BARHL2 Methylation Using Gastric Wash DNA or Gastric Juice Exosomal DNA is a Useful Marker For Early Detection of Gastric Cancer in an H. pylori-Independent Manner.

OBJECTIVES: The main purpose of this study was to develop a methylation analysis pipeline by using gastric wash-derived DNA and/or gastric juice-derived exosomal DNA (exoDNA), and to evaluate its suitability for the early detection of gastric cancer (GC) in clinical settings. METHODS: We analyzed alterations of BarH-like 2 homeobox protein (BARHL2) in GC cell lines and tissues, as well as in DNA obtained from 128 gastric washes and 30 gastric juice-derived exosomes. GC cell lines were transfected with plasmids encoding BARHL2 and subjected to proliferation, colony formation, and gene expression analyses. RESULTS: High levels of BARHL2 methylation were detected in three of seven GC cell lines; consistent with this, these cell lines expressed low levels of BARHL2. Treatment of these cell lines with 5-aza-2'-deoxycytidine restored BARHL2 expression. Levels of BARHL2 methylation in 18 normal and 14 atrophic gastritis samples were low irrespective of Helicobacter pylori infection. High levels of BARHL2 methylation were observed in gastric wash-derived DNA obtained from early GC patients before endoscopic resection (ER), but methylation was significantly lower after curative ER. Analysis using gastric juice-derived exoDNA samples revealed that BARHL2 methylation yielded an area under the curve of 0.923 with 90% sensitivity and 100% specificity with respect to discriminating GC patients from non-GC controls. BARHL2 nuclear immunoreactivity was found in all normal gastric epithelial cells and in cells from patients with gastritis and adenoma. In contrast, loss of BARHL2 expression was observed in the vast majority of the GC tissues. Finally, transfection of BARHL2 into MKN7 and MKN45 cell lines significantly inhibited their proliferation and ability to form colonies. CONCLUSIONS: Methylation analysis of BARHL2 using gastric wash-derived DNA and/or gastric juice-derived exoDNA could be useful for early detection of GC in clinical settings.

Correlation between hepatic blood flow and liver function in alcoholic liver cirrhosis.

AIM: To elucidate the correlation between hepatic blood flow and liver function in alcoholic liver cirrhosis (AL-LC). METHODS: The subjects included 35 patients with AL-LC (34 men, 1 woman; mean age, 58.9 ± 10.7 years; median age, 61 years; range: 37-76 years). All patients were enrolled in this study after obtaining written informed consent. Liver function was measured with tests measuring albumin (Alb), prothrombin time (PT), brain natriuretic peptide (BNP), branched amino acid and tyrosine ratio (BTR), branched chain amino acid (BCAA), tyrosine, ammonia (NH3), cholinesterase (ChE), immunoreactive insulin (IRI), total bile acid (TBA), and the retention rate of indocyanine green 15 min after administration (ICG R15). Hepatic blood flow, hepatic arterial tissue blood flow (HATBF), portal venous tissue blood flow (PVTBF), and total hepatic tissue blood flow (THTBF) were simultaneously calculated using xenon computed tomography. RESULTS: PVTBF, HATBF and THTBF were 30.2 ± 10.4, 20.0 ± 10.7, and 50.3 ± 14.9 mL/100 mL/min, respectively. Alb, PT, BNP, BTR, BCAA, tyrosine, NH3, ChE, IRI, TBA, and ICG R15 were 3.50 ± 0.50 g/dL, 72.0% ± 11.5%, 63.2 ± 56.7 pg/mL, 4.06 ± 1.24, 437.5 ± 89.4 µmol/L, 117.7 ± 32.8 µmol/L, 59.4 ± 22.7 µg/dL, 161.0 ± 70.8 IU/L, 12.8 ± 5.0 µg/dL, 68.0 ± 51.8 µmol/L, and 28.6% ± 13.5%, respectively. PVTBF showed a significant negative correlation with ICG R15 (r = -0.468, P <0.01). No significant correlation was seen between ICG 15R, HATBF and THTBF. There was a significant correlation between PVTBF and Alb (r = 0.2499, P < 0.05), and NH3 tended to have an inverse correlation with PVTBF (r = -0.2428, P = 0.0894). There were also many significant correlations between ICG R15 and liver function parameters, including Alb, NH3, PT, BNP, TBA, BCAA, and tyrosine (r = -0.2156, P < 0.05; r = 0.4318, P < 0.01; r = 0.4140, P < 0.01; r = 0.3610, P < 0.05; r = 0.5085, P < 0.001; r = 0.4496, P < 0.01; and r = 0.4740, P < 0.05, respectively). CONCLUSION: Our investigation showed that there is a close correlation between liver function and hepatic blood flow.

