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Series GSE261709 Query DataSets for GSE261709
Status Public on Apr 15, 2024
Title Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci
Organism Homo sapiens
Experiment type Other
Summary Only a portion of cancer patients respond favorably to immunotherapy, indicating the need for new biomarkers and targets. Here, we identify common somatic and germline 3´ untranslated region (3´UTR) variants across the human transcriptome from 375 gastric cancer patients from The Cancer Genome Atlas (39.5% somatic). By performing gene expression quantitative trait loci (eQTL) and immune landscape QTL (ilQTL) analysis, we discover 3´UTR variants with cis effects on expression and immune landscape phenotypes, such as immune cell infiltration. To distinguish between causal and correlative effects of 3´UTR eQTLs in immune-related genes, we perform a massively parallel reporter assay. Our approach identifies numerous 3´UTR eQTLs and ilQTLs (e.g. in ADAR1), providing a unique resource for the identification of immunotherapeutic targets and biomarkers. Our prioritized ilQTL variant signature predicts response to immunotherapy better than standard-of-care PD-L1 expression in independent patient cohorts, showcasing the untapped potential of non-coding mutations in cancer.
 
Overall design To assess the effect of 3'UTR variants on gene expression we performed a massively parallel reporter assay (MPRA) in two stomach cancer cell lines (AGS, SNU719) in triplicate.
 
Contributor(s) Miliotis C, Karagkouni D, Mattioli K, Slack FJ, Vlachos IS
Citation(s) 38773080
Submission date Mar 15, 2024
Last update date Jun 05, 2024
Contact name Christos Miliotis
E-mail(s) cnmiliotis@gmail.com
Organization name BIDMC
Department Cancer Center
Street address 330 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (7)
GSM8149344 AGS, rep1
GSM8149345 AGS, rep2
GSM8149346 AGS, rep3
Relations
BioProject PRJNA1088465

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE261709_RAW.tar 690.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA

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