DNA methylation analysis in the gastric tissue collected from health check-up cohort.
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE199898 | GEO | 2023/10/31
REPOSITORIES: GEO
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Project description:DNA methylation analysis in the gastric tissue collected from health check-up cohort.
| PRJNA821904 | ENA
Project description:Despite the effort in defining the molecular mechanisms for the drug resistance, predictors of response to chemotherapy have yet to be developed in gastric cancer. With microarray of whole human genes, we determined 29 genes associated with the response to cisplatin and docetaxel combination chemotherapy for metastatic gastric cancer. We obtained Fresh-frozen samples of tumor tissue and background gastric mucosa tissue from 19 patients with gastric cancer by endoscopic biopsy before DCS therapy. Total RNA was extracted from individual microdissected populations of cancer cells and background mucosa cells using RNAeasy mini kits and amplified with a random primer, WT-Ovation FFPE RNA Amplification System V2; NuGEN, Cincinnati, Ohio) according to the manufacturer’s protocols. The amplified fragmented RNA was hybridized on a Whole Human Genome Oligo Microarray Chip (Agilent Technologies) containing 44,000 cDNA clones.
2014-08-31 | E-GEOD-31811 | biostudies-arrayexpress
Project description:As the important layer of the stomach wall, gastric mucosa is related to many functions of digestion. According to the anatomical location, the human stomach is divided into seven regions. In order to get an entire profiling of the 7 regions at proteomic and transcriptomic levels, we collected 7 biopsies from each health volunteer, 49 total were used for integrative analysis, and measured the regional-specific gene products to define the reference intervals of gene expression for outliers screening and prognostic gene detection. Collectively, we presented profiling of normal gastric mucosa at different levels and defined reference ranges of gene expression to study the specific characteristics of abnormal and cancer samples, providing a better understanding of stomach physiological function in studies of gastric disease mechanism.
2024-04-01 | GSE250499 | GEO
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: 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.
2014-09-18 | E-GEOD-61493 | biostudies-arrayexpress
Project description:Background and purposeType 2 diabetes mellitus patients have an increased fracture risk despite having higher areal bone mineral density (aBMD) measured by DXA. This apparent paradox might be explained by the overestimation of BMD by DXA due to the higher fat mass in type 2 diabetes mellitus patients. Volumetric BMD (vBMD) as assessed by quantitative CT (QCT) is not influenced by fat mass. We assessed the association of vBMD and fasting plasma glucose in a large cohort of Chinese subjects and compared the vBMD in healthy and diabetic subjects. In addition, we compared the relation between aBMD, vBMD, glucose and fat mass in a subset of this cohort.Materials and methods10309 participants from the China Biobank project underwent QCT based on chest low dose CT to compute vBMD of L1 and L2 vertebrae and FPG measurements between 2018 and 2019. Among them, 1037 subjects also had spine DXA scans. Data was analyzed using linear regression models.ResultsIn the total cohort (5889 men and 4420 women, mean age 53 years, range 30-96), there was no significant association between vBMD and FPG after adjustment for age (women: p=0.774; men: p=0.149). 291 women and 606 men fitted the diagnostic criteria of diabetes. Both women and men with diabetes had lower vBMD compared to non-diabetic subjects, but this became non-significant after adjusting for age in the total cohort (women: p=0.817; men: p=0.288) and after propensity score matching based on age (women: p=0.678; men: p=0.135). In the DXA subcohort, aBMD was significantly higher in men with diabetes after adjusting for age and this difference disappeared after further adjusting for total fat area (p=0.064).ConclusionWe did not find any effect of fasting plasma glucose or diabetes on the volumetric BMD measured with QCT after adjustment for age. Therefore, vBMD measured with QCT might be a more reliable measurement to diagnose osteoporosis and assess fracture risk than aBMD measured with DXA in diabetic patients.
| S-EPMC8763321 | biostudies-literature
Project description:The expression profiles of normal gastric mucosa were described by advanced technology such as SWATH and RNA-seq.
2018-07-25 | PXD047977 |
Project description:ObjectivesThis study aimed to investigate the relationship between cardiovascular mortality in elderly Asians and decline in renal function.DesignA retrospective cohort study.SettingCommunity-based health examination database from Taipei city.ParticipantsAt the beginning, the database included 315 045 health check-up visits of 97 803 elderly persons aged ≥65 years old from 2005 to 2012. After excluding missing values and outliers, there were 64 732 elderly persons with at least two visits retained for further analyses.Primary outcome measuresKidney function indicators include estimated glomerular filtration rate (eGFR) and urine protein, and rapid decline in eGFR was defined as slope ≤ -5 mL/min/1.73 m2 per year. The endpoint outcome was defined as the cardiovascular deaths registered in the death registry encoded by the International Classification of Diseases. We applied a Cox proportional hazards model to analyse the association between renal function and cardiovascular mortality.ResultsIn this study, we found 1264 elderly persons died from cardiovascular diseases, for whom the data included 4055 previous health check-up visits. We observed significant and independent associations of eGFR <60 mL/min/1.73 m2 (HR (95% CI) of 60>eGFR≥45 and eGFR<45 in males: 2.85 (1.33 to 6.09) and 3.98 (1.84 to 8.61); in females: 3.66 (1.32 to 10.15) and 6.77 (2.41 to 18.99)), positive proteinuria (HR (95% CI) of +/-, +,++ and +++, ++++ in males: 1.51 (1.29 to 1.78) and 2.31 (1.51 to 3.53); in females: 1.93 (1.54 to 2.42) and 4.23 (2.34 to 7.65)) and rapid decline in eGFR (HR (95% CI) in males: 3.24 (2.73 to 3.85); in females: 2.83 (2.20 to 3.64) with higher risk of cardiovascular mortality. The joint effect of increased concentration of urine protein and reduced eGFR was associated with a higher risk of cardiovascular mortality.ConclusionsRenal function and rapid decline in renal function are independent risk factors for cardiovascular mortality in the elderly.
