Evaluation of a Direct Reverse Transcription Loop-Mediated Isothermal Amplification Method without RNA Extraction (Direct RT-LAMP) for the Detection of Lymph Node Metastasis in Early Breast Cancer / Journal of the Korean Cancer Association, 대한암학회지

Purpose@#Assessing lymph node metastasis, tumor-derived DNA, or tumor-derived RNA has previously been studied in place of immunohistochemical assay. Because a direct reverse transcription loop-mediated isothermal amplification method (direct RT-LAMP) has been previously developed in order to rapidly identify viruses in place of RNA extraction, our team hypothesized that a direct RT-LAMP assay can be employed as a substitute in order to detect tumor involvement of lymph nodes within breast cancer patients. @*Materials and Methods@#A total amount of 92 lymph nodes removed across 40 patients possessing breast cancer were collected at Kyungpook National University Chilgok Hospital between the months of November 2015 and February 2016. All samples were then evaluated and contrasted via both a direct RT-LAMP assay and routine histopathologic examination. @*Results@#The sensitivity and specificity of the direct RT-LAMP assay were 85.7% and 100%, respectively. The positive predictive value and negative predictive value were 100% and 94.4%, respectively. @*Conclusion@#Direct RT-LAMP assay is capable of facilitating the detection of sentinel lymph node metastasis within breast cancer patients intraoperatively possessing an excellent sensitivity via a cost-effective and time-saving manner.

Uracil-DNA glycosylase-treated reverse transcription loop-mediated isothermal amplification for rapid detection of avian influenza virus preventing carry-over contamination

Here, we describe a uracil-DNA glycosylase (UNG)-treated reverse transcription loop-mediated isothermal amplification (uRT-LAMP) for the visual detection of all subtypes of avian influenza A virus (AIV). The uRT-LAMP assay can prevent unwanted amplification by carryover contamination of the previously amplified DNA, although the detection limit of the uRT-LAMP assay is 10-fold lower than that of the RT-LAMP without a UNG treatment. To the best of our knowledge, this is the first successful application of deoxyuridine triphosphate/UNG strategy in RT-LAMP for AIV detection, and the assay can be applied for the rapid, and reliable diagnosis of AIVs, even in contaminated samples.

Replication of the results of genome-wide and candidate gene association studies on telomere length in a Korean population

BACKGROUND/AIMS: A number of genome-wide and candidate gene association studies have identified polymorphisms associated with telomere length in Caucasian populations. This study was conducted to determine the impacts of 17 polymorphisms identified in Caucasians on telomere length in a Korean population. METHODS: Ninety-four healthy individuals were enrolled in this study. Relative telomere length of chromosomes from peripheral blood samples was measured using quantitative polymerase chain reaction. RESULTS: Two polymorphisms, rs10936599 of MYNN and rs412658 of ZNF676, were found to be associated w ith telomere length (under dominant model, p = 0.04; under recessive model, p = 0.001). Three polymorphisms, rs2853669, rs7705526, and rs2736108, at the TERT locus were also associated with telomere length (under recessive model, p = 0.01, p = 0.02, and p = 0.01, respectively). The genotypes of the five polymorphisms associated with short telomere length were considered bad genotypes; telomere length was significantly decreased with increasing number of bad genotypes (p= 1.7 x 10(-5)). CONCLUSIONS: We have identified polymorphisms associated with telomere length in a Korean population.

Genome-Wide Association Study of Lung Cancer in Korean Non-Smoking Women

Lung cancer in never-smokers ranks as the seventh most common cause of cancer death worldwide, and the incidence of lung cancer in non-smoking Korean women appears to be steadily increasing. To identify the effect of genetic polymorphisms on lung cancer risk in non-smoking Korean women, we conducted a genome-wide association study of Korean female non-smokers with lung cancer. We analyzed 440,794 genotype data of 285 cases and 1,455 controls, and nineteen SNPs were associated with lung cancer development (P < 0.001). For external validation, nineteen SNPs were replicated in another sample set composed of 293 cases and 495 controls, and only rs10187911 on 2p16.3 was significantly associated with lung cancer development (dominant model, OR of TG or GG, 1.58, P = 0.025). We confirmed this SNP again in another replication set composed of 546 cases and 744 controls (recessive model, OR of GG, 1.32, P = 0.027). OR and P value in combined set were 1.37 and < 0.001 in additive model, 1.51 and < 0.001 in dominant model, and 1.54 and < 0.001 in recessive model. The effect of this SNP was found to be consistent only in adenocarcinoma patients (1.36 and < 0.001 in additive model, 1.49 and < 0.001 in dominant model, and 1.54 and < 0.001 in recessive model). Furthermore, after imputation with HapMap data, we found regional significance near rs10187911, and five SNPs showed P value less than that of rs10187911 (rs12478012, rs4377361, rs13005521, rs12475464, and rs7564130). Therefore, we concluded that a region on chromosome 2 is significantly associated with lung cancer risk in Korean non-smoking women.

