Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1189879 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31480136_1.fastq.gz | Fastqsanger.gz | |||
| SRR31480136_2.fastq.gz | Fastqsanger.gz | |||
| SRR31480137_1.fastq.gz | Fastqsanger.gz | |||
| SRR31480137_2.fastq.gz | Fastqsanger.gz | |||
| SRR31480138_1.fastq.gz | Fastqsanger.gz |
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Project description:Chronic inflammation is a common underlying condition associated with tumor development, accounting for approximately 20% of human cancers. This association is especially apparent in Hepatocellular carcinoma (HCC), which often develops on the background of chronic hepatitis and hepatic fibrosis, slowly unfolding on a background of chronic inflammation. HCC is one of the most common tumors worldwide, exhibiting a very poor prognosis and high mortality rate with limited available therapeutic tools. The etiology of liver cancer is well known, however there is still a lack of precise knowledge about pathogenesis of HCC. IL-6 have been shown to be of importance for liver protection and prevention of liver injury in animal models of acute sclerosing cholangitis and correlate with increased HCC in human patients. Using a murine model of chronic cholangitis based on the ablation of the Mdr2 gene, this study has examined the role of IL-6 signaling in chronic hepatitis and in the subsequent development of liver cancer. The main observations of this study are that IL-6 signaling in male Mdr2-KO mice protects from the development of liver injury and fibrosis, but simultaneously promotes tumor initiation. Thus, IL-6 deficiency in male Mdr2-KO mice dissociates the tight correlation between liver fibrosis and the development of inflammation-associated HCC. To reveal the affected molecular pathways that lead to increased cholestasis and bile acid–induced liver injury, but reduced tumorigenesis in the male IL-6 deficient Mdr2-KO/IL6-KO mice, we performed gene array analysis and identified distinct classes of differentially-expressed genes in these mice. We performed genome-scale gene expression profiling by Affymetrix analysis on tumor-free livers samples from Mdr2-KO, Mdr2-KO/IL6-KO, and wild type C57BL/6 mice at the age of 14 months.
2015-05-01 | E-GEOD-37468 | biostudies-arrayexpress
Project description:Background. Abcb4 (-/-) mice secrete phosphatidylcholine-deficient bile and develop sclerosing cholangitis (SC). The cholangitis involves differential hepatic transcription of genes whose products govern inflammation, activation of hepatic stellate cells and fibrosis. This study was undertaken to test the hypothesis that several genes involved in regulation of tissue inflammation and fibrosis display transcription rates that reflect SC disease activity. Methods. Abcb4 (-/-) mice fed cholic acid (CA) display high SC activity and ursodeoxycholic acid (UDCA) fed mice display low SC activity. Differential hepatic transcription of genes was accordingly measured in abcb4 (-/-) mice maintained on CA- and UDCA-supplemented diets using cDNA microarrays. Abcb4 (+/+) mice served as controls. The differential transcription of selected genes was verified by real time polymerase chain reaction. Liver tissue pathology was quantified by histopathology scoring and immunohistochemistry to visualize bile duct cells and activated hepatic stellate cells. Results. Differential transcription of Ccl2, Ccl20, Cxcl10, Nfκb1, Nfκb2, Tgfβ1, Tgfβ2, Sparc, Ctgf, Lgals3, Elf3, Spp1, Pdgfa, Pdgfrb, Col1a1, Col1a2 and Col4a1 genes paralleled the differing SC activities of cholic acid- and UDCA-fed abcb4 (-/-) mice. Histopathology scores and immunohistochemistry showed greatly enhanced activation of hepatic stellate cells during high SC activity due to CA feeding. Conclusion. Differential transcription of several genes relating to tissue inflammation and hepatic stellate cell activation parallels SC activity in abcb4 (-/-) mice. Data on their differential transcription may be used to gauge SC disease activity.