| S-EPMC8458353 | biostudies-literature
Project description:Patients were recruited at the Departments of Abdominal Surgery and Endoscopy of the Hospital do Cancer AC Camargo (São Paulo/Brazil) during a 4-year period (2001 to 2004). All patients signed a pre-informed consent and the study was approved by the internal ethics committee. Tissue samples were either snap frozen in liquid nitrogen (when obtained by surgery) or collected in RNAlaterTM (Ambion®, Austin, Texas USA, when obtained by biopsy). For all samples, diagnosis was confirmed by H&E staining at the time of RNA extraction. Biopsy samples of the esophageal and gastric mucosa obtained by endoscopy had information of the correct anatomical location using a standard diagram. Frozen samples were dissected and only those having at least 70% of tumor cells were processed. A total of 71 samples were analyzed: 39 esophagus and esophagogastric junction samples (9 normal mucosa, 6 esophagitis mucosa, 10 Barrett's mucosa - 4 for the long type and 6 for the short type, and 14 tumor samples of adenocarcinoma) and 32 stomach samples (6 normal body and antrum mucosa, 5 normal cardiac mucosa, 9 intestinal metaplasia mucosa, 7 samples of intestinal type adenocarcinoma and 5 samples of diffuse type carcinoma). For Barrett's samples, diagnosis required evidence of intestinal metaplasia together with tongues or segments of red columnar-appearing epithelium extending upwards from the esophagogastric junction. A long Barrett's esophagus was defined as longer ?3cm and a short Barrett's esophagus by ?3cm of columnar epithelium (Spechler, 2004). The tumor samples of esophagus and esophagogastric junction were not differentiated. For the gastric adenocarcinoma samples were used the Laurén's classification (Laurén, 1965) and the others gastric sample were previously described (Meireles et al, 2003). Keywords: other
2005-05-09 | GSE2444 | GEO
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
2008-06-18 | E-GEOD-5081 | biostudies-arrayexpress
Project description:BACKGROUND & AIMS: Gastric cancer results from a combination of Helicobacter pylori (H pylori) infection, exposure to dietary carcinogens, and predisposing genetic make-up. Because the role of these factors in gastric carcinogenesis cannot be determined readily in human beings, the present study examined the role of an oral carcinogen and H pylori infection in rhesus monkeys. METHODS: Gastroscopies were performed in 23 monkeys assigned to 4 groups: controls; nitrosating carcinogen ethyl-nitro-nitrosoguanidine administration alone; and inoculation of a virulent H pylori strain alone (H), or in combination with ethyl-nitro-nitrosoguanidine (EH). Follow-up gastroscopies and biopsies were performed at 3-month intervals for 5 years for pathologic and molecular studies. RESULTS: Postinoculation, H and EH groups showed persistent infection and antral gastritis. Starting at 2 and 5 years, respectively, gastric intestinal metaplasia and intraepithelial neoplasia developed in 3 EH monkeys but in no other groups. Transcriptional analysis of biopsies at 5 years revealed group-specific expression profiles, with striking changes in EH monkeys, plus a neoplasia-specific expression profile characterized by changes in multiple cancer-associated genes. Importantly, this neoplastic profile was evident in nonneoplastic mucosa, suggesting that the identified genes may represent markers preceding cancer. CONCLUSIONS: Gastric intraglandular neoplasia is induced in primates when H pylori infection is associated with consumption of a carcinogen similar to the nitrosaminesfound in pickled vegetables, suggesting that H pylori and the carcinogen synergistically induce gastric neoplasia in primates. Monkey arrays used for analysis of the affect of Helicobacter pylori and diet on development of gastric cancer. Each RNA was hybridized against a common reference. Biopsy numbers represent the following in terms of descriptions used in publication of the paper... Each set of numbers/descriptions is organized in the following order: Biopsy#; Monkey#; Group Code on Fig 5 Biopsy #4674; AB24; E; E1 Biopsy #4684; 16G; E; E2 Biopsy #4716; 89G; H; H1 Biopsy #4724; 54H; H; H2 Biopsy #4720; 20G; H; H3 Biopsy #4710; 92F; C; C1 Biopsy #4714; 26G; C; C2 Biopsy #4712; 92G; C; C3 Biopsy #4726; 08G; H; H4 Biopsy #4722; 57G; H; H5 Biopsy #4718; 85G; H; H6 Biopsy #4694; 48H; HE NON; HE1 Biopsy #4686; 59H; HE NON; HE2 Biopsy #4690; 81G; HE NEO; HE3 Biopsy #4696; 36G; HE NEO; HE4 Biopsy #4692; 63G; HE NEO; HE5 Biopsy #4680; 76G; E; E3 Biopsy #4682; 52G; E; E4 Biopsy #4678; 15G; E; E5 Biopsy #4676; 93G; E; E6 Biopsy #4688; 47H; HE NON; HE6 A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. Infection: Rhesus monkeys were infected with H. pylori (+/-) Compound Based Treatment: Rhesus monkeys were treated with ENNG (N-ethyl-N-nitrosoguanidine) (+/-)
2009-10-07 | GSE18434 | GEO