Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA116545 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A genome-wide integrated methylome and transcriptome analysis of the early stage of hepatocellular carcinoma development that induced by HBx. The HBV x (HBx) protein, which plays a critical role in the development of HCC, was shown to interact with several epigenetic factors, such as DNMT3A and HDAC1. Most HBx transgenic (TG) mice spontaneously develop HCC at about 1 year of age, providing genetic validation of the oncogenic potential of HBx even in the absence of viral integration and chronic inflammation. Therefore, it would be intriguing to study the regulatory role of HBx in the epigenome and its impact on HCC development. We performed a genome-wide analysis to examine the differences in DNA methylation patterns and RNA transcriptions between cancer and normal liver cells. High-throughput sequencing analysis of MIRA (methylated CpG island recovery assay) and mRNA at 3 mouth old age mouse liver
2013-06-19 | E-GEOD-48052 | biostudies-arrayexpress
Project description:PURPOSE: To provide a detailed gene expression profile of the normal postnatal mouse cornea. METHODS: Serial analysis of gene expression (SAGE) was performed on postnatal day (PN)9 and adult mouse (6 week) total corneas. The expression of selected genes was analyzed by in situ hybridization. RESULTS: A total of 64,272 PN9 and 62,206 adult tags were sequenced. Mouse corneal transcriptomes are composed of at least 19,544 and 18,509 unique mRNAs, respectively. One third of the unique tags were expressed at both stages, whereas a third was identified exclusively in PN9 or adult corneas. Three hundred thirty-four PN9 and 339 adult tags were enriched more than fivefold over other published nonocular libraries. Abundant transcripts were associated with metabolic functions, redox activities, and barrier integrity. Three members of the Ly-6/uPAR family whose functions are unknown in the cornea constitute more than 1% of the total mRNA. Aquaporin 5, epithelial membrane protein and glutathione-S-transferase (GST) omega-1, and GST alpha-4 mRNAs were preferentially expressed in distinct corneal epithelial layers, providing new markers for stratification. More than 200 tags were differentially expressed, of which 25 mediate transcription. CONCLUSIONS: In addition to providing a detailed profile of expressed genes in the PN9 and mature mouse cornea, the present SAGE data demonstrate dynamic changes in gene expression after eye opening and provide new probes for exploring corneal epithelial cell stratification, development, and function and for exploring the intricate relationship between programmed and environmentally induced gene expression in the cornea. Keywords: other
2004-01-02 | GSE887 | GEO
Project description:Hepatoarcinogenesis is a slow and multistep process. We used Hepatitis B virus X antigen (HBx) induced Hepatocellular carcinoma (HCC) as model. We also identify the biomarkers, the pathways and networks underlying HCC formation in this animal model. We analyzed the events from the early, middle, and late stages, in order to predict and prevent the development of cancer. At each specific stage, we analyzed the expression level that differed at least two-fold between HBx transgenic and wild-type mouse liver. Statistical approaches were used to identify genes displaying an increasing or decreasing trend throughout hepatocarcinogenesis. The liver was excised from 6-week-, 8-month-, 12-month-, 14-month-, and 16-month-old HBx transgenic mice (A106 strain) and RNA samples were isolated. In both 14-month- and 16-month-old mice, samples were obtained from both the tumor tissue and the normal.
2010-09-16 | E-GEOD-15251 | biostudies-arrayexpress
Project description:Hepatoarcinogenesis is a slow and multistep process. We used Hepatitis B virus X antigen (HBx) induced Hepatocellular carcinoma (HCC) as model. We also identify the biomarkers, the pathways and networks underlying HCC formation in this animal model. We analyzed the events from the early, middle, and late stages, in order to predict and prevent the development of cancer. At each specific stage, we analyzed the expression level that differed at least two-fold between HBx transgenic and wild-type mouse liver. Statistical approaches were used to identify genes displaying an increasing or decreasing trend throughout hepatocarcinogenesis.