2008-08-20 | GSE11507 | GEO
Project description:Primary biliary cholangitis (PBC) is a cholestatic autoimmune liver disease secondary to an autoreactive T cell response against intrahepatic small bile ducts. Multiple murine models have demonstrated the critical role of effector CD8+T cells in this response and our work has used IL-12p40-/-IL-2Rα-/- mice (DKO mice) to study this issue. Herein we first demonstrated that use of either a CD8a knock-out or an anti-CD8a antibody prevents/reduces biliary immunopathology. Bulk and single-cell RNA sequencing analysis identifies CD8+ tissue resident memory T cells (Trm) in the liver of DKO mice, which highly express activation and cytotoxicity associated markers and have the ability to induce apoptosis of bile duct epithelial cells. Liver CD8+Trm cells also upregulate expression of several immune checkpoint molecules and in particular we identified PD-1 as a specific liver CD8+Trm cell marker in this model. Based on these data we constructed a novel chimeric antigen receptor containing a PD-L1 extracellular domain to target PD-1-expressing CD8+Trm cells. Importantly, treatment of DKO mice with PD-1 targeting CAR-T cells selectively depleted liver CD8+Trm cells in vivo and alleviated autoimmune cholangitis.
2023-09-05 | GSE241014 | GEO
Project description:Chronic inflammation is a common underlying condition associated with tumor development, accounting for approximately 20% of human cancers. This association is especially apparent in Hepatocellular carcinoma (HCC), which often develops on the background of chronic hepatitis and hepatic fibrosis, slowly unfolding on a background of chronic inflammation. HCC is one of the most common tumors worldwide, exhibiting a very poor prognosis and high mortality rate with limited available therapeutic tools. The etiology of liver cancer is well known, however there is still a lack of precise knowledge about pathogenesis of HCC. IL-6 have been shown to be of importance for liver protection and prevention of liver injury in animal models of acute sclerosing cholangitis and correlate with increased HCC in human patients. Using a murine model of chronic cholangitis based on the ablation of the Mdr2 gene, this study has examined the role of IL-6 signaling in chronic hepatitis and in the subsequent development of liver cancer. The main observations of this study are that IL-6 signaling in female Mdr2-KO mice protects from the development of liver injury and fibrosis, but simultaneously reduced tumor initiation. To reveal the affected molecular pathways that lead to increased cholestasis and bile acid ?induced liver injury, and increased tumorigenesis in the female IL-6 deficient Mdr2-KO/IL6-KO mice, we performed gene array analysis and identified distinct classes of differentially-expressed genes in these mice. We performed genome-scale gene expression profiling by Affymetrix analysis on tumor-free livers samples from Mdr2-KO, Mdr2-KO/IL6-KO, and wild type C57BL/6 mice at the age of 14 months.
2015-05-01 | E-GEOD-37559 | biostudies-arrayexpress
Project description:Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts. Due to a limited understanding of the underlying pathogenesis of disease, there remains a paucity of treatment options. As such, we sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that outside PSC scar regions, hepatocytes are transitioning to bile duct cells, whereas within the scars, there is an accumulation of immune cells. Of these cells, macrophages that typically contribute to tissue repair were enriched in immunoregulatory genes and were less responsive to stimulation. These cells are likely involved in maintaining hepatic inflammation and could be targeted in novel therapeutic development.
2024-01-18 | GSE247128 | GEO
Project description:Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts. Due to a limited understanding of the underlying pathogenesis of disease, there remains a paucity of treatment options. As such, we sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that outside PSC scar regions, hepatocytes are transitioning to bile duct cells, whereas within the scars, there is an accumulation of immune cells. Of these cells, macrophages that typically contribute to tissue repair were enriched in immunoregulatory genes and were less responsive to stimulation. These cells are likely involved in maintaining hepatic inflammation and could be targeted in novel therapeutic development.
2024-01-18 | GSE243977 | GEO
Project description:Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts. Due to a limited understanding of the underlying pathogenesis of disease, there remains a paucity of treatment options. As such, we sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that outside PSC scar regions, hepatocytes are transitioning to bile duct cells, whereas within the scars, there is an accumulation of immune cells. Of these cells, macrophages that typically contribute to tissue repair were enriched in immunoregulatory genes and were less responsive to stimulation. These cells are likely involved in maintaining hepatic inflammation and could be targeted in novel therapeutic development.
