Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole transcriptome analysis of iPSC derived hepatic organoids cultures

ABSTRACT: A heatmap, which focused upon 2458 genes that were involved in stem cell differentiation and liver development, was prepared to visualize the relative relationship between the transcriptomes of iPSCs, PHHs, human liver tissue and HO1. The dendrogram indicates that HO1 is more closely related to liver tissue than to PHHs; this is because cholangiocytes are present in HO1 and liver, but are absent (or rare) in PHHs. Examination of the genes within this heatmap indicated that there was a lack of expression of pluripotent genes in HO1; and that HO1 had an increased level of expression of cellular markers for liver lineages and liver development, which included mature hepatocytes, bile duct cells and NOTCH signaling components. A cluster analysis of 1510 genes indicates that there were major changes in the transcriptome after the cells that were dissociated from an HO1 were transferred from the growth medium into the differentiation medium. As with the HO1s, the gene expression profile of HO2s resembled that of PHHs and human liver. Of importance, the level of expression of mRNAs that are of importance for various human liver functions (ADH4, CYP3A4, TTR, GSRA1, TDO2, GSTA1 and FAH) were markedly increased in HO2s.

ORGANISM(S): Homo sapiens

PROVIDER: GSE138549 | GEO | 2019/10/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Whole transcriptome analysis of iPSC-derived hepatic organoids cultures

Project description:A heatmap, which focused upon 2458 genes that were involved in stem cell differentiation and liver development, was prepared to visualize the relative relationship between the transcriptomes of iPSCs, PHHs, human liver tissue and HO1. The dendrogram indicates that HO1 is more closely related to liver tissue than to PHHs; this is because cholangiocytes are present in HO1 and liver, but are absent (or rare) in PHHs. Examination of the genes within this heatmap indicated that there was a lack of expression of pluripotent genes in HO1; and that HO1 had an increased level of expression of cellular markers for liver lineages and liver development, which included mature hepatocytes, bile duct cells and NOTCH signaling components. A cluster analysis of 1510 genes indicates that there were major changes in the transcriptome after the cells that were dissociated from an HO1 were transferred from the growth medium into the differentiation medium. As with the HO1s, the gene expression profile of HO2s resembled that of PHHs and human liver. Of importance, the level of expression of mRNAs that are of importance for various human liver functions (ADH4, CYP3A4, TTR, GSRA1, TDO2, GSTA1 and FAH) were markedly increased in HO2s.

2017-10-21 | GSE101770 | GEO

mRNA sequencing of ADH4 overexpression in HBV-associated hepatoma cell line HepG2.2.15

Project description:Liver cancer is the sixth most common cancer globally and the third leading cause of cancer-related death. Alcohol dehydrogenase families (ADHs), which predominantly exist in the livers of humans and animals, serve as essential enzymes in the metabolism of short-chain alcohols and ω-oxidation of certain fatty acids, playing crucial roles in numerous physiological processes. A cluster of genes consisting of seven alcohol dehydrogenase-encoding genes (ADH1A, ADH1B, ADH1C, ADH4, ADH5, ADH6 and ADH7) is situated on chromosome 4q and encodes ADHs. Loss of Chromosome 4q is a frequent occurrence in liver cancer, leading to the loss of an entire cluster of seven genes. As a result, there is typically a decrease in the expression of ADHs (ADH1A, ADH1B, ADH1C, ADH4 and ADH6) in liver cancer. Amongst these, ADH4 is the most substantially downregulated gene, which affects both overall survival (OS) and disease-free survival (DFS) in liver cancer patients. Furthermore, a thorough investigation was previously conducted to identify possible biomarkers for predicting liver cancer recurrence. The results showed that in liver cancer, ADH4 was significantly downregulated and this downregulation indicated a higher likelihood of recurrence in liver cancer patients. As a consequence, further research was conducted on the role of ADH4 in liver cancer progression.

2023-08-19 | GSE241204 | GEO

Transcriptomic analysis of PHHs isolated from hCLiP-transplanted mouse chimeric liver

Project description:Transcriptome of PHHs isolated from hCLiP-transplanted mouse chimeric liver was compared with those of cryopreserved PHHs.

2019-07-04 | GSE133779 | GEO

Expression data from oral squamous cell carcinomas, 3A and HO1-N-1

Project description:Co-culture with human oral squamous cell carcinoma cells, 3A or NEM, or culture with each of their conditioned medium induced many osteoclasts from osteoclast precursor cells, which were generated by a 24-h pretreatment of RANKL or TNF-α. However, HO1-N-1 cells did not induce any osteoclasts. Osteoprotegerin, a decoy RANKL receptor, denosumab, an anti-RANKL antibody drug, and infliximab, an anti-TNF-α antibody drug, did not prevent this tumor-associated osteoclastogenesis. We compared the expression of molecules associated with osteoclastogenesis between 3A and HO1-N-1 cells.

