Virus Dataset Detail

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Dataset Information
Accession GSE158935
Status 2021/11/1
Title Genome-wide transcriptome analysis of KSHV long-term-infected endothelial (LTC) and parental uninfected TIVE cells [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: To characterize genome-wide mRNA expression profiles in the context of Kaposi’s sarcoma-associated herpesvirus (KSHV)-induced oncogenesis using isogenic cell lines for a Kaposi's sarcoma (KS) xenograft model: KSHV-infected human endothelial cells (LTC) that form tumors with properties closely resembling KS lesions in nude mice and uninfected parental (TIVE) cells. Methods: mRNA expression profiles of LTC and TIVE cells were generated by deep sequencing using Illumina. In addition, mRNA profiles of LTC transfected with miR-127-3p or negative control (NC) mimic were generated by deep sequencing. Results: We analyzed global transcriptome changes in LTC compared to TIVE cells and identified significant upregulation of many cell cycle and oncogenic signaling pathways. In addition, we assessed global transcriptome changes in LTC transfected with miR-127-3p mimic and found a significant decrease in the levels of E2F and Myc targets, indicating that miR-127-3p suppresses E2F and Myc transcriptional activities. Conclusions: This study provides a detailed analysis of the cellular transcriptome in LTC and TIVE cells using RNA sequencing technology. Our study identifies miR-127-3p as a potent tumor suppressor miRNA that acts as a negative regulator of the CDK-RB-E2F cell cycle signaling pathway and the oncogenic Myc network in the context of KSHV oncogenesis and establishes a strong rationale for developing this miRNA as a therapeutic agent against KS.
Samples
GSM ID Sample info Characteristics Description
GSM4816036 LTC_NC_rep2 tissue source:Human umbilical cord; cell type source:Human umbilical vein endothelial cells; cell type:Kaposi's sarcoma-associated herpesvirus (KSHV)-infected human endothelial cells (LTC); treatment:Transfected with 30 nM NC mimic for 3 days; library construction method:Illumina TruSeq stranded mRNA sample preparation; reference assembly:GRCh38 processed data file: comparison_2.xlsx
GSM4816037 LTC_127_rep1 tissue source:Human umbilical cord; cell type source:Human umbilical vein endothelial cells; cell type:Kaposi's sarcoma-associated herpesvirus (KSHV)-infected human endothelial cells (LTC); treatment:Transfected with 30 nM miR-127 mimic for 3 days; library construction method:Illumina TruSeq stranded mRNA sample preparation; reference assembly:GRCh38 processed data file: comparison_2.xlsx
GSM4816038 LTC_127_rep2 tissue source:Human umbilical cord; cell type source:Human umbilical vein endothelial cells; cell type:Kaposi's sarcoma-associated herpesvirus (KSHV)-infected human endothelial cells (LTC); treatment:Transfected with 30 nM miR-127 mimic for 3 days; library construction method:Illumina TruSeq stranded mRNA sample preparation; reference assembly:GRCh38 processed data file: comparison_2.xlsx
GSM4816033 LTC tissue source:Human umbilical cord; cell type source:Human umbilical vein endothelial cells; cell type:Kaposi's sarcoma-associated herpesvirus (KSHV)-infected human endothelial cells (LTC); treatment:none; library construction method:Illumina TruSeq small RNA sample preparation; reference assembly:GRCh37 processed data file: comparison_1.xlsx
GSM4816034 TIVE tissue source:Human umbilical cord; cell type source:Human umbilical vein endothelial cells; cell type:uninfected parental cells (TIVE) cells.; treatment:none; library construction method:Illumina TruSeq small RNA sample preparation; reference assembly:GRCh37 processed data file: comparison_1.xlsx
GSM4816035 LTC_NC_rep1 tissue source:Human umbilical cord; cell type source:Human umbilical vein endothelial cells; cell type:Kaposi's sarcoma-associated herpesvirus (KSHV)-infected human endothelial cells (LTC); treatment:Transfected with 30 nM NC mimic for 3 days; library construction method:Illumina TruSeq stranded mRNA sample preparation; reference assembly:GRCh38 processed data file: comparison_2.xlsx
Platform GPL16791  GPL24676  : Illumina HiSeq 2500 (Homo sapiens);Illumina NovaSeq 6000 (Homo sapiens)
Literature 34725152  
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xCell Plot
* p<0.05 ** p<0.01