RET Fusion Genes in Korean Non-Small Cell Lung Cancer

Recently, rearranged during transfection (RET) fusions have been identified in approximately 1% of non-small cell lung cancer (NSCLC). To know the prevalence of RET fusion genes in Korean NSCLCs, we examined the RET fusion genes in 156 surgically resected NSCLCs using a reverse transcriptase polymerase chain reaction. Two KIF5B-RET fusions and one CCDC6-RET fusion were identified. All three patients were females and never smokers with adenocarcinomas. RET fusion genes were mutually exclusive from EGFR, KRAS mutations and EML4-ALK fusion. RET fusion genes occur 1.9% (3 of 156) of surgically treated NSCLC patients in Koreans.

EML4-ALK Fusion Gene in Korean Non-Small Cell Lung Cancer

A fusion gene between echinoderm microtubule-associated protein-like 4 (EML4) and the anaplastic lymphoma kinase (ALK) has been identified in non-small cell lung cancers (NSCLCs). Although a few studies have evaluated EML4-ALK fusion genes in Korean NSCLCs, the prevalence of different EML4-ALK fusion variants has yet to be clearly assessed. Herein, we have examined the profiles of EML4-ALK fusion gene variants in Korean patients of NSCLCs. EML4-ALK fusion genes have been detected in 10 (6.0%) of 167 patients of NSCLCs and in 9 (7.4%) of 121 patients of adenocarcinoma. Of the 10 patients with fusion genes identified, 8 (80%) were E13;A20 (variant 1) and 2 (20%) were E6;A20, with an additional 33-bp sequence derived from intron 6 of EML4 (variant 3b). These results indicate that the profiles of EML4-ALK fusion gene variants in Korean patients of NSCLC may differ from those in other ethnic populations. Herein, we describe for the first time the profiles of EML4-ALK fusion variants of Korean patients with NSCLCs.

Telomerase Activity and the Risk of Lung Cancer

Telomerase play a key role in the maintenance of telomere length and chromosome integrity. We have evaluated the association between telomerase activity and the risk of lung cancer in peripheral blood. Telomerase activity in peripheral blood mononuclear cells was measured by a PCR-designed telomeric repeat amplification protocol in 63 lung cancer patients and 190 healthy controls that were matched for age, gender, and smoking status. Telomerase activity was significantly lower in the lung cancer patients than in controls (mean +/- standard deviation; 1.32 +/- 1.65 vs 2.60 +/- 3.09, P < 1 x 10(-4)). When telomerase activity was categorized into quartiles based on telomerase activity in the controls, the risk of lung cancer increased as telomerase activity reduced (Ptrend = 1 x 10(-4)). Moreover, when the subjects were categorized based on the median value of telomerase activity, subjects with low telomerase activity were at a significantly increased risk of lung cancer compared to subjects with high telomerase activity (adjusted odds ratio = 3.05, 95% confidence interval = 1.60-5.82, P = 7 x 10-4). These findings suggest that telomerase activity may affect telomere maintenance, thereby contributing to susceptibility to lung cancer.

Association between Lung Cancer Susceptibility Variants Identified by Genome-Wide Association Studies and the Survival of Non-Small Cell Lung Cancer

PURPOSE: Nowadays, chromosomal regions containing genes associated with the risk of lung cancer are identified by a number of genome-wide association studies (GWASs). As part of the study, GWAS has identified the association of six chromosomal regions, 1q23, 4q22, 4q31, 5p15, 6p21, and 15q25, as being associated with lung cancer risk in the European population. We investigated the impact of genetic variants identified in GWASs for lung cancer susceptibility on the survival outcomes in patients with early stage non-small cell lung cancer (NSCLC). MATERIALS AND METHODS: Three hundred and sixty-three patients with surgically resected NSCLC were enrolled. Eight single nucleotide polymorphisms (SNPs), rs2808630 on 1q23, rs7671167 on 4q22, rs1489759 and rs2202507 on 4q31, rs2736100 and rs402710 on 5p15, rs1052486 on 6p21 and rs16969968 on 15q25, were genotyped using a polymerase chain reaction-restriction fragment length polymorphism assay. The associations between genotypes and overall survival (OS) and disease-free survival (DFS) were analyzed. RESULTS: None of the eight SNPs were significantly associated with OS or DFS. In addition, when the patients were categorized according to age, gender, smoking status, tumor histology and pathologic stage, there were no significant associations between the eight SNPs and the survival outcomes. CONCLUSION: These results suggest that the genetic variants identified by GWASs for lung cancer susceptibility may not affect the prognosis of early stage NSCLC.

