Epigenetic and genetic inactivation of tumor suppressor miR-135a in non-small-cell lung cancer.

BACKGROUND: Despite therapeutic advances, lung cancer prognosis remains poor. Loss of heterozygosity (LOH) in the 3p21 region is well documented in lung cancer, but the specific causative genes have not been identified. MATERIALS AND METHODS: Here, we aimed to examine the clinical impact of miR-135a, located in the 3p21 region, in lung cancer. miR-135a expression was assessed using quantitative real-time polymerase chain reaction. LOH was analyzed at microsatellite loci D3S1076 and D3S1478, and promoter methylation status was determined by pyrosequencing of resected samples of primary non-small-cell lung cancer (NSCLC). The regulation of telomerase reverse transcriptase (TERT) was evaluated in lung cancer cells H1299 by luciferase report assays after treatment with miR-135a mimics. RESULTS: miR-135a was significantly downregulated in squamous cell cancer (SCC) tumor tissues compared to normal tissues (p = 0.001). Low miR-135a expression was more frequent in patients with SCC (p = 2.9 × 10-4 ) and smokers (p = 0.01). LOH and hypermethylation were detected in 27.8% (37/133) and 17.3% (23/133) of the tumors, respectively. Overall, 36.8% (49/133) of the NSCLC cases harbored either miR-135a LOH or promoter hypermethylation. The frequencies of LOH and hypermethylation were significantly associated with SCCs (p = 2 × 10-4 ) and late-stage (p = 0.04), respectively. MiR-135a inhibited the relative luciferase activity of psiCHECK2-TERT-3'UTR. CONCLUSION: These results suggest that miR-135a may act as a tumor suppressor to play an important role in lung cancer carcinogenesis, which will provide a new insight into the translational value of miR-135a. Further large-scale studies are required to confirm these findings.

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.

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.

Validation of loop-mediated isothermal amplification to detect Helicobacter pylori and 23S rRNA mutations: A prospective, observational clinical cohort study.

BACKGROUND: Identifying point mutations in 23S rRNA closely associated with clarithromycin resistance can increase the eradication rate of Helicobacter pylori (H pylori). In this study, we verified the sensitivity, specificity, and reliability of a newly developed loop-mediated isothermal amplification (LAMP) assay kit to detect H pylori and 2143G and 2182C mutations in 23S rRNA. METHODS: LAMP assay to detect H pylori and a mutant strain with 2143G and 2182C was conducted with the Isopollo® H pylori & ClaR kit. A prospective, open-label, observational study was conducted to validate the reliability of the LAMP assay in both a development cohort and a bedside direct LAMP cohort. RESULTS: The LAMP assay had good sensitivity, as it could detect as few as 10-100 copies of H pylori and mutants with 2143G and 2182C in 23S rRNA, and good specificity, as it did not react with other bacterial species. In the development cohort with 622 participants, the LAMP assay showed good agreement with RUT for detecting H pylori (kappa value 0.923, P < .001) and had exactly the same results as sequencing analysis for 2143G and 2182C point mutations. The direct LAMP cohort including 93 patients had 97.7% (42/43) of concordance in detecting 2143G and 2182C point mutations compared to the PCR-based sequencing analysis. CONCLUSION: The Isopollo® H pylori & ClaR LAMP assay was a valid method for detecting H pylori and for 2143G and 2182C point mutations in 23S rRNA in a clinical setting.

Development of a tablet PC-based portable device for colorimetric determination of assays including COVID-19 and other pathogenic microorganisms.

There has been a strong and urgent demand to diagnose community transmission-driven coronavirus disease 2019 (COVID-19) after it crossed borders. A large number of rapid and accurate tests and diagnoses are required at drive-through test stations, community clinics and hospitals. Isothermal amplification technology, such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), provides excellent alternatives for resource limited test environments. LAMP has been shown to be comparable with polymerase chain reaction (PCR) and can be performed in less than 30 min by non-laboratory staff without ribonucleic acid (RNA) extractions commonly associated with PCR. LAMP tests on assays with SARS-CoV-2 and other pathogenic microorganisms, such as Dengue, Malaria, and Influenza viruses and Helicobacter pylori show color changes allowing test results to be interpreted by the color change of the assays. However, visual inspection of a large number of assays is prone to human error and manual record keeping makes test result tracking for an epidemiologic investigation very difficult and inefficient. The epidemiologic investigation is an essential part of the fight against community transmission-driven viruses. We have developed a very accurate and reliable, human error free, tablet PC-based portable device for colorimetric determination of assays including SARS-CoV-2 and other pathogenic microorganisms.