2010-09-16 | GSE15251 | GEO
Project description:Hepatitis B virus (HBV) infection promotes liver cancer initiation by inducing inflammation and cellular stress, but its impact in established tumors is not well understood. We used affinity purification mass spectrometry to comprehensively map a network of 145 physical interactions between HBV and human proteins in hepatocellular carcinoma (HCC). A subset of the host factors targeted by HBV proteins are preferentially mutated in non-HB¬V-associated HCC suggesting that their interaction with HBV influences HCC biology. These include proteins involved in mRNA splicing, mitogenic signaling and DNA repair, with the latter set interacting with the HBV oncoprotein X (HBx). We show that HBx remodels the PP2A phosphatase complex by excluding striatin regulatory subunits from the PP2A holoenzyme. We find that HBx effects on PP2A cause Hippo kinase activation, particularly in cells with high striatin levels. In parallel, HBx activates mTOR complex 2 (mTORC2) to prevent YAP degradation. mTORC2 effects on YAP can be observed in human HCC specimens and mouse HCC models and can be targeted with mTOR kinase inhibitors. Thus, HBV interaction with host proteins rewires HCC signaling rather than directly activating mitogenic pathways. These findings provide a new paradigm for the cellular effects of a tumor promoting virus and support a model where HBV may have therapeutic actionable effects on HCC biology.
2024-11-23 | PXD055366 | Pride
Project description:Hepatitis B virus (HBV) has been clearly recognized as an etiological factor for hepatocellular carcinoma (HCC). HBV encodes the potentially oncogenic HBx protein. We aimed to elucidate the molecular mechanism of HCC caused by HBx and to discover the biomarker related to HCC by HBx. Three experimental groups, 3, 9 and 13 month aged HBx Tg mice and age matched normal wild type B6 mouse which have same background of HBx Tg mice were used to find differentially expressed genes during HCC. Keywords: Genetic modification 3-month-old, 9-month-old, 13-month-old wild type B6 mice vs 3-month-old, 9-month-old, 13-month-old HBx transfected mice; Biological replicates at each timepoint; 9 controls vs 9 HBx-mice
2010-06-19 | E-GEOD-12723 | biostudies-arrayexpress
Project description:Hepatitis B virus (HBV) has been clearly recognized as an etiological factor for hepatocellular carcinoma (HCC). HBV encodes the potentially oncogenic HBx protein. We aimed to elucidate the molecular mechanism of HCC caused by HBx and to discover the biomarker related to HCC by HBx. Three experimental groups, 3, 9 and 13 month aged HBx Tg mice and age matched normal wild type B6 mouse which have same background of HBx Tg mice were used to find differentially expressed genes during HCC. Keywords: Genetic modification
2008-09-11 | GSE12723 | GEO
Project description:A genome-wide integrated ChIP-seq analysis of the early stage of hepatocellular carcinoma development that induced by HBx. The HBV x (HBx) protein, which plays a critical role in the development of HCC, was shown to interact with several epigenetic factors, such as DNMT3A and HDAC1. Most HBx transgenic (TG) mice spontaneously develop HCC at about 1 year of age, providing genetic validation of the oncogenic potential of HBx even in the absence of viral integration and chronic inflammation. Therefore, it would be intriguing to study the regulatory role of HBx in the epigenome and its impact on HCC development. We performed a genome-wide analysis to examine the differences in histone modification and RNA pol II enrichment pattern between cancer and normal liver cells.
2019-01-20 | GSE77023 | GEO
Project description:A genome-wide integrated DNA methylation analysis of the early stage of hepatocellular carcinoma development that induced by HBx. The HBV x (HBx) protein, which plays a critical role in the development of HCC, was shown to interact with several epigenetic factors, such as DNMT3A and HDAC1. Most HBx transgenic (TG) mice spontaneously develop HCC at about 1 year of age, providing genetic validation of the oncogenic potential of HBx even in the absence of viral integration and chronic inflammation. Therefore, it would be intriguing to study the regulatory role of HBx in the epigenome and its impact on HCC development. We performed a genome-wide analysis to examine the differences in DNA methylation enrichment pattern between cancer and normal liver cells.
2019-01-21 | GSE77059 | GEO