2019-01-09 | GSE123411 | GEO

TSA attenuates the progression of c-Myc-driven hepatocarcinogenesis by pAKT-ADH4 pathway

Project description:Histone deacetylase inhibitors (HDACi), such as Trichostatin A (TSA), hold enormous promise for the treatment of HCC. In this study, we investigated the effects of TSA treatment on a c-Myc-induced HCC model in mice. TSA treatment delayed the development of HCC, and liver function indicators such as ALT, AST, liver weight ratio, and spleen weight ratio indicated the effectiveness of TSA treatment. Oil red staining further demonstrated that TSA attenuated lipid accumulation in the HCC tissues of mice. Through mRNA sequencing, we identified that TSA mainly affected cell cycle and fatty acid degradation genes, with alcohol dehydrogenase 4 (ADH4) potentially being the core molecular downstream target. QPCR, immunohistochemistry, and western blot analysis revealed that ADH4 expression was repressed by c-Myc and recovered after TSA treatment both in vitro and in vivo. Furthermore, we observed that the levels of total NAD+ and NADH, NAD+, NAD+/NADH, and ATP concentration increased after c-Myc transfection in liver cells but decreased after TSA intervention. The levels of phosphorylated protein kinase B (p-AKT) and p-mTOR were identified as targets regulated by TSA, and they governed the ADH4 expression and the downstream regulation of total NAD+ and NADH, NAD+, NAD+/NADH, and ATP concentration. Overall, our study suggests that TSA has a therapeutic effect on c-Myc-induced HCC through the AKT-mTOR-ADH4 pathway.

2024-08-01 | GSE244814 | GEO

Radiomic and gEnomic approaches for the enhanced DIagnosis of REnal Cancer (REDIRECt): A translational pilot study

Project description:Introduction: The aim of this pilot study is to establish a radiogenomic characterisation of a clear-cell renal cell carcinoma (ccRCC) subpopulation, focusing on the transcriptomic underpinnings of radiomic features. Materials & Methods: To establish the viability of conducting a combined analysis of both radiomic and genomic data, a pilot cohort of 6 patients with <5cm G2 unilateral non-metastatic T1a-b ccRCC, who underwent surgery, was evaluated. Transcriptomic analysis was conducted through RNA-seq on tumor samples, while radiomic data was extracted from pre-operative 4 phase contrast-enhanced multidetector CT scans. Genomic heterogeneity was assessed with principal component analysis run on unrestricted data, on a clear-cell renal cell carcinoma associated gene list with zero-centered Reads Per Kilobase of transcript, per million mapped reads values. The underlying pathways and gene ontologies were established with enrichment analysis. In addition, Pearson’s correlation between radiomic data and the transcription of significant genes was fitted, and dendrogram and heatmap plots were drawn. Results: Even in a clinically homogeneous population, the employed analyses have demonstrated that RCC should be regarded as an intrinsically heterogeneous disease. The analysis of the radiomic features and gene expression correlation using heatmap and dendrogram showed four distinct radiogenomic correlation patterns: with one including 5 radiomic features, and the other three including 2 features each. Conclusion: The current pilot study is the first investigation demonstrating an innovative radiogenomic characterisation of clear-cell RCC. Based on such observations, further investigation into the radiomic and genomic approaches for the enhanced diagnosis of RCC is warranted.

2019-06-28 | GSE133460 | GEO

Omics-characterization of tebufenpyrad effects on human primary hepatocytes

Project description:The biological effects of the pesticide and complex I inhibitor tebufenpyrad (TEBU) on liver cells were investigated by proteomic approaches. Cellular contents and culture media were analyzed in dose-response experiments on human primary hepatocytes (PHHs).

2022-10-06 | PXD030887 | Pride

A two-step de-differentiation and maturation of primary human hepatocytes in vitro with efficient metabolic and regenerative capacities

Project description:Hepatocytes hold significant promise for applications in drug screening, disease modeling, and clinical cell transplantation. Generating large amouts of hepatocyte in vitro for those application is still challenging. We have previously established a 5C medium for long-term culture and functional maintanace human primary hepatocytes (PHHs) in vitro. However, 5C condtion could not support hepatocyte expansion, which limited its application. In this study, we established a new hepatocyte expansion medium (NHEM) for efficient hepatocyte expansion, which turned the PHHs into hepatic progenitor-like cells (HPLCs). We also generated an optimized 6C condtion for HPLCs maturation. Overall, this study provide a new strategy to generate large amounts of hepatocytes in vitro.

2024-09-23 | GSE261965 | GEO

A two-step de-differentiation and maturation of primary human hepatocytes in vitro with efficient metabolic and regenerative capacities

2024-09-23 | GSE261962 | GEO

Human induced pluripotent stem cell culture on a non-coated dish using medium supplemented with milk fat globule epidermal growth factor 8

Project description:201B7 cells were cultured on iMatrix-511 for 4 days after cell seeding in Stem Fit AK03 medium or CTS Essential 8 medium (2 samples each), and separately, different 201B7 cells (2 samples each) were cultured in Stem Fit AK03 medium or gelatin solution (10%) + MFGE 8 (2 µg/mL) in CTS Essential 8 medium for 4 days from cell seeding. A hierarchical cluster analysis of the 10 cell types is shown (Figure 2A). The 5,919 probes with variable expression are shown in a heatmap. Comparisons between samples based on 'human ES cell' were made using a hierarchical cluster analysis, and 4,825 probes with variable expression in each of the four comparisons are shown in the heatmap (Figure 2B). Comparisons between samples based on 'human iPSC N116213' were performed using a hierarchical cluster analysis, and 4,886 probes with variable expression in each of the four comparisons are also shown in a heatmap (Figure 2C).

2023-04-20 | GSE230084 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data