An updated review of gastric cancer in the next-generation sequencing era: insights from bench to bedside and vice versa.

Gastric cancer (GC) is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide. There is an increasing understanding of the roles that genetic and epigenetic alterations play in GCs. Recent studies using next-generation sequencing (NGS) have revealed a number of potential cancer-driving genes in GC. Whole-exome sequencing of GC has identified recurrent somatic mutations in the chromatin remodeling gene ARID1A and alterations in the cell adhesion gene FAT4, a member of the cadherin gene family. Mutations in chromatin remodeling genes (ARID1A, MLL3 and MLL) have been found in 47% of GCs. Whole-genome sequencing and whole-transcriptome sequencing analyses have also discovered novel alterations in GC. Recent studies of cancer epigenetics have revealed widespread alterations in genes involved in the epigenetic machinery, such as DNA methylation, histone modifications, nucleosome positioning, noncoding RNAs and microRNAs. Recent advances in molecular research on GC have resulted in the introduction of new diagnostic and therapeutic strategies into clinical settings. The anti-human epidermal growth receptor 2 (HER2) antibody trastuzumab has led to an era of personalized therapy in GC. In addition, ramucirumab, a monoclonal antibody targeting vascular endothelial growth factor receptor (VEGFR)-2, is the first biological treatment that showed survival benefits as a single-agent therapy in patients with advanced GC who progressed after first-line chemotherapy. Using NGS to systematically identify gene alterations in GC is a promising approach with remarkable potential for investigating the pathogenesis of GC and identifying novel therapeutic targets, as well as useful biomarkers. In this review, we will summarize the recent advances in the understanding of the molecular pathogenesis of GC, focusing on the potential use of these genetic and epigenetic alterations as diagnostic biomarkers and novel therapeutic targets.

Evaluation of hepatic tissue blood flow using xenon computed tomography with fibrosis progression in nonalcoholic fatty liver disease: comparison with chronic hepatitis C.

AIMS: The present study evaluated the utility of xenon computed tomography (Xe-CT) as a noninvasive diagnostic procedure for the measurement of hepatic tissue blood flow (TBF) in patients with nonalcoholic fatty liver disease (NAFLD) or chronic hepatitis C (CH-C). METHODS: Xe-CT was performed in 93 patients with NAFLD and in 109 patients with CH-C. Subjects were classified into one of three groups, based on fibrosis stage: group 1, no bridging fibrosis; group 2, bridging fibrosis; and group 3, liver cirrhosis. Correlations between hepatic TBFs in each fibrosis stage were examined. RESULTS: In group 1, portal venous TBF (PVTBF), hepatic arterial (HATBF), and total hepatic TBF (THTBF) were significantly lower in patients with in nonalcoholic steatohepatitis (NASH) than in those with CH-C (p < 0.001, p < 0.05, p < 0.001, respectively). In group 2, PVTBF and THTBF were significantly lower in patients with in NASH than in those with CH-C (p < 0.001, p < 0.05, respectively). In group 3, hepatic TBFs were not significantly different when comparing patients with NASH and those with CH-C. CONCLUSIONS: PVTBF decreased due to fat infiltration. Therefore, hemodynamic changes occur relatively earlier in NAFLD than in CH-C. Patients with NASH should be monitored carefully for portal hypertensive complications in the early fibrosis stage.