Clinical relevance of point mutations in the 23S rRNA gene in Helicobacter pylori eradication: A prospective, observational study.

Clarithromycin-based triple therapy is prescribed worldwide for Helicobacter pylori eradication. However, increases in the clarithromycin resistance of H pylori are thought to be responsible for eradication failure. Here, we studied whether point mutations in domain V of the 23S rRNA gene can affect H pylori eradication failure in a prospective, open-label, observational study. Of the 755 enrolled patients, 299 patients (39.6%) had positive Campylobacter-like organism (CLO) tests. DNA sequencing analysis of H pylori 23S rRNA in 295 patients revealed that 2143G was the most frequent point mutation (24.7% of patients), followed by the 2182T mutation (11.5%). The overall eradication failure rate was 20.9% (42/201) in clarithromycin-based triple therapy. Patients with the 2143G had an approximately 60% eradication failure rate, which suggested that 2143G was a high-risk genotype for eradication failure. Patients with the 2182C genotype without 2143G had an 8.7% failure rate, and patients without 2143G or 2182C had only a 4.3% failure rate. The presence of 2143G, which was associated with previous eradication history and female sex, was an independent risk factor for eradication failure. In conclusion, the 2143G point mutation in the 23S rRNA of H pylori was an independent risk factor for eradication failure in clarithromycin-based triple therapy. Personalized tailored therapy based on the genotypes of 23S rRNA can increase eradication success rates in H pylori infections.

An improved reverse transcription loop-mediated isothermal amplification assay for sensitive and specific detection of serotype O foot-and-mouth disease virus.

A sensitive and specific swarm primer-based reverse transcription loop-mediated isothermal amplification (sRT-LAMP) assay for the detection of serotype O foot-and-mouth disease virus (FMDV) was developed and evaluated. The assay specifically amplified the VP3 gene of serotype O FMDV, but did not amplify the VP3 gene of other serotype FMDVs or any other viruses. The limit of detection of the assay was 102 TCID50/mL or 103 RNA copies/µL, which is 100 times lower than that of the RT-LAMP assay without swarm primers. The new assay is 10 times more sensitive than reverse transcription-polymerase chain reaction (RT-PCR) and is comparable to the sensitivity of real time RT-PCR (qRT-PCR). Evaluation of the assay using different serotypes of FMDV strains showed 100% agreement with the RT-PCR results. The previously reported serotype O FMDV-specific RT-LAMP assay did not detect 20 out of 22 strains of serotype O FMDVs, probably due to multiple mismatches between the primer and template sequences, showing that it is not suitable for detecting the serotype O FMDVs circulating in Pool 1 region countries, including Korea. In contrast, the developed sRT-LAMP assay with improved primers can rapidly and accurately diagnose serotype O FMDVs circulating in Pool 1 region countries and will be a useful alternative to RT-PCR and qRT-PCR.

A Paper-Based Device for Performing Loop-Mediated Isothermal Amplification with Real-Time Simultaneous Detection of Multiple DNA Targets.

Paper-based diagnostic devices have many advantages as a one of the multiple diagnostic test platforms for point-of-care (POC) testing because they have simplicity, portability, and cost-effectiveness. However, despite high sensitivity and specificity of nucleic acid testing (NAT), the development of NAT based on a paper platform has not progressed as much as the others because various specific conditions for nucleic acid amplification reactions such as pH, buffer components, and temperature, inhibitions from technical differences of paper-based device. Here, we propose a paper-based device for performing loop-mediated isothermal amplification (LAMP) with real-time simultaneous detection of multiple DNA targets. We determined the optimal chemical components to enable dry conditions for the LAMP reaction without lyophilization or other techniques. We also devised the simple paper device structure by sequentially stacking functional layers, and employed a newly discovered property of hydroxynaphthol blue fluorescence to analyze real-time LAMP signals in the paper device. This proposed platform allowed analysis of three different meningitis DNA samples in a single device with single-step operation. This LAMP-based multiple diagnostic device has potential for real-time analysis with quantitative detection of 102-105 copies of genomic DNA. Furthermore, we propose the transformation of DNA amplification devices to a simple and affordable paper system approach with great potential for realizing a paper-based NAT system for POC testing.

