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Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development.

ABSTRACT: The liver performs a number of essential functions for life. The development of such a complex organ relies on finely regulated gene expression profiles which change over time in the development and determine the phenotype and function of the liver. We used high-density oligonucleotide microarrays to study the gene expression and transcription regulation at 14 time points across the C57/B6 mouse liver development, which include E11.5 (embryonic day 11.5), E12.5, E13.5, E14.5, E15.5, E16.5, E17.5, E18.5, Day0 (the day of birth), Day3, Day7, Day14, Day21, and normal adult liver. With these data, we made a comprehensive analysis on gene expression patterns, functional preferences and transcriptional regulations during the liver development. A group of uncharacterized genes which might be involved in the fetal hematopoiesis were detected.

SUBMITTER: Li T

PROVIDER: S-EPMC2995988 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature

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Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development.

Li Tingting T Huang Jian J Jiang Ying Y Zeng Yan Y He Fuchu F Zhang Michael Q MQ Han Zeguang Z Zhang Xuegong X

Genomics 20081210 3

The liver performs a number of essential functions for life. The development of such a complex organ relies on finely regulated gene expression profiles which change over time in the development and determine the phenotype and function of the liver. We used high-density oligonucleotide microarrays to study the gene expression and transcription regulation at 14 time points across the C57/B6 mouse liver development, which include E11.5 (embryonic day 11.5), E12.5, E13.5, E14.5, E15.5, E16.5, E17.5 ...[more]

PMID: 19015022

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Project description:It is generally accepted that exposure to particulate matter (PM) increases the risk of cardiovascular-related morbidity and mortality, though the exact mechanism behind this has yet to be elucidated. Oxidative stress plays a potentially important role in the mechanism of toxicity, with Nrf2 serving as a major antioxidant gene. In the current study, a Nrf2 knockout mouse model was used in combination with an individual ventilated cage (IVC)-based real-ambient PM exposure system to assess the potential cardiotoxicity induced by real-ambient PM exposure and the potential role of Nrf2 and related signaling in this endpoint. After 6- or 11-weeks exposure to PM, ICP-mass spectrometry was used to assess the metal depositions in the heart tissue following PM exposure. Functional and morphological changes in the hearts were investigated with echocardiography and histopathology, and oxidative stress levels were assessed with a serum malondialdehyde content assay. In the further mechanistic study, an RNA-seq technique was utilized to assess the gene transcription status in the hearts of C57/B6 mice exposed to PM with or without Nrf2 knockout. The expression levels of genes of interest were then further investigated with quantitative real-time PCR and western blotting. The results indicated that PM exposure resulted in significant elevation of sodium, potassium, selenium, and ferrum levels in mouse heart tissue. Meanwhile, significantly altered heart function and morphology were observed. Interestingly, Nrf2 knockout led to abolishment of PM-induced effects in several functional parameters but not the morphological changes. Meanwhile, elevated malondialdehyde content was observed in Nrf2 knockout animals. RNA-seq results revealed thousands of genes altered by PM exposure and/or Nrf2 knockout, and this affected several pathways, such as MAPK, phagosome, calcium signaling, and JAK-STAT. In subsequent molecular studies, enhanced nuclear translocation of Nrf2 was also observed following PM exposure, while the MAPK signaling pathway along with related JAK-STAT and TGF-β1 pathway genes, such as p38MAPK, AKT, TAK1, JAK1, STAT3, GRB2, TGFb1, and SMAD2, were confirmed to be affected by PM exposure and/or Nrf2 knockout. The data suggested that PM may induce cardiotoxicity in C57/B6 mice in which Nrf2 plays both protective and detrimental roles involving cardiac-related pathways, such as MAPK, JAK-STAT, and TGF-β1.

Project description:Short-and long-term exposure to particulate matter (PM) has been associated with cardiovascular disease (CVD). It is well recognized that oxidative stress is a potential major mechanism in PM-induced vascular injuries, in which the nuclear factor E2-related factor 2 (Nrf2) signaling pathway plays a critical role. In the current study, a Nrf2 knockout mouse model was used in combination with an individual ventilated cage (IVC)-based real-ambient PM exposure system to assess the potential vascular injury and the potential role of Nrf2 in the angiotensin II (Ang II)-associated vascular injury. After 6-or 11-week exposure to PM, the histopathology assay revealed that PM exposure resulted in the thickening of the walls of vascular. After 6 weeks exposure to PM, the ELISA assay revealed that PM exposure resulted in the elevated plasma concentration of Ang II. The expression levels of genes of interest were then further investigated with quantitative real-time PCR. Notably, the results showed that Angiotensinogen (AGT), Angiotensin converting enzyme (ACE) and Angiotensin type I receptor (AT1R) were involved in PM-induced pathological changes. Western blotting for ACE showed similar results. Moreover, the extent of vascular thickening and the Ang II elevation was most prominent in the Nrf2 gene knockout PM exposure group (KOE). Furthermore, the expression of Nrf2 downstream relevant genes (HO1, Nqo1, Gclc, Gsta4) were significantly enhanced in the wildtype PM exposure group (WTE), while those were remarkably suppressed in the Nrf2 gene knockout groups. The ELISA result of monocyte chemoattractant protein-1 (MCP-1) serum levels in the KOE group was significantly higher in relation to that in the Nrf2 knockout control group (KOC). In summary, PM exposure is associated with thickening of vascular wall, while Nrf2 knockout may further enhance this effect. A potential mechanistic contributor of such effects is the activation of ACE/ANGII/AT1R axis, in which Nrf2 played a regulatory role.

Project description:BackgroundCancer progression can be tracked by gene expression changes that occur throughout early-stage to advanced-stage cancer development. The accumulated genetic changes can be detected when gene expression levels in advanced-stage are less variable but show high variability in early-stage. Normalizing advanced-stage expression samples with early-stage and clustering of the normalized expression samples can reveal cancers with similar or different progression and provide insight into clinical and phenotypic patterns of patient samples within the same cancer.ObjectiveThis study aims to investigate cancer progression through RNA-Seq expression profiles across the multi-stage process of cancer development.MethodsRNA-sequenced gene expression of Diffuse Large B-cell Lymphoma, Lung cancer, Liver cancer, Cervical cancer, and Testicular cancer were downloaded from the UCSC Xena database. Advanced-stage samples were normalized with early-stage samples to consider heterogeneity differences in the multi-stage cancer progression. WGCNA was used to build a gene network and categorized normalized genes into different modules. A gene set enrichment analysis selected key gene modules related to cancer. The diagnostic capacity of the modules was evaluated after hierarchical clustering.ResultsUnnormalized RNA-Seq gene expression failed to segregate advanced-stage samples based on selected cancer cohorts. Normalization with early-stage revealed the true heterogeneous gene expression that accumulates across the multi-stage cancer progression, this resulted in well segregated cancer samples. Cancer-specific pathways were enriched in the normalized WGCNA modules. The normalization method was further able to stratify patient samples based on phenotypic and clinical information. Additionally, the method allowed for patient survival analysis, with the Cox regression model selecting gene MAP4K1 in cervical cancer and Kaplan-Meier confirming that upregulation is favourable.ConclusionThe application of the normalization method further enhanced the accuracy of clustering of cancer samples based on how they progressed. Additionally, genes responsible for cancer progression were discovered.

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Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development.

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Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development.

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