A Functional Polymorphism in the CHRNA3 Gene and Risk of Chronic Obstructive Pulmonary Disease in a Korean Population

A genome-wide association study has identified the 15q25 region as being associated with the risk of chronic obstructive pulmonary disease (COPD) in Caucasians. This study intended as a confirmatory assessment of this association in a Korean population. The rs6495309C > T polymorphism in the promoter of nicotinic acetylcholine receptor alpha subunit 3 (CHRNA3) gene was investigated in a case-control study that consisted of 406 patients with COPD and 394 healthy control subjects. The rs6495309 CT or TT genotype was associated with a significantly decreased risk of COPD when compared to the rs6495309 CC genotype (adjusted odds ratio = 0.69, 95% confidence interval = 0.50-0.95, P = 0.023). The effect of the rs6495309C > T on the risk of COPD was more evident in moderate to very severe COPD than in mild COPD under a dominant model for the variant T allele (P = 0.024 for homogeneity). The CHRNA3 rs6495309C > T polymorphism on chromosome 15q25 is associated with the risk of COPD in a Korean population.

Polymorphisms in Apoptosis-Related Genes and TP53 Mutations in Non-Small Cell Lung Cancer

Apoptosis plays an essential role in the elimination of mutated or transformed cells from the body. Therefore, polymorphisms of apoptosis-related genes may lead to an alteration in apoptotic capacity, thereby affecting the occurrence of TP53 mutations in lung cancer. We investigated the relationship between potentially functional polymorphisms of apoptosis-related genes and TP53 mutations in non-small cell lung cancer (NSCLC). Twenty-seven single nucleotide polymorphisms in 20 apoptosis-related genes were genotyped by a sequenome mass spectrometry-based genotyping assay in 173 NSCLCs and the associations with TP53 mutations in the entire coding exons (exons 2-11), including splicing sites of the gene, were analyzed. None of the 27 polymorphisms was significantly associated with the occurrence of TP53 mutations. This suggests that apoptosis-related genes may not play an important role in the occurrence of TP53 mutations in lung cancer.

TP53 Mutations in Korean Patients with Non-small Cell Lung Cancer

Although TP53 mutations have been widely studied in lung cancer, the majority of studies have focused on exons 5-8 of the gene. In addition, TP53 mutations in Korean patients with lung cancers have not been investigated. We searched for mutations in the entire coding exons, including splice sites of the gene, in Korean patients with non-small cell lung cancer (NSCLC). Mutations of the gene were determined by direct sequencing in 176 NSCLCs. Sixty-nine mutations (62 different mutations) were identified in 65 tumors. Of the 62 mutations, 12 were novel mutations. TP53 mutations were more frequent in males, ever-smokers and squamous cell carcinomas than in females, never-smokers and adenocarcinomas, respectively (all comparisons, P<0.001). Missense mutations were most common (52.2%), but frameshift, nonsense, and splice-site mutations were frequently observed at frequencies of 18.8%, 15.9% and 10.1%, respectively. Of the 69 mutations, 9 (13.0%) were found in the oligomerization domain. In addition, the proportion of mutations in the oligomerization domain was significantly higher in adenocarcinomas than in squamous cell carcinomas (23.5% vs. 2.9%, P=0.01). Our study provides clinical and molecular characteristics of TP53 mutations in Korean patients with NSCLCs.

The Relationship between MDR1 Polymorphisms and the Response to Etoposide/Cisplatin Combination Chemotherapy in Small Cell Lung Cancer / 결핵및호흡기질환

No abstract available.

DNMT3b 39179G>T polymorphism and risk of primary lung cancer in Koreans / 대한내과학회지

