Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Identification of pathogenic microRNAs in Helicobacter pylori-associated gastric cancer

ABSTRACT: To identify dysregulated miRNA(s) upon infection with H. pylori during different pre-malignant and malignant stages of gastric cancer in a mouse model miRNA expression in pre-neoplastic and neoplastic lesions in murine stomachs induced by H. pylori and N-methyl-N-nitrosourea (MNU) after 12 months was profiled by miRNA expression array.

ORGANISM(S): Mus musculus

SUBMITTER: Jing Shen

PROVIDER: E-GEOD-62503 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Epigenetic silencing of miR-490-3p reactivates the chromatin remodeler SMARCD1 to promote Helicobacter pylori-induced gastric carcinogenesis.

Shen Jing J Xiao Zhangang Z Wu William K K WK Wang Maggie H MH To Ka F KF Chen Yangchao Y Yang Weiqin W Li May S M MS Shin Vivian Y VY Tong Joanna H JH Kang Wei W Zhang Lin L Li Minxing M Wang Lin L Lu Lan L Chan Ruby L Y RL Wong Sunny H SH Yu Jun J Chan Matthew T V MT Chan Francis K L FK Sung Joseph J Y JJ Cheng Alfred S L AS Cho Chi H CH

Cancer research 20141212 4

Chromatin remodeling has emerged as a hallmark of gastric cancer, but the regulation of chromatin regulators other than genetic change is unknown. Helicobacter pylori causes epigenetic dysregulation to promote gastric carcinogenesis, but the roles and functions of microRNAs (miRNA) in this multistage cascade are not fully explored. In this study, miRNA expression in preneoplastic and neoplastic lesions in murine stomachs induced by H. pylori and N-methyl-N-nitrosourea (MNU) was profiled by miRNA ...[more]