Quantitative and sensitive protein detection strategies based on aptamers.

Aptamers are functional oligonucleotides of single-stranded RNA or DNA that can selectively recognize their targets with high affinity. Hence, they have been widely developed for analytical, diagnostic, and therapeutic applications. In this review, we have summarized recent advances in the development of aptamer-based detection systems. Aptamers can be amplified exponentially by PCR, which is one of the advantages of aptamers over antibodies. Recently, we have developed immuno-aptamers that bind to mouse or rabbit IgG and constructed a novel sensitive detection system based on a conventional ELISA, called the immuno-aptamer PCR assay. In this article, the aptamer-based ready-to-use sensors and another PCR-based aptamer assays are also described; moreover, we have discussed highly sensitive aptamer-based detection systems.

Characterization of DNA hypermethylation in two cases of peritoneal mesothelioma.

Malignant mesothelioma (MM) is a rare disease with a poor prognosis. Pleural mesothelioma, which is the most common type of MM, is considered to be caused by asbestos exposure and is increasing in incidence, with about 15,000 new cases diagnosed worldwide annually. On the other hand, peritoneal mesothelioma is a very rare type of MM; thus, its pathogenesis is even less understood than pleural mesothelioma. Recent research on the pathogenesis of malignant pleural mesothelioma has indicated that both epigenetic and genetic alterations contribute to tumorigenesis. Here, we hypothesize that peritoneal mesothelioma also has an epigenetic alteration in the same genes (Kazal-type serine peptidase inhibitor domain 1 (KAZALD1), transmembrane protein 30B (TMEM30B), and mitogen-activated protein kinase 13 (MAPK13)). Our goal is to identify DNA methylation of these three candidate genes in two peritoneal mesothelioma cases. Laser capture microdissection was used to separate diseased sections of formalin-fixed paraffin-embedded samples from one surgically resected tissue (epithelial type) and one autopsy tissue (sarcomatous type). Genomic DNA was subsequently extracted by the standard phenol chloroform method. The DNA was then treated with sodium bisulphite, and pyrosequencing analysis was used to quantitatively analyze the methylation of candidate genes reported to be hypermethylated in malignant pleural mesothelioma (KAZALD1, TMEM30B, and MAPK13). TMEM30B and MAPK13 were not methylated in either case. However, KAZALD1 was highly methylated in sarcomatoid-type peritoneal mesothelioma. We first report that the KAZALD1 gene was hypermethylated in sarcomatoid-type malignant peritoneal mesothelioma.

Hypermethylation of Sox17 gene is useful as a molecular diagnostic application in early gastric cancer.

Although minimal invasive treatment is widely accepted in the early stages of gastric cancer (GCa), we still do not have any appropriate risk markers to detect residual neoplasia and the potential for recurrence. We previously reported that aberrant DNA methylation is an early and frequent process in gastric carcinogenesis and could be useful for the detection of gastric neoplasia. Our goal is to find and identify some candidate genes, using genome-wide DNA methylation analysis, as a treatment marker for early gastric cancer (EGC). We performed methylated CpG island amplification microarray analysis using 12 gastric washes (six each of pre- and post-endoscopic treatment in each of the same patients). We finally focused on Sox17 gene. We examined the DNA methylation status of Sox17 in a validation set consisting of 128 wash samples (pre, 64; post, 64) at EGC. We next carried out functional studies to identify Sox17. Sox17 showed significant differential methylation between pre- and post-treatments in EGC patients (Sox17, p < 0.0001). Moreover, treating GCa cells that lacked Sox17 expression with a methyltransferase inhibitor, 5-aza-2'-deoxycytidine, restored the gene's expression. Additionally, the introduction of exogenous Sox17 into silenced cells suppressed colony formation. Gastric wash-based DNA methylation analysis could be useful for early detection of recurrence following endoscopic resection in EGC patients. Our data suggest that the silencing of Sox17 occurs frequently in EGC and may play a key role in the development and progression of the disease.

