Analysis of gastric microbiota by pyrosequencing in Korea
Ontology highlight
ABSTRACT: Sequencing of 16S ribosomal RNA (rRNA) gene, which has improved the characterization of microbial community, has made it possible to detect a low level Helicobacter pylori (HP) sequences even in HP-negative subjects which were determined by a combination of conventional methods. This study was conducted to obtain a cutoff value for HP colonization in gastric mucosa biopsies and gastric juices by the pyrosequencing method. Corresponding author: Department of Internal Medicine, Seoul National University Bundang Hospital, Seoungnam, Gyeonggi-do, Korea; Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com). Microbial DNA from gastric mucosal samples [gastric antrum (n=63, mucosal biopsy), follow-up sample on gastric antrum (n=16, mucosal biopsy), and gastric body (n=18, mucosal biopsy)] and gastric juices (n=4, not mucosal biopsy) was amplified by nested PCR using universal bacterial primers, and the 16S rRNA genes were pyrosequenced.
Project description:Sequencing of 16S ribosomal RNA (rRNA) gene, which has improved the characterization of microbial community, has made it possible to detect a low level Helicobacter pylori (HP) sequences even in HP-negative subjects which were determined by a combination of conventional methods. This study was conducted to obtain a cutoff value for HP colonization in gastric mucosa biopsies and gastric juices by the pyrosequencing method. Corresponding author: Nayoung Kim, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoungnam, Gyeonggi-do, Korea; Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com).
Project description:The whole-genome oligonucleotide microarray analysis gives an opportunity for studying the unidentified gene expression background of the idiopathic and H.pylori related gastric erosive alterations. Using microarrays we compared the whole genome gene expression profile of HP+ and HP- gastric erosions and normal adjacent mucosa to explain the possible role and response to HP infection and to get morphology related mRNA expression patterns. Experiment Overall Design: Total RNA was extracted from frozen gastric biopsy specimens of patients with Helicobacter pylori positive (HP+) and Helicobacter pylori negative (HP-) antrum erosions (ER+), and the corresponding, adjacent normal mucosae (ER-) and hybridized on Affymetrix HGU133 Plus 2.0 microarrays
Project description:The study was undertaken to identify microRNAs differently expressed by intestinal type of gastric cancer using miRNA microarray. The miRNA expression in the intestinal type of gastric cancer depending on H. pylori infection suggest that different gastric cancer pathogenesis could be exist between H. pylori-positive and -negative gastric cancer. Total RNA was extracted from cancerous region and non-cancerous regions in formalin fixed paraffin embedded tissues of intestinal type gastric cancer patients who were H. pylori-positive (n=8) or -negative (n=8). Corresponding author: Nayoung Kim, M.D., Department of Internal Medicine, Seoul National University Bundang Hospital (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com).
Project description:The goal of this project was to compare the metabolite profiles of the: mouse gastric antrum and the mouse gastric corpus, the mouse gastric antrum and the mouse gastric antrum isolated glands, and the mouse gastric corpus and the mouse gastric corpus isolated glands.
Project description:For the identification of miRNA biomarker of pancreatic cancer, total RNA containing miRNA was extracted from the serum samples using Affymetrix miRNA 4.0 and the serum miRNA purification kit (Genolution, Seoul, Korea)
Project description:In this study, 56 semen samples were collected from healthy Korean males aged 18 to 70 and data was obtained utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).
Project description:DNA methylation profiles were compared between gastric mucosae samples without Helicobacter pylori (HP) infection (low risk : G1), those with HP eradication without gastric cancer (intermediate risk : G2), and those with HP eradication with gastric cancer (high risk : G3).
Project description:Persistent colonization of the gastric mucosa by Helicobacter pylori (Hp) elicits chronic inflammation and aberrant epithelial cell proliferation, which increases the risk of gastric cancer. We examined the ability of microRNAs to modulate gastric cell proliferation in response to persistent Hp infection and found that epigenetic silencing of miR-210 plays a key role in gastric disease progression. Importantly, DNA methylation of the miR-210 gene was increased in Hp-positive human gastric biopsies as compared to Hp-negative controls. Moreover silencing of miR-210 in gastric epithelial cells promoted proliferation. We identified STMN1 and DIMT1 as miR-210 target genes and demonstrated that inhibition of miR-210 expression augmented cell proliferation by activating STMN1 and DIMT1. Together, our results highlight inflammation-induced epigenetic silencing of miR-210 as a mechanism of induction of chronic gastric diseases, including cancer, during Hp infection.
Project description:Interventions: Drug : 1.At the time of EMR/ESD: Rapid Urease test/anti-helicobacter IgG Ab/ histology --> If two of them are (+), diagnosis of HP infection could be made. During endoscopy, designated biopsy for the evaluation of gastric atrophy should be performed (baseline data)
2.Patients are assigned to HP (+) or HP (-) group according to the HP status. (Each 120 patients)
3.HP (+) group should undergo eradication therapy after anti-ulcer medication (8weeks, LFDT 30mg + rebamipide SR 150mg bid), and diagnosis of successful eradication should be followed with urea breath test 4weeks later of last dose.
4.HP (-) group should undergo anti-ulcer medication (8weeks, LFDT 30mg + rebamipide SR 150mg bid).
5.In this time, patients are randomly allocated to rebamipide group (60 patients from each group) or placebo group (60 patients from each group).
EGD with biopsy should be repeated to evaluate the regression of atrophy at the time of 12mo, 24mo, 36mo, 48mo, 60mo, respectively.
Primary outcome(s): The primary outcome of this study is to evaluate the difference in the effect of between rebamipide and placebo on regression of gastric atrophy and intestinal metaplasia.
Primary Purpose : Treatment, Intervention Model : Parallel, Blinding/Masking : , Blinding Target : Subject, Investigator, Caregiver, Allocation : RCT
Project description:In order to investigate the gene expression changes in human embryonic stem cells (hESCs) during differentiation, we performed a microarray analysis from RNAs isolated from undifferentiated hESCs and their differentiated cells incubated for 1 week or 2 weeks in ESC medium. Human SNUhES3 ESCs (Seoul National University Hospital, Seoul, Korea) were cultured on mitotically-arrested STO feeder cells (ATCC, Manassas, USA) in DMEM/F12 supplemented with 20% knockout serum replacement (KSR). The embryoid bodies were incubated for 1 or 2 weeks in the above ESC medium without bFGF. Cells were then lysed and RNA was isolated.