PMID: 25503559

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Project description:In the present study, we aimed to determine the genes involved in inflammatory process of diabetic nephropathy. ICAM-1+/+ and ICAM-1-/- mice aged 8 weeks were divided into four groups: 1) nondiabetic ICAM-1+/+ mice (ND-WT), 2) nondiabetic ICAM-1-/- mice (ND-KO), 3) streptozotocin (STZ)-induced diabetic ICAM-1+/+ mice (DM-WT), and 4) STZ-induced diabetic ICAM-1-/- mice (DM-KO). Three months after the induction of diabetes, total RNA was extracted from each specimen of renal cortex. We examined gene expression profiles of four groups. We identified 193 genes; the ratio of expression level of DM-WT was >2 or <0.5 of that of DM-KO. Of 193 genes, hierarchical clustering identified 33 genes that were significantly upregulated only in DM-WT but not remarkable in ND-WT and ND-KO. Functional annotation of these 33 genes revealed that the significant functions of them were related to the immune or inflammatory process: immune response, response to stimulus, defense response, immune effector process and antigen processing and presentation. These genes contained several inflammatory related genes, such as chemokine (C-X-C motif) ligand 10, chemokine (c-c motif) ligand 12, and chemokine (c-c motif) ligand 8. In this cluster, we focused on cholecystokinin (CCK) because CCK is one of the most up-regulated genes. Real-time RT-PCR revealed that CCK mRNA expression was significantly up-regulated in DM-WT compared with DM-KO. These results suggest that CCK may play a critical role in the progression of diabetic nephropathy by controlling inflammation in diabetic kidney. Male ICAM-1-/- mice (C57BL/6J background) were purchased from The Jackson Laboratory (Bar Harbor, ME). Male C57BL/6J mice (ICAM-1+/+) mice were used as controls. ICAM-1+/+ and ICAM-1-/- mice aged 8 weeks were divided into four groups (n = 5 each): 1) nondiabetic ICAM-1+/+ mice (ND-WT), 2) nondiabetic ICAM-1-/- mice (ND-KO), 3) streptozotocin (STZ)-induced diabetic ICAM-1+/+ mice (DM-WT), and 4) STZ-induced diabetic ICAM-1-/- mice (DM-KO). Mice in the diabetic groups received an intraperitoneal injection of STZ (Sigma Chemical, St.Louis, MO) at 200 mg/kg in citrate buffer (pH 4.5). Blood glucose levels were determined 7 days after STZ injection and only mice with blood glucose concentrations >16 mmol/L were used in the study. Nondiabetic ICAM-1+/+ and ICAM-1-/- mice received citrate buffer injections only. All mice had free access to standard diet and tap water. All animal procedures were performed according to the Guidelines for Animal Experiments at Okayama University Medical School, Japanese Government Animal Protection and Management Law (no. 105), and Japanese Government Notification on Feeding and Safekeeping of Animals (no. 6). Three months after the induction of diabetes, all mice were killed, and the kidneys were harvested. Total RNA was extracted from each specimen of renal cortex using standard protocol from RNeasy midi kit (Qiagen, Valencia, CA) at 3 months. The concentration and the quality of the total RNA sample were assessed by Agilent Bioanalyzer. Biotin-labeled target cRNA was prepared using First and Second strand cDNA Synthesis Kit (Amersham Biosciences, No. 320000) and In Vitro Transcription Kit (Amersham Biosciences, No.320001). Incubate total RNA (5 Î¼g), diluted bacterial mRNA spike controls and T7 oligo (dT) primer for 10 min at 70 C. Add first-strand reaction components and incubate 1 hour at 42C. Add the first-strand cDNA product to the second-strand reaction components and incubate for 2 hours at 16 C. Double-strand cDNA was purified using QIAquick purification kit (Qiagen), eluted twice, each time with 30Î¼l of nuclease-free water then dried in a SpeedVac concentrator. Prepare IVT mix of biotinylated UTP, ribonucleotides, and the 10x T7 enzyme mix and add to the resuspended cDNA. Incubate at 37C for 14 hours. Purify cRNA using RNeasy Mini Kit (Qiagen) and elute the cRNA twice, each time with 50 Î¼l nuclease-free water. Measure the absorbance at 260 nm and 280 nm to determine the ratio (A260:A280=2). In 25 Î¼l total volume, add 10 Î¼g of cRNA to 5 Î¼l of 5x fragmentation buffer and incubate at 94 C for 20 min. Bring 10 Î¼g of fragmented cRNA, 78 Î¼l of hybridization buffer component A, and 130 Î¼l of hybridization buffer component B to a final volume of 260 Î¼l with water. Incubate at 90C for 5 min and immediately chill on ice for 5 min. Slowly inject 250 Î¼l of hybridization reaction mixture into array input port and seal ports with sealing strips. Set the shaker speed to 300 rpm and incubate slides for 18 hours at 37C in an Innove 4080 shaker. Remove the Flex Chamber using the hybridization removal tool. Then, place the bioarrays into the bioarray rack while it sits inside the medium reagent reservoir containing 0.75xTNT. Transfer the bioarray rack to the large reagent reservoir containing preheated 0.75xTNT, and incubate at 46 C for exactly 1 hour. Fill each slot of the small reagent reservoir with 3.4 ml of Cy5-Streptavidin working solution. Transfer the bioarray rack from the large reagent reservoir in to the small reagent reservoir and incubate bioarrays at RT for 30 min. Wash the bioarrays four times with 1xTNT at RT for 5 min. Rinse the bioarrays in 0.1xSSC/0.05%Tween by moving rack up and down 5 times in 5 seconds. Immediately follow the rinse with centrifugation to dry bioarrays, and store dried bioarrays in the dark. We scanned bioarrays with Axon GenePix 4000B and analyzed with CodeLink Expression Analysis software version 2.3.2. The 10,000 spot intensities on the scanned microarray image were normalized to a median value of 1 and data were exported for analysis with CodeLink Expression Analysis software version 2.3.2

Dataset Information

Identification of pathogenic microRNAs in Helicobacter pylori-associated gastric cancer

Publications

Epigenetic silencing of miR-490-3p reactivates the chromatin remodeler SMARCD1 to promote Helicobacter pylori-induced gastric carcinogenesis.

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