Browse
Submit Data
Databases
API
Help

Dataset Information

55 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Helicobacter Pylori Genome Project (HpGP)

ABSTRACT: Helicobacter pylori is a common bacterial infection. It can lead to severe stomach problems, including stomach cancer. Researchers want to look at samples of the bacteria. These H. pylori strains will be taken from chronically infected people. They want to identify the genetic and epigenetic differences in H. pylori strains. This could help predict which people who get infected with the bacteria will get stomach cancer. This could lead to the cancer being detected earlier. It could also mean less people get stomach cancer. Objectives: To study genetic variations of H. pylori strains based on samples from chronically infected people. To identify the features of strains that might lead to severe stomach problems or stomach cancer. Eligibility: People ages 30-70 years who need an upper endoscopy or who were recently diagnosed with stomach cancer Design: Participants will be screened by the doctor who does their procedure and a study nurse. Participants who have endoscopy will have ~6 biopsies removed. These are tissue samples. They are about the size of a grain of rice. Participants will allow the study team to access reports from their stomach exam. Participants with stomach cancer will donate some of the tissue that will be removed during their clinical care. They will allow the study team to access reports of their surgery. They will also allow them to access the microscope slides of their stomach.

DISEASE(S): Intestinal Metaplasia,Metaplasia,Non-atrophic Gastritis,Gastric Cancer,Stomach Neoplasms,Gastritis

PROVIDER: 2216372 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

ACCESS DATA

Json Xml

Similar Datasets

Rhesus monkeys challenged with H. pylori and ENNG

Project description:Gene expression was studied in samples from the stomach of Rhesus monkeys that have been infected with Helicobacter pylori and treated with a known carcinogen (Ethyl-nitro-nitrosoguanidine (ENNG)) that is similar to known nitrosamine dietary carcinogens. The samples represent the following: Biopsy 4689 is from animal 81G taken 55 months after inoculation with H. pylori and the start of the carcinogen ENNG Biopsy 4691 is from animal 63G taken 55 months after inoculation with H. pylori and the start of the carcinogen ENNG Biopsy 4709 is from animal 92F taken after 55 months of observation and no treatment (control). Gastric biopsies were obtained at the indicated times and RNA was harvested from the sample. All hybridizations were conducted against a common reference that was prepared using commercially obtained RNA isolated from the stomach of uninfected monkeys.

2013-06-07 | GSE38586 | GEO

A Novel Human Gastric Primary Cell Culture System for Modeling Helicobacter Pylori Infection In Vitro

Project description:We identified specific long-term culture conditions that allow the formation of 3-dimensional human gastric spheroids, which can be differentiated by withdrawal of Wnt3A and R-spondin1 to human gastric organoids. These cultures can expand indefinitely and exhibit important characteristics of human stomach tissue. Furthermore, these 3-dimensional cultures can be transferred into 2-dimensional primary epithelial cell layers, which can be successfully infected with H. pylori and thereby provide ideal conditions to study infections in vitro.

2014-12-10 | GSE58473 | GEO

Remodeling of the gastric environment in Helicobacter pylori-induced atrophic gastritis

Project description:Helicobacter pylori colonization of the human stomach is a strong risk factor for gastric cancer. To investigate H. pylori-induced gastric molecular alterations, we used a Mongolian gerbil model of gastric carcinogenesis. Histologic evaluation revealed varying levels of atrophic gastritis (a premalignant condition characterized by parietal and chief cell loss) in H. pylori-infected animals, and transcriptional profiling revealed a loss of markers for these cell types. We then assessed the spatial distribution and relative abundance of proteins in the gastric tissues using imaging mass spectrometry and liquid chromatography with tandem mass spectrometry (LC-MS/MS). We detected striking differences in protein content of corpus and antrum tissues. 492 proteins were preferentially localized to the corpus in uninfected animals. The abundance of 91 of these proteins was reduced in H. pylori-infected corpus tissues exhibiting atrophic gastritis compared to infected corpus tissues with non-atrophic gastritis or uninfected corpus tissues; these included numerous proteins with metabolic functions. Fifty proteins localized to the corpus in uninfected animals were diffusely delocalized throughout the stomach in infected tissues with atrophic gastritis; these included numerous proteins with roles in protein processing. Corresponding alterations were not detected in animals infected with a H. pylori ∆cagT mutant (lacking Cag type IV secretion system activity). These results indicate that H. pylori can cause loss of proteins normally localized to the gastric corpus as well as diffuse delocalization of corpus-specific proteins, resulting in marked changes in the normal gastric molecular partitioning into distinct corpus and antrum regions.

