from an in-gel digest. Serum samples were obtained from men with biopsy-confirmed prostate cancer, high-grade prostatic intraepithelial neoplasia, and benign histologic features, from men with clinically defined benign prostatic hyperplasia, and from controls without prostatic disease. These samples were analyzed for the presence of the biomarker by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. RESULTS: The 50.8-kDa protein was identified by peptide mass fingerprinting as being related to vitamin D-binding protein. It was found in 96% of the sera from individuals with prostate cancer (n = 52) including 11 of 12 specimens that exhibited prostate-specific antigen values of less than 4 ng/mL. The 50.8-kDa protein was found in 10 of 19 samples from men with prostatic intraepithelial neoplasia; however, it was not detected in the sera of 5 (75%) of 20 individuals with benign prostatic histologic features, 7 (70%) of 10 with clinical benign prostatic hyperplasia, 8 (80%) of 10 patients who had previously undergone radical prostatectomy, or 48 (96%) of 50 specimens from healthy controls. CONCLUSIONS: Although the study cohort was relatively small, the data suggest that an assay for the 50.8-kDa protein may be useful for the early detection of prostate cancer. Additional elucidation of its structure may yield insight into the development of this disease.