Overexpression of microRNA-196b Accelerates Invasiveness of Cancer Cells in Recurrent Epithelial Ovarian Cancer Through Regulation of Homeobox A9.

BACKGROUND/AIM: Although microRNAs (miRNAs) are known to influence messenger RNA post-transcriptional control and contribute to human tumorigenesis, little is known about the differences in miRNA expression between primary and recurrent epithelial ovarian cancer (EOC). The purpose of this study was to assess the differential miRNA expression between primary and recurrent EOC and to investigate whether miR-196b could regulate the expression of the Homeobox A9 (HOXA9) gene, and thus affect the invasiveness of cancer cells in recurrent EOC. MATERIALS AND METHODS: Microarrays were used to generate the expression profiles of 6658 miRNAs from samples of 10 patients with EOC. miRNA expression patterns were compared between primary and recurrent EOC. Aberrantly expressed miRNA, associated genes, and invasion activities were validated by a luciferase assay and an in vitro invasion assay. RESULTS: miRNA microarray analysis identified 33 overexpressed miRNAs (including miR-196b) and 18 under expressed miRNAs in recurrent EOC from 6658 human miRNAs. HOXA9 expression was inversely correlated with miR-196b levels in recurrent EOC. We noted that miR-196b induced ovarian cancer cell invasiveness in recurrent EOC by an in vitro invasion assay. CONCLUSION: Overexpression of miR-196b may contribute to invasion activities in recurrent EOC by regulating the HOXA9 gene. Moreover, miR-196b can be a potential biomarker in recurrent EOC.

Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the visual detection of European and North American porcine reproductive and respiratory syndrome viruses.

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for visual detection of European (EU) and North American (NA) porcine reproductive and respiratory syndrome viruses (PRRSVs) were established and evaluated with reference PRRSV strains and clinical samples. The assay was performed in two reaction tubes containing each set of primers specific for EU or NA-PRRSV at 58°C for 40min, and the results could be visually detected by the naked eye, using hydroxynaphthol blue dye. The detection limit of the assay was 1 or 0.1 TCID50/0.1mL for EU or NA PRRSV, respectively, which was comparable to that of the previously described real-time RT-PCR (qRT-PCR). The detection rate of the assay on 130 field samples was 72.3%, relatively higher than that of qRT-PCR (70.8%), and there was high overall percentage agreement between the two assays. The high specificity, sensitivity, and reliability of the RT-LAMP assay described in this study renders it useful for the rapid and differential diagnosis of EU and NA PRRSVs, even in under-equipped laboratories.

Impact of Genetic Variation in MicroRNA-binding Site on Susceptibility to Colorectal Cancer.

The present study analyzed single nucleotide polymorphisms (SNPs) located at putative microRNA(miRNA)-binding sites of the 3'-untranslated region (UTR) in different genes and investigated their impact on the susceptibility to colorectal cancer (CRC). Ninety-two SNPs were selected using an in silico analysis of 3'-UTR SNPs in an SNP database and their miRNA binding efficiency was calculated using several miRNA databases and the HapMap database. Two independent study sets were used: 380 healthy controls and 371 patients with colorectal adenocarcinoma for the discovery set, and 521 healthy controls and 524 patients with colorectal adenocarcinoma for the validation set. The SNP genotyping was performed using a Sequenom MassARRAY. In addition, a luciferase assay was used to investigate whether miR-370 modulated docking protein 3 (DOK3) gene expression when rs2279398G>A was included in the DOK3 3'-UTR region. For the discovery set, 16 out of 92 SNPs were significantly associated with the risk of CRC in at least one of the genetic models. The validation set showed that among these 16 SNPs, DOK3 rs2279398G>A was significantly associated with reduced risk of CRC in a recessive model [adjusted odds ratio (aOR)=0.65, 95% confidence interval (CI)=0.44-0.97, p=0.03]. In a combined analysis, DOK3 rs2279398G>A was associated with a significantly reduced risk of CRC in a co-dominant and recessive model (aOR=0.84, 95% CI=0.73-0.96, p=0.012; aOR=0.65, CI=0.49-0.88, p=0.004, respectively). Significantly lower Renilla activity was also observed with the rs2279398 AA construct when compared to the rs2279398 GG construct (p<0.001). DOK3 rs2279398G>A may affect the expression of DOK3 by altering the miRNA binding efficiency at the miRNA-binding sites of the 3'-UTR in DOK3, thereby impacting CRC tumorigenesis.