2023-12-04 | PXD046333 | Pride

Rhesus monkeys challenged with H. pylori and ENNG

2013-06-07 | E-GEOD-38586 | biostudies-arrayexpress

Gene expression profiling of gastric cells infected by Helicobacter pylori

Project description:Helicobacter pylori are gram-negative bacteria that colonize the human stomach and are the major etiological factor in gastric carcinoma development. The aim of this work was to evaluate changes in gene expression in gastric cells induced by H. pylori. The human gastric carcinoma-derived cell line AGS was infected with H. pylori strain 60190 (ATCC 49503) for 24 hours. RNA was extracted from three independent experiments.

2016-03-01 | E-GEOD-70394 | biostudies-arrayexpress

Gastric Cancer Precursor Lesions (GCPL) Study

Project description:Background: Gastric cancer is a leading cause of cancer deaths around the world. This disease is a serious problem in places like East Asia, Central and South America, and Eastern Europe. Researchers want to study the causes of gastric cancer and its precursors. They want to reduce the number of people with stomach cancer. Objectives: To learn more about bacteria factors and other causes of gastric cancer. To study potential markers associated with precancerous gastric lesions (intestinal metaplasia). Eligibility: Adults ages 40-70 years at certain hospitals in Chile who: Are going to have upper gastrointestinal endoscopies OR have stomach cancer and need surgery Design: Participants will give gastric tissue samples. Some participants will donate a portion of the stomach tissue that is removed as part of their clinical care. Participants will give access to reports of their stomach exam. They will allow researchers to photograph the microscope slides of their tissue samples. Participants will answer questions. The topics of the questions include: Age, height, weight Education Habits including tobacco and alcohol Personal and family history of disease Reproductive history Diet Some participants will give blood, urine, saliva, and stool samples. Study staff will collect the blood. They will tell the participants how to collect the other samples themselves.

| 2247086 | ecrin-mdr-crc

H. pylori strain content variation after five year infection of macaques measured by array CGH

Project description:Helicobacter pylori strains USU101 was infected into macaques, some of which were treated with the dietary carcinogen ENNG. After 5 years, H. pylori isolates were obtained by endoscopy followed by culture. The resulting strains were analyzed for differences in gene content by array CGH.

2014-08-18 | GSE60405 | GEO

The role of CTH in the innate immune response to H. pylori

Project description:RNA sequencing by Illumina NovaSeq6000 was performed on F4/80 positive cells isolated from the gastric tissue of mice infected or not with H. pylori SS1 for 16 weeks to determine the role of CTH in the innate immune response in the stomach.

2022-05-18 | GSE158817 | GEO

A Novel Human Gastric Primary Cell Culture System for Modeling Helicobacter Pylori Infection In Vitro

2014-12-10 | E-GEOD-58473 | biostudies-arrayexpress

To identify alterations induced in gastric mucosa of mice exposed to Pteridium aquilinum and/or infected with Helicobacter pylori

Project description:The aim of this study is to identify alterations induced in gastric mucosa of mice exposed to Pteridium aquilinum and/or infected with Helicobacter pylori, in order to identify genes that are induced by bracken fern exerts exacerbating effects on gastric lesions associated to the infection. Six groups of C57Bl/6 mice were be used: 1) control, 2) infected Helicobacter pylori, 3) treated with Bracken fern extract orogastrically, 4) treated with Bracken fern extract in drinking water, 5) infected Helicobacter pylori + treated with Bracken fern extract orogastrically, 6) infected Helicobacter pylori + treated with Bracken fern extract in drinking water. The infection procedure was performed using an orogastric inoculation of H.pylori (strain SS1) twice in the first week. The RNA isolation was done in triplicate (3 mice per each condition). Further evaluation of morphological alterations on gastric mucosa, proliferative index and induction of DNA strand breaks will be performed in the mice stomach exposed to Pteridium aquilinum infected or not with Helicobacter pylori. Alterations of glycosylation in gastric tissues will also evaluated.

2011-09-07 | E-GEOD-31991 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data