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Series GSE142381 Query DataSets for GSE142381
Status Public on Jun 01, 2020
Title DNA Demethylation promotes ERV expression and activation of immune signaling in renal cell cancer cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Recently, we reported that expression of endogenous retroviruses (ERVs), a class of transposable element, is associated with response to immune checkpoint blockade (ICB) in renal cell carcinoma (RCC). Aberrant expression of ERVs can activate host antiviral responses, as well as produce neoantigens. ERV expression is repressed by DNA methylation and can be activated by DNA hypomethylating agents. Here, we investigate whether Decitabine, a DNA hypomethylating agent, can activate ERV expression and host antiviral defenses in RCC to potentially enhance response to ICB. Decitabine induced expression of ERV3-2 and ERV4700 in RCC cells lines, which was accompanied by activation of host antiviral defense genes and increased secretion of inflammatory cytokines. We validated this effect in primary human RCC cell lines. Knockout of RIG-I and MDA5 dsRNA sensors attenuated activation of antiviral responses associated with Decitabine treatment, and RIG-I and MDA5 immunoprecipitations showed increased ERV binding in RCC cells treated with Decitabine. Bioinformatic analysis of RNAseq data showed the Decitabine-induced gene signature could be associated with increased CD8 infiltration and response to ICB. Conditioned media from Decitabine treated RCC cells was capable of inducing host anti-viral defense in naïve RCC cells and could modestly improve activation of T-cells from healthy donors. Further, conditioned media from RCC cells treated with Decitabine significantly enhanced T-cell migration. In a small retrospective cohort of metastatic RCC patients treated with single-agent PD-1/PD-L1 blockade, activation of some host antiviral defense genes was significantly higher in responders compared with nonresponders. Thus, modulation of ERV expression by Decitabine to activate host antiviral defenses could represent a novel therapeutic strategy to enhance RCC patient response to immune checkpoint blockade.
Overall design RNAseq profiles in HKC and 786-0 kidney cells treated with DMSO or Decitabine (100nM or 300nM)\
Contributor(s) de Cubas AA, Rathmell WK
Citation(s) 32493845
Submission date Dec 19, 2019
Last update date Jun 29, 2020
Contact name Aguirre A de Cubas
Organization name Vanderbilt University Medical Center
Department Hematology and Oncology
Lab Rathmell Lab
Street address 2220 Pierce Ave
State/province TN
ZIP/Postal code 37232
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (12)
GSM4226504 1533-ADC-1: HKC_wt_D0-1
GSM4226505 1533-ADC-2: HKC_wt_D0-2
GSM4226506 1533-ADC-3: HKC_wt_D300-1
BioProject PRJNA596778
SRA SRP238226

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE142381_RAW.tar 37.4 Mb (http)(custom) TAR (of TXT)
GSE142381_VSN.Data.Matrix.txt.gz 2.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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