Gastric wash-based molecular testing for antibiotic resistance in Helicobacter pylori.

BACKGROUND: A number of noninvasive tests have been developed to establish the presence of Helicobacter pylori infection. However, thus far these tests have only been capable of detecting its presence. An increasing number of antibiotic-resistant H. pylori infections have been reported and they are known to be correlated with 23S rRNA single nucleotide polymorphisms (SNPs). We hypothesized that genomic analysis of H. pylori recovered from gastric washes could not only be less invasive, but also useful as a screening test and for assessing the outcome of eradication therapy. METHODS: Biopsy specimens and gastric washes were collected from 100 patients during endoscopic examination. Then we analyzed 23S rRNA, ureA, and cagA genes using PCR and high-throughput pyrosequencing analysis. RESULTS: Forty-five percent (44/97) of patients tested positive for ureA and 42.3% (41/97) tested positive by a rapid urease test. One hundred percent (35/35) of patients who tested positive by both methods were observed to have the cagA gene. Among these 35 patients, 23S rRNA SNPs were present in 34.3% (12/35). CONCLUSIONS: Gastric wash-based PCR and a pyrosequencing assay were used to rapidly detect and estimate the number of 23S rRNA SNPs in clinical isolates of H. pylori. Not only is this a less invasive technique, but it can also diagnose drug resistance.

ValFold: Program for the aptamer truncation process.

UNLABELLED: DNA or RNA aptamers have gained attention as the next generation antibody-like molecules for medical or diagnostic use. Conventional secondary structure prediction tools for nucleic acids play an important role to truncate or minimize sequence, or introduce limited chemical modifications without compromising or changing its binding affinity to targets in the design of improved aptamers selected by Systematic Evolution of Ligands by EXponential enrichment (SELEX). We describe a novel software package, ValFold, capable of predicting secondary structures with improved accuracy based on unique aptamer characteristics. ValFold predicts not only the canonical Watson-Crick pairs but also G-G pairs derived from G-quadruplex (known structure for many aptamers) using the stem candidate selection algorithm. AVAILABILITY: The database is available for free at http://code.google.com/p/valfold/

Development of a sphingosylphosphorylcholine detection system using RNA aptamers.

Sphingosylphosphorylcholine (SPC) is a lysosphingolipid that exerts multiple functions, including acting as a spasmogen, as a mitogenic factor for various types of cells, and sometimes as an inflammatory mediator. Currently, liquid chromatography/tandem mass spectrometry (LC/MS/MS) is used for the quantitation of SPC. However, because of the complicated procedures required it may not be cost effective, hampering its regular usage in a routine practical SPC monitoring. In this report, we have generated RNA aptamers that bind to SPC with high affinity using an in vitro selection procedure and developed an enzyme-linked aptamer assay system using the minimized SPC aptamer that can successfully distinguish SPC from the structurally related sphingosine 1-phosphate (S1P). This is the first case of the Systematic Evolution of Ligands by EXponential enrichment (SELEX) process being performed with a lysosphingolipid. The SPC aptamers would be valuable tools for the development of aptamer-based medical diagnosis and for elucidating the biological role of SPC.

Antibody-specific aptamer-based PCR analysis for sensitive protein detection.

Nucleic acid amplification techniques were applied to the enzyme linked immunosorbent assay (ELISA) with an antibody-specific aptamer, R18. This novel detection system is a modification of the original immuno-polymerase chain reaction (immuno-PCR), but oligonucleotide-labeled antibodies are not required in the assay. This method is performed with the usual ELISA protocol, using an RNA aptamer for rabbit IgG instead of the conventional secondary antibody. After the assay plate was washed, quantitative reverse transcription (RT)-PCR was performed. Ribonuclease (RNase) inhibitors are not needed for this method. The detection limit of the quantitative RT-PCR is over 100 times more sensitive than the original ELISA method, even with the same sandwich-antibody combination. Only 1 mg of aptamer is sufficient for more than 10 million assays. This aptamer-based quantitative PCR successfully detected 16 attomoles (16 x 10(-18)) of vascular endothelial growth factor (VEGF). This is a cost-effective and easy method to increase the sensitivity of the rabbit antibody-based ELISA systems. The new method is referred to as immuno-aptamer PCR (iaPCR), to distinguish it from the original immuno-PCR.