BACKGROUND: DNA methylation is the main mechanism of epigenetic modification of genes and plays an important role in carcinogenesis. The methylation of promoter can inactivate the tumor suppressor gene by repression of transcription. We investigated the relationship between the 39179G>T (-579bp from exon 1B) polymorphism in DNMT3b gene, which is involved in de novo methylation, and the risk of primary lung cancer in Koreans. METHODS: The DNMT3b 39179G>T genotypes were determined using PCR-RFLP method in 392 primary lung cancer patients and 391 healthy controls who were frequency (1:1) matched based on age and sex. RESULTS: Although the frequencies of GG, GT, TT genotypes among cases (0.8%, 19.9%, 79.3%, respectively) were not significantly different from those among controls (1.5%, 25.1%, 73.4%, respectively), the frequency of wild-type G allele among cases was significantly different from that of controls (14.1% vs 10.7%, p=0.05). The combined GT and GG genotype was associated with a significantly decreased risk of lung cancer [adjusted odds ratio (OR)=0.71, 95% confidence interval (CI)=0.51~1.00, p=0.05] when TT genotype was used as reference. When the lung cancers were categorized by tumor histology, the combined GT and GG genotype was associated with a significantly decreased risk of adenocarcinoma (adjusted OR=0.46, 95% CI=0.26~0.80, p=0.006). In adenocarcinoma, the decreased risk of the combined GT and GG genotype was statistically significant in older patients (>or=61 years, adjusted OR=0.23, 95% CI=0.09~0.58, p=0.002) and in heavier smokers (>or=35 pack years, adjusted OR=0.34, 95% CI=0.13~0.88, p=0.028) in stratification analyses. CONCLUSION: DNMT3b 39179G>T polymorphism may be a genetic determinant of lung cancer, especially adenocarcinoma in Koreans.

The GSTT1 Genotype as A Marker for Susceptibility to Lung Cancer in Korean Female Never-Smokers / 결핵

BACKGROUND: Most previous studies regarding the role of GSTMl and GSTT1 on lung cancer risk have been focused mainly on male smokers. However, epidemiological characteristics, histologic types and risk factors are different in female and male lung cancers, we investigated the association between these genotypes and lung cancer risk in males and females separately. MATERIALS AND METHODS: The study population consisted of 253 lung cancer (153 males and 100 females) and 243 controls (140 males and 103 females). GSTM1 and GSTT1 genotypes were determined by a multiplex PCR. RESULTS: In the male population, neither GSTM1 nor GSTT1 null genotype showed significant difference between cases and controls. In the female population, the frequencies of GSTM1 null genotype showed no significant difference between cases and controls. However, the frequencies of GSTT1 null genotype was significantly higher in cases (70.3%) than controls (55.3%, odds ratio (OR)=2.18; 95% confidence interval (CI=l.21-3.93). When the female population was stratified by age and smoking status, the ORs for GSTT1 null genotype were significantly higher in subgroups of ≤60 years (OR=4.82; 95% CI=l.61-14.4) and never-smokers (OR=4.29; 95% CI=1.94-9.48) but not in subgroups of >60 years or smokers. When stratifying the female never-smokers by age, the ORs for GSTT1 null genotype were significantly higher in both age groups of ≤60 years (OR=7.64; 95% CI=2.00-29.2) and >60 years (OR=2.89; 95% CI=1.05-7.94). CONCLUSION: We found that GSTT1 null genotype was associated with an increased risk of lung cancer in Korean female never-smokers. This result suggests that GSTT1 null genotype could be used as a biomarker for genetic susceptibility to lung cancer in Korean female never-smokers.

Microsatellite Instability in Non-Small Cell Lung Cancer / 결핵

PURPOSE: Microsatellite instability (MSI) is frequently used as an indicative of microsatellite mutator phenotype (MMP) tumors. MSI has been observed in a fraction of non-small cell lung cancer (NSCLC). However, its role in tumorigenesis of NSCLC remains unknown. We evaluated the frequency and pattern of MSI in NSCLC, and compared the clinical parameters of MSI-positive tumors with those of MSS (microsatellite stable) tumors. MATERIALS AND METHODS: Twenty surgically resected NSCLCs were analyzed for 15 microsatellite markers located at chromosome 3p and 9p. Patients' peripheral blood lymphocytes were used as the source of the normal DNA. RESULTS: 1) Of 20 cases, 8 (40%) demonstrated MSI. 2) Instability observed more commonly in tri- and tetra-nucleotide repeats rather than dinucleotide repeats. In all cases, instability appeared as a shift of individual allelic bands. 3) LOH was observed in 10 (50%) of 20 tumors analyzed. 4) Of 20 cases, MSI-H tumor (showing MSI in the majority of markers) was absent. There were 5 MSI-L tumors (showing MSI in a greater than 10% of markers). 5) No significant difference was observed between MSI-L tumors and MSI-negative tumors in clinicopathologic features such as pack-year history of smoking, histologic subtype, and the stage of disease. There was also no significant difference in the incidence of LOH according to the status of MSI. CONCLUSION: These data strongly suggest that MSI has different roles in lung and colon cancer. MMP pathway appears far less important in the tumorigenesis of NSCLC, caused mainly by cigarette smoke, with little familial tendency.