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Analysis of gene expression in co-culture of PBMCs with colon cancer cell lines by High-Throughput Sequencing

ABSTRACT: (Objectives) The goal of this study is to investigate paracrine effect of peripheral blood mononuclear cells (PBMCs) on colon cancer cell lines. (Method) Transcription profiles of PBMCs (control) and PBMCs co-cultured with colon cancer cell lines (treatment) were generated by deep sequencing, in triplicate for SW480 and duplicate for HT29, using Illumina HiSeq 4000. (Results and conclusion) Transcriptome analysis of PBMCs has shown the gene expression changed when co-cultured with colon cancer cell lines. The result revealed significantly up- and down-regulated genes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE110989 | GEO | 2020/12/31

REPOSITORIES: GEO

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Analysis of gene expression in co-culture of PBMCs with breast cancer cell lines by High-Throughput Sequencing

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Analysis of gene expression in co-culture of PBMCs with lung cancer cell lines by High-Throughput Sequencing

Project description:Objective: The goal of this study is to investigate paracrine effect of Peripheral Blood Mononuclear Cells (PBMCs) on lung cancer cell lines. Method: Transcription profiles of PBMCs (control) and PBMCs co-cultured with lung cancer cell lines (treatment) were generated by deep sequencing,in triplicate, using Illumina HiSeq 4000. Results and Conclusions: With demonstrating of RNA sequencing approach, PBMCs has been shown the gene expression changed when co-cultured with lung cancer cell lines. The result revealed that up-regulated genes were 8,073 and 8,070 genes co-cultured with A549 and H292, respectively. In the other hand, down-regulated genes were 8,341 and 8,342 genes co-cultured with A549 and H292, respectively. Comparing the data to expression array databases from lung cancer patients, up-regulated genes were shown 29 genes co-cultured with A549 and 37 genes with H292 which, among them, there were 2 genes, ANKRD37 and BUB3, found in both treatments. Down-regulated genes were found 24 and 35 genes in the co-culture of A549 an d H292, respectively, that no similar genes found in both treatments.

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Analysis of gene expression in co-culture of PBMCs with Hepatocellular carcinoma by High-Throughput Sequencing

Project description:Objectives: To characterize the transcripts profile of PBMCs when co-cultured with HCC cell lines using High-Throughput Sequencing and To validate the differentially expressed genes via quantitative reverse transcription polymerase chain reaction (qRT-PCR) in PBMCs of HCC pateints. Methods: Transcription profiles of PBMC (control) and PBMC co-cultured with liver cancer cell lines (treatment) were generated by deep sequencing, in triplicate, using Illumina Illumina HiSeq 4000. Results and conclusion: Transcriptome analysis of PBMCs has revealed the presence of biological process alterations when co-cultured with HCC cell lines and qRT-PCR validation have indicated that four genes were up-reglurated in HCC patients when compared with healthy donors including IL1b, INHBA, PLOD2, PRG4.

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Project description:Analysis of differentially expressed genes in colon cancer cell lines SW480 and HT29 with and without stably expressed ERbeta gene, with and without 10ng/mL TNFa treatment for 2 and 24 hours. Total RNA obtained from colon cancer cell lines SW480 and HT29 with and without stably expressed ERbeta gene, with and without 10ng/mL TNFa treatment for 2 and 24 hours.

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Analysis of gene expression in co-culture of PBMCs with Head and Neck cancer cells line by High-Throughput Sequencing

Project description:(Objectives) The goal of this study is to investigate paracrine effect of Peripheral Blood Mononuclear Cells (PBMCs) on Head and Neck cancer cell lines. (Method) Transcription profiles of PBMCs (control) and PBMCs co-cultured with Head and Neck cancer cell lines (treatment) were generated by deep sequencing, in triplicate for HN17 and duplicate for HN4, using Illumina HiSeq 4000. (Results and conclusion) Transcriptome analysis of PBMCs has shown the gene expression changed when co-cultured with HN cell lines. The result revealed significantly down-regulated genes. On the other hand, up-regulated gene, ZCCHC6 were used to validated with qRT-PCR in HNSCC patient blood. The synopsis of this study demonstrates paracrine effect on PBMC of HNSCC patient to significantly up expression of ZCCHC6 gene when compared with healthy donors.

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2020-10-30 | GSE155343 | GEO

LncRNA expression analysis of Clostridium butyricum-induced cell apoptosis in colon cancer SW480 cells

Project description:To compare lncRNAs and mRNAs expression profiles in colon cancer after co-cultured with CB and without CB, we extracted total RNA of colon cancer cell line(SW480) after co-cultured with CB(SW480/CB) and paired control without CB(SW480/ctr), and identified the dysregulated lncRNAs and mRNAs using Agilent Human lncRNAs/mRNAs microarrays.

2015-05-30 | GSE66731 | GEO

ERbeta modulation of NFkB pathway in colon cancer cell lines SW480 and HT29

2020-08-13 | GSE65979 | GEO

Analysis of gene expression in co-culture of PBMCs with ovarian cancer cell lines by High-Throughput Sequencing

Project description:(Objectives) The goal of this study is to investigate paracrine effect of peripheral blood mononuclear cells (PBMCs) on ovarian cancer cell lines. (Methods) Transcription profiles of PBMC (control) and PBMC co-cultured with ovarian cancer cell lines (treatment) were generated by deep sequencing, in triplicate, using Illumina HiSeq X Ten. (Results and Conclusions) Transcriptome analysis of PBMCs has revealed the expression change when co-cultured with EOC cell lines with significantly in up-regulated genes; CDKN1B, GIMAP8 and SNN. The qRT-PCR validation have indicated that GIMAP8 was high expressed in EOC patients when compared with healthy female. We summarized that PBMCs were changed their expression as a result of paracrine signals from ovarian cancer cells.

2020-12-31 | GSE110745 | GEO

Diverse effect of WWOX overexpression in HT29 colon cancer cell line.

Project description:The WWOX gene is a tumor suppressor probably involved in regulation of cell cycle and apoptosis and downregulated in variety of cancer types.However, its role in colon cancerogenesis is unknown. The aim of this study was to characterize how WWOX may be involved in colon cancerogenesis or cancer progression, how it influences the basic cancer cell features and modifies cell expression profile.Our observations suggest that in HT29 colon cancer cell line increased expression of WWOX may result in transition of cancer cells into more normal- like colon epithelium phenotype, on the other hand in SW480 WWOX revealed the well-known tumour suppressor properties. However, as the colon cancer is very heterogeneous disease, obtained discrepancies may reflect the known differences between cell lines and cancerogenesis pathway, which they undergone. HT29 colon cancer cells were stably transfected with WWOX cDNA. HT29 cells transfected with an empty vector served as a control. Total mRNA was isolated to look for gene-expression differences induced by the WWOX overexpression.

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