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.

Homeobox A9 directly targeted by miR-196b regulates aggressiveness through nuclear Factor-kappa B activity in non-small cell lung cancer cells.

MicroRNAs (miRNAs) are recognized as crucial posttranscriptional regulators of gene expression, and play critical roles as oncogenes or tumor suppressors in various cancers. Here, we show that miR-196b is upregulated in mesenchymal-like-state non-small cell lung cancer (NSCLC) cells and lung cancer tissues. Moreover, miR-196b upregulation stimulates cell invasion and a change in cell morphology to a spindle shape via loss of cell-to-cell contacts. We identified homeobox A9 (HOXA9) as a target gene of miR-196b by using public databases such as TargetScan, miRDB, and microRNA.org. HOXA9 expression is inversely correlated with miR-196b levels in clinical NSCLC samples as compared to that in corresponding control samples, and with the migration and invasion of NSCLC cells. Ectopic expression of HOXA9 resulted in a suppression of miR-196b-induced cell invasion, and HOXA9 reexpression increased E-cadherin expression. Furthermore, HOXA9 potently attenuated the expression of snail family zinc finger 2 (SNAI2/SLUG) and matrix metallopeptidase 9 (MMP9) by controlling the binding of nuclear factor-kappa B to the promoter of SLUG and MMP9 genes, respectively. Therefore, we suggest that HOXA9 plays a central role in controlling the aggressive behavior of lung cancer cells and that miR-196b can serve as a potential target for developing anticancer agents. © 2015 Wiley Periodicals, Inc.

A Panel of Genetic Polymorphism for the Prediction of Prognosis in Patients with Early Stage Non-Small Cell Lung Cancer after Surgical Resection.

BACKGROUND: This study was conducted to investigate whether a panel of eight genetic polymorphisms can predict the prognosis of patients with early stage non-small cell lung cancer (NSCLC) after surgical resection. MATERIALS AND METHODS: We selected eight single nucleotide polymorphisms (SNPs) which have been associated with the prognosis of lung cancer patients after surgery in our previous studies. A total of 814 patients with early stage NSCLC who underwent curative surgical resection were enrolled. The association of the eight SNPs with overall survival (OS) and disease-free survival (DFS) was analyzed. RESULTS: The eight SNPs (CD3EAP rs967591, TNFRSF10B rs1047266, AKT1 rs3803300, C3 rs2287845, HOMER2 rs1256428, GNB2L1 rs3756585, ADAMTSL3 rs11259927, and CD3D rs3181259) were significantly associated with OS and/or DFS. Combining those eight SNPs, we designed a prognostic index to predict the prognosis of patients. According to relative risk of death, a score value was assigned to each genotype of the SNPs. A worse prognosis corresponded to a higher score value, and the sum of score values of eight SNPs defined the prognostic index of a patient. When we categorized the patients into two groups based on the prognostic index, high risk group was significantly associated with worse OS and DFS compared to low risk group (aHR for OS = 2.21, 95% CI = 1.69-2.88, P = 8.0 x 10-9, and aHR for DFS = 1.58, 95% CI = 1.29-1.94, P = 1.0 x 10-5). CONCLUSIONS: Prognostic index using eight genetic polymorphisms may be useful for the prognostication of patients with surgically resected NSCLC.

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 × 10(-5)). CONCLUSIONS: We have identified polymorphisms associated with telomere length in a Korean population.

MicroRNA-146a inhibits epithelial mesenchymal transition in non-small cell lung cancer by targeting insulin receptor substrate 2.

