GEO DataSets

(Submitter supplied) Hepatocellular carcinoma (HCC) is the second most common cause of cancer related death. NAFLD affects a large proportion of the US population. Its incidence and prevalence are increasing to epidemic proportions around the world and is known to increase the risk of HCC. We studied how intrahepatic lipids affect adaptive immunity and HCC development in different murine models of NASH and HCC. Linoleic acid, a fatty acid found in NAFLD caused a selective loss of hepatic CD4+ but not CD8+ T cells leading to accelerated hepatocarcinogenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

12 Samples

Download data: CEL

(Submitter supplied) Purpose: To identify the impact of Acox1 on cellular metabolism and inflammation related to non-alcoholic fatty liver disease, within the context of obesogenic dietary stress. Methods: Hepatic mRNA profiles were obtained in triplicate for control and Acox1Lampe1 mice on chow diet or obesogenic diet. Profiles were generated using the Illumina HiSeq2000, reads that passed quality inspection were processed through the TopHap/Cufflinks pipeline. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TXT

(Submitter supplied) Hepatocellular carcinoma (HCC) has dismal treatment responses to systemic therapies and is caused by both, viral and non-viral etiologies, including non-alcoholic steatohepatitis (NASH) 1–5. NASH - triggered by high caloric intake and sedentary lifestyle - has become an important driver for HCC development. Immunotherapy has been recently approved for HCC but stratification of responders versus non-responders has remained an unmet need 5–8. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Genomic DNA was extracted from tumors that developed in C57BL/6 mice fed with CD-HFD for 12 months alone or fed with CD-HFD for 12 months followed by 8 weeks of treatment with anti-PD-1. DNA extracted from five pooled tail-clips of C57BL/6 mice was used as reference DNA.

Organism:

Mus musculus

Type:

Genome variation profiling by array

Platforms:

GPL16796 GPL28130

21 Samples

Download data: TXT

(Submitter supplied) Whereas some cancer types (e.g. melanoma) can be efficiently treated with immunotherapy, others lack measurable positive effects (e.g. PDAC ). Moreover, stratification of responders/non-responders is only possible in some cancer types (e.g. melanoma).  Hepatocellular carcinoma (HCC) has a dismal prognosis, limited treatment options and survival benefit, and represents a potential cancer entity for successful immunotherapy. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

37 Samples

Download data: TXT

(Submitter supplied) The pathophysiological mechanisms that drive non-alcoholic fatty liver disease (NAFLD) progression remain poorly understood. This multicenter study characterized the transcriptional changes that occur as liver disease progresses. 216 snap frozen liver biopsies, comprising 206 NAFLD cases with different fibrosis stages and 10 controls were studied. Samples underwent high-throughput RNA sequencing. This study provides novel insights into transcriptional changes during liver disease evolution and progression as well as proof of principle that transcriptomic changes reveal potentially tractable biomarkers for NAFLD fibrosis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

216 Samples

Download data: TXT

(Submitter supplied) To identify pro-tumorigenic signaling cascades in livers of Fah-/- mice, gene expression patterns were compared between tumor prone Fah-/- mice and immunocompromised mice in which tumor development was found to be reduced

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

6 Samples

Download data: TXT

(Submitter supplied) Only a small fraction of patients with HCC benefit from immune checkpoint inhibitor (ICI) therapy. Recently published studies suggest that HCC in patients with NASH does not respond the ICI therapy. Indeed, we demonstrate that anti-PD1 therapy is not working in several murine NASH models. CD8+ T cells were identified as the effector of anti-PD1 therapy. We observed a proinflammatory phenotype if hepatic CD8+ T cells that does not explain the inefficacy of anti-PD1 therapy in NASH. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL30557

12 Samples

Download data: RCC

(Submitter supplied) We show that chronic inflammation and fibrosis in mice with non-alcoholic fatty liver disease (NASH) is accompanied by accumulation of immunoglobulin A (IgA) positive plasmocytes. These cells suppress activation of cytotoxic T cells (CTL) derived from liver infiltrating CD8+ cells. CD8+ T cell ablation greatly accelerates HCC appearance, genetic or pharmacological targeting of IgA and PD-L1 expressing plasmocytes attenuates hepatic carcinogenesis and induces CTL-dependent regression of established HCC.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

41 Samples

Download data: TXT

(Submitter supplied) To investigate mechanism involved in the development of NAFLD-driven hepatocarcinoma (HCC), we used genome microarray expression profiling. The aim was to identify genes which upregulation could be controlled by E2F1 and/or E2F2 in NAFLD -driven HCC. For that, HCC was induced in wild type (WT), E2f1 knockout mice (E2f1-/-) and E2f2 knockout mice (E2f2-/-) by administration of the procarcinogenic agent diethylnitrosamine (DEN) combined with a feeding of high fat diet (HFD) for 32 weeks.The microarray results were then validated by RT-qPCR. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

12 Samples

Download data: TXT

(Submitter supplied) To assess the effect of steatosis and oxidative stress on progression of liver fibrosis, we have employed whole genome microarray expression profiling as a discovery platform to identify genes that are related with oxidative stress- and steatosis-induced hepatic fibrogenesis. When wild type mice were fed high-fat/high-sucrose diet for 24 weeks, expression of 69 genes was changed more than 10-fold compared with wild type animals fed normal diet, 11 of which were categorized to lipid metabolic process. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

8 Samples

Download data: TXT

(Submitter supplied) The molecular features of hepatocellular carcinoma arising from non-alcoholic fatty liver disease (NAFLD-HCC) are not well known. In this study, we investigated the mechanism by which NAFLD-HCC survives in a fat-rich environment. We found that caveolin (CAV)-1 was overexpressed in clinical specimens from NAFLD-HCC patients. HepG2, HLE, and HuH-7 HCC cell lines showed decreased proliferation in the presence of the saturated fatty acids palmitic acid and stearic acid, although only HLE cells expressed high levels of CAV-1. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

6 Samples

Download data: CEL

(Submitter supplied) In this study we want to compare the gene expression profile of CD44+CXCR6+ CD8+ T cells from the liver of ND and CD-HFD mice with hepatic CD44+CXCR6neg and splenic CD44+ CX3CR1neg CD8 T cells of ND and CD-HFD mice. This comparison will reveal transcriptional signatures of hepatic CD44+CXCR6+ CD8+ T cells in CD-HFD responsible for causing liver pathology in NASH.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

35 Samples

Download data: TXT

(Submitter supplied) T-cell exhaustion denotes a hypofunctional state of T lymphocytes commonly found in cancer, but how tumor cells drive T-cell exhaustion remains elusive. We found oncogenic reprograming of HCC methionine recycling with elevated 5-methylthioadenosine (MTA) and S-adenosylmethionine (SAM) to be tightly linked to T-cell exhaustion. We used an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to assay the genome-wide chromatin accessibility of T cells during activation and SAM/MTA treatment.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: NARROWPEAK