RNA aptamers specifically interact with the Fc region of mouse immunoglobulin G.

We have designed the in vitro selection method to obtain some aptamers such as a general antibody-probing agent, which might bind to the constant regions of mouse immunoglobulin G (IgG) subclasses. As a consequence, one of the selected aptamers found to recognize mouse IgG1, 2a, and 3 subclasses. According to the binding assay, it is suggested that this aptamer recognizes the constant regions of mouse IgG subclass. In addition, this aptamer could recognize the only native form of mouse IgGs but the denatured IgGs. These features show the advantage of the aptamer as an antibody-probing agent rather than the usual secondary antibodies.

X-ray structures of Aerococcus viridans lactate oxidase and its complex with D-lactate at pH 4.5 show an alpha-hydroxyacid oxidation mechanism.

L-Lactate oxidase (LOX) belongs to a family of flavin mononucleotide (FMN)-dependent alpha-hydroxy acid-oxidizing enzymes. Previously, the crystal structure of LOX (pH 8.0) from Aerococcus viridans was solved, revealing that the active site residues are located around the FMN. Here, we solved the crystal structures of the same enzyme at pH 4.5 and its complex with d-lactate at pH 4.5, in an attempt to analyze the intermediate steps. In the complex structure, the D-lactate resides in the substrate-binding site, but interestingly, an active site base, His265, flips far away from the D-lactate, as compared with its conformation in the unbound state at pH 8.0. This movement probably results from the protonation of His265 during the crystallization at pH 4.5, because the same flip is observed in the structure of the unbound state at pH 4.5. Thus, the present structure appears to mimic an intermediate after His265 abstracts a proton from the substrate. The flip of His265 triggers a large structural rearrangement, creating a new hydrogen bonding network between His265-Asp174-Lys221 and, furthermore, brings molecular oxygen in between D-lactate and His265. This mimic of the ternary complex intermediate enzyme-substrate-O(2) could explain the reductive half-reaction mechanism to release pyruvate through hydride transfer. In the mechanism of the subsequent oxidative half-reaction, His265 flips back, pushing molecular oxygen into the substrate-binding site as the second substrate, and the reverse reaction takes place to produce hydrogen peroxide. During the reaction, the flip-flop action of His265 has a dual role as an active base/acid to define the major chemical steps. Our proposed reaction mechanism appears to be a common mechanistic strategy for this family of enzymes.

Rabbit antibody detection with RNA aptamers.

Antibody-based detection systems are widely used, but in the cases of immunoprecipitations and enzyme-linked immunoassays, they can be laborious. These techniques require the preparation of at least two kinds of non-cross-reactive immunoglobulin Gs (IgGs), usually made from different species against the single target molecule. Aptamers composed of nucleic acids possess strict recognition ability for the target molecule's three-dimensional structure and, thus, are considered to act like IgG. In this study, experimental trials were designed to combine the advantages of IgG and aptamers. For this purpose, aptamers against rabbit IgG were identified by in vitro selection. One of the obtained aptamers had a dissociation constant lower than 15 pM to the rabbit IgG. It bound specifically to the constant region of the rabbit IgG, and no binding was observed with mouse or goat IgG. Moreover, this aptamer recognized only the native form of rabbit IgG and could not bind the sodium dodecyl sulfate (SDS)-denatured form. These features show the advantage of using the aptamer as a secondary probing agent rather than the usual secondary antibodies.