During cancer progression, some tumor cells show changes in their plasticity by morphological and phenotypical conversions, as an expression of mesenchymal markers and loss of epithelial markers, collectively referred to as epithelial-mesenchymal transition (EMT). EMT has been increasingly recognized as a critical phenomenon in lung cancer progression. The goal of this study was to identify microRNAs involved in lung cancer progression. A microarray and qRT-PCR were performed to investigate the miRNA expression profiles in mesenchymal-like lung cancer cells. The role of miR­146a in lung cancer progression was measured by invasion and migration assays in vitro. Bioinformatics and luciferase report assays were used to identify the target of miR­146a. The expression of miR­146a was reduced in mesenchymal-like lung cancer cell lines. The overexpression of miR­146a induced a marked reduction of the mesenchymal marker and increase the epithelial marker in lung cancer cell lines. Moreover, the overexpression of miR­146a suppressed lung cancer cell migration and invasion. Co-treatment with miR­146a and gefitinib treatment showed a significant reduction of invasion in the resistant lung cancer cells induced by EMT. The expression of miR­146a was downregulated in advanced lung cancer tissues. Insulin receptor substrate 2 (IRS2), an adaptor protein that modulates normal growth, metabolism, survival, and differentiation, was identified as a target of miR­146a. miR­146a regulated the expression of IRS2 at the mRNA and protein levels. These data demonstrate for the first time that miR­146a suppresses lung cancer progression by repressing IRS2 expression. This provides new insight into the post-transcriptional regulation of lung cancer progression by miRNAs, a potential approach for the treatment of lung cancer.

Expression Analysis of p16, c-Myc, and mSin3A in Non-small Cell Lung Cancer by Computer Aided Scoring and Analysis (CASA).

BACKGROUND: Immunohistochemical analysis (IHC) of tissue microarray (TMA) slides enables large sets of tissue samples to be analyzed simultaneously on a single slide. However, manual evaluation of small cores on a TMA slide is time consuming and error prone. METHODS: We describe a computer aided scoring and analysis (CASA) method to allow facile and reliable scoring of IHC staining using TMA containing 300 non-small cell lung cancer (NSCLC) cases. In the two previous published papers utilizing our TMA slides of lung cancer we examined 18 proteins involved in the chromatin machinery. We developed our study using more proteins of the chromatin complex and several transcription factors that facilitate the chromatin machinery. Then, a total of 78 antibodies were evaluated by CASA to derive a normalized intensity value that correlated with the overall staining status of the targeting protein. The intensity values for TMA cores were then examined for association to clinical variables and predictive significance individually and with other factors. RESULTs: Using our TMA, the intensity of several protein pairs were significantly correlated with an increased risk of death in NSCLC. These included c-Myc with p16, mSin3A with p16 and c-Myc with mSinA. Predictive values of these pairs remained significant when evaluated based on standard IHC scores. CONCLUSIONS: Our results demonstrate the usefulness of CASA as a valuable tool for systematic assessment of TMA slides to identify potential predictive biomarkers using a large set of primary human tissues.

Functional intronic ERCC1 polymorphism from regulomeDB can predict survival in lung cancer after surgery.

We searched for potential regulatory single nucleotide polymorphisms (SNPs) in excision repair cross-complementing group 1 (ERCC1) using RegulomeDB, a database integrating information from the Encyclopedia of DNA Elements (ENCODE) project, and investigated their association with survival after surgery in non-small cell lung cancer (NSCLC). Among 364 SNPs found within ERCC1 region using RegulomeDB, four top priority SNPs (rs2298881C>A, rs1049739A>G, rs10415949A>G and rs6509214G>T) were selected for this study. The four SNPs were investigated in 316 patients. A replication study was performed (n = 579). Of the four SNPs analyzed in the discovery set, rs2298881C>A and rs6509214G>T were significantly associated with survival outcomes. The association was consistently observed only for rs2298881C>A in the validation cohort. In combined analysis, rs2298881C>A was significantly associated with worse overall survival and disease-free survival (P = 0.0002 and 0.02, respectively). A decreased reporter gene expression for rs2298881 A allele was observed compared with C allele by luciferase assay (P = 0.02). ERCC1 rs2298881C>A, an intronic SNP, is the first genetic polymorphism with functional evidence of regulating its expression, and the SNP is associated with prognosis of NSCLC. Our result supports the role of RegulomeDB as a comprehensive source of prioritized candidate SNPs for genetic association studies.

Differential MicroRNA Expression Profiles in Primary and Recurrent Epithelial Ovarian Cancer.

