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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

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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

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

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

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

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

Transmitted/founder hepatitis C viruses induce cell type- and genotype-specific differences in innate signaling within the liver

Project description:Primary human hepatocytes (PHHs) are a liver-specific cell subtype, and we have shown that these cells respond in a unique manner to the introduction of hepatitis C viral RNA (HCV vRNA) derived from different genotypes of the virus. We used microarray to analyze the transcriptional differences between the PHHs exposed to the different genotypes of HCV to further shed light on their differential effects on HCV innate immune responses in vitro HCV vRNA from either genotype 3a HCV or genotype 1a HCV was introduced into the PHH cells for 8 hours. Total RNA was then harvested to determine transcriptional differences.

2014-12-20 | E-GEOD-64400 | biostudies-arrayexpress

HBV Infection and DNA Stimulation Induce a Unique Innate Immune Response in Hepatocytes

Project description:Background and Aims: Recent identification of intracellular DNA sensing pathways and involvement in numerous diverse disease processes including viral pathogenesis and autoimmunity suggests a role for these processes in liver pathology. The presence of these pathways in the liver and their role in HBV infection is unknown. Methods: In order to characterize the role of DNA sensing pathways in the liver, we utilized in vitro models. Microarray was performed on DNA treated and HBV infected hepatoma primary human hepatocytes. Results: Here we show that HBV infection and foreign DNA results in a significant innate immune response characterized by the production of inflammatory chemokines. The goal of this study is to characterize the changes in gene expression triggered by HBV and foreign DNA in primary human hepatocytes. PHHs were infected with HBV (MO.I = 50) for 40 hours. PHHs were transfected with 1Î¼g/mL of ISD/dsDNA90 for 12 or 24 hours. Three replicates were performed for each condition.

2016-08-09 | E-GEOD-69590 | biostudies-arrayexpress

Transmitted/founder hepatitis C viruses induce cell type- and genotype-specific differences in innate signaling within the liver

2014-12-20 | GSE64400 | GEO

Radiation enhances melanoma response to immunotherapeutic and synergizes with benzodiazepines to promote improved anti-tumor activity

Project description:The RNA-Seq data of 17 brain metastatic samples short-read sequences were aligned to the hg19 human reference genome using STAR (v 2.4.1a). featureCounts was used to count the reads of the mapped bam files. SAMseq was used to conduct differential expression analysis among the two treatment groups. SAMseq was utilized as it accounts for potential correlation in expression among genes and its permutation-based testing method was deemed more appropriate for a smaller sample size. After identifying the differentially expressed genes (FDR cut-off, 0.05), expression levels were normalized with the samr R package before being log2 transformed. This data was utilized to generate a heatmap with the patients sorted with supervised clustering based upon their immunotherapy/radiation groups and the gene dendrogram was created with Pearson’s Correlation Coefficient and with the Ward D2 linkage method. Differentially expressed genes (FDR<0.05[KD1] ) were subjected to pathway analysis using MetaCore.

2019-05-21 | GSE131521 | GEO

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