2023-10-06 | GSE240429 | GEO
Project description:Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts. Due to a limited understanding of the underlying pathogenesis of disease, there remains a paucity of treatment options. As such, we sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that outside PSC scar regions, hepatocytes are transitioning to bile duct cells, whereas within the scars, there is an accumulation of immune cells. Of these cells, macrophages that typically contribute to tissue repair were enriched in immunoregulatory genes and were less responsive to stimulation. These cells are likely involved in maintaining hepatic inflammation and could be targeted in novel therapeutic development.
2024-01-18 | GSE245620 | GEO
Project description:Chronic inflammation is a common underlying condition associated with tumor development, accounting for approximately 20% of human cancers. This association is especially apparent in Hepatocellular carcinoma (HCC), which often develops on the background of chronic hepatitis and hepatic fibrosis, slowly unfolding on a background of chronic inflammation. HCC is one of the most common tumors worldwide, exhibiting a very poor prognosis and high mortality rate with limited available therapeutic tools. The etiology of liver cancer is well known, however there is still a lack of precise knowledge about pathogenesis of HCC. IL-6 have been shown to be of importance for liver protection and prevention of liver injury in animal models of acute sclerosing cholangitis and correlate with increased HCC in human patients. Using a murine model of chronic cholangitis based on the ablation of the Mdr2 gene, this study has examined the role of IL-6 signaling in chronic hepatitis and in the subsequent development of liver cancer. The main observations of this study are that IL-6 signaling in male Mdr2-KO mice protects from the development of liver injury and fibrosis, but simultaneously promotes tumor initiation. Thus, IL-6 deficiency in male Mdr2-KO mice dissociates the tight correlation between liver fibrosis and the development of inflammation-associated HCC. To reveal the affected molecular pathways that lead to increased cholestasis and bile acid–induced liver injury, but reduced tumorigenesis in the male IL-6 deficient Mdr2-KO/IL6-KO mice, we performed gene array analysis and identified distinct classes of differentially-expressed genes in these mice.
2015-05-01 | GSE37468 | GEO
Project description:Background and aim: The molecular mechanisms underlying the progression of nonalcoholic fatty liver (NAFL) to nonalcoholic steatohepatitis (NASH) remain unclear; however, the role of autophagy in these mechanisms has attracted extensive attention. This study aimed to investigate the role of chaperone-mediated autophagy (CMA) in NAFL-to-NASH progression and elucidate the underlying mechanisms. Methods: Hepatic CMA activity was analyzed in patients with NASH and mouse models of NASH. LAMP2A was knocked down or overexpressed to assess the effects of hepatocyte-specific CMA on NAFL-to-NASH progression. Mice were fed a high-fat diet or a methionine–choline-deficient diet to induce NAFL or NASH. Palmitic acid was used to mimic lipotoxicity-induced hepatocyte damage in vitro. The promoter activity of FOXM1 was evaluated via chromatin immunoprecipitation and dual-luciferase reporter assay. Results: Hepatic CMA activity was substantially low in patients and mice with NASH. Knockdown of LAMP2A resulted in hepatocyte-specific CMA deficiency, which promoted hepatic inflammation and fibrosis in mice with NASH. In addition, CMA deficiency exacerbated endoplasmic reticulum (ER) stress and hepatocyte damage in vivo and in vitro. Mechanistically, CMA deficiency in hepatocytes increased cholesterol accumulation by blocking the degradation of HMGCR, a rate-limiting enzyme of cholesterol synthesis, and the accumulated cholesterol subsequently induced ER stress and hepatocyte damage. Restoration of hepatocyte-specific CMA activity effectively ameliorated diet-induced NASH and ER stress in vivo and in vitro. FOXM1 negatively regulated the transcription of LAMP2A by directly binding to its promoter. Upregulation of FOXM1 impaired CMA and enhanced ER stress, which in turn increased FOXM1 expression, resulting in a vicious circle and promoting the development of NASH. Conclusions: This study highlights the role of the FOXM1/CMA/ER stress axis in NAFL-to-NASH progression and proposes novel therapeutic targets for NASH.
2025-02-19 | GSE274949 | GEO