BACKGROUND/AIM: Although it has been shown that microRNAs influence messenger RNA post-transcriptional control and can attribute to human tumorigenesis, little is known regarading the differences in microRNA expression between primary and recurrent epithelial ovarian cancer (EOC). The purpose of the present study was to assess the differential expression of microRNA between primary and recurrent EOC. MATERIALS AND METHODS: Between September 2013 and May 2014, the expression of microRNAs in tumor tissues from 5 primary and 5 recurrent EOC cases were analyzed. The tumor histotype was serous cystadenocarcinoma in all patients. Total RNA was extracted from tumor samples and microRNA expression levels were measured by performing microarray analysis. Expression levels were compared between the two groups and analyzed statistically. RESULTS: Several microRNAs were differentially expressed in recurrent EOC compared to primary EOC, including 18 under-expressed microRNAs and 33 over-expressed microRNAs among 6,658 human microRNAs. Four specific microRNAs were the most significantly over-expressed in recurrent EOC: miR-551b, miR-19b, miR-196b and miR-3198. Moreover, 4 specific microRNAs were the most significantly down-expressed in recurrent EOC: miR-8084, miR-3201, miR-3613 and miR-7515. CONCLUSION: Based on our data, dysregulation of microRNA expression was associated with the recurrence of EOC. Moreover, significantly over- and down-regulated microRNAs can be useful biomarkers for the prediction of recurrence in EOC.

Common Oncogene Mutations and Novel SND1-BRAF Transcript Fusion in Lung Adenocarcinoma from Never Smokers.

Lung adenocarcinomas from never smokers account for approximately 15 to 20% of all lung cancers and these tumors often carry genetic alterations that are responsive to targeted therapy. Here we examined mutation status in 10 oncogenes among 89 lung adenocarcinomas from never smokers. We also screened for oncogene fusion transcripts in 20 of the 89 tumors by RNA-Seq. In total, 62 tumors had mutations in at least one of the 10 oncogenes, including EGFR (49 cases, 55%), K-ras (5 cases, 6%), BRAF (4 cases, 5%), PIK3CA (3 cases, 3%), and ERBB2 (4 cases, 5%). In addition to ALK fusions identified by IHC/FISH in four cases, two previously known fusions involving EZR- ROS1 and KIF5B-RET were identified by RNA-Seq as well as a third novel fusion transcript that was formed between exons 1-9 of SND1 and exons 2 to 3' end of BRAF. This in-frame fusion was observed in 3/89 tested tumors and 2/64 additional never smoker lung adenocarcinoma samples. Ectopic expression of SND1-BRAF in H1299 cells increased phosphorylation levels of MEK/ERK, cell proliferation, and spheroid formation compared to parental mock-transfected control. Jointly, our results suggest a potential role of the novel BRAF fusion in lung cancer development and therapy.

Association between GWAS-identified genetic variations and disease prognosis for patients with colorectal cancer.

Genome-wide association studies (GWASs) have already identified at least 22 common susceptibility loci associated with an increased risk of colorectal cancer (CRC). This study examined the relationship between these single nucleotide polymorphisms (SNPs) and the clinical outcomes of patients with colorectal cancer. Seven hundred seventy-six patients with surgically resected colorectal adenocarcinoma were enrolled in the present study. Twenty-two of the GWAS-identified SNPs were genotyped using a Sequenom MassARRAY. Among the 22 SNPs, two (rs1321311G>T in CDKN1A and rs10411210C>T in RHPN2) were significantly associated with the survival outcomes of CRC in a multivariate survival analysis. In a recessive model, the rs1321311 TT genotype (vs. GG + GT) and rs10411210 TT genotype (vs. CC + CT) were associated with a worse prognosis for disease-free survival (adjusted HR = 1.90; 95% confidence interval = 1.00-3.60; P = 0.050, adjusted HR = 1.94; 95% confidence interval = 1.05-3.57; P = 0.034, respectively) and overall survival (adjusted HR = 2.05; 95% confidence interval = 1.00-4.20; P = 0.049, adjusted HR = 2.06; 95% confidence interval = 1.05-4.05; P = 0.036, respectively). None of the other SNPs was significantly associated with any clinicopathologic features or survival. The present results suggest that the genetic variants of the CDKN1A (rs1321311) and RHPN2 (rs10411210) genes can be used as prognostic biomarkers for patients with surgically resected colorectal cancer.