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Series GSE141878 Query DataSets for GSE141878
Status Public on Dec 12, 2019
Title Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Tumor-reactive CD8+ tumor infiltrating lymphocytes (TILs) represent a subtype of T cells that could recognize and destroy tumor specifically. Understanding the regulatory mechanism of tumor-reactive CD8+ T cells has important therapeutic implications. Yet the DNA methylation status of this T cell subtype has not been elucidated. In this study, we segregated tumor-reactive and bystander CD8+ TILs, as well as naïve and effector memory CD8+ T cell subtypes as controls from colorectal cancer (CRC) patients, to compare their transcriptome and methylome characteristics. Transcriptome profiling confirmed previous conclusion that tumor-reactive TILs have an exhausted tissue-resident memory signature. Whole-genome methylation profiling identified a distinct methylome pattern of tumor-reactive CD8+ T cells, with tumor-reactive markers (CD39 and CD103) being specifically demethylated. In addition, dynamic changes were observed during the transition of naïve T cells into tumor-reactive CD8+ T cells. Transcription factor (TF) binding motif enrichment analysis identified several immune-related TFs, including three exhaustion-related genes (NR4A1, BATF and EGR2) and VDR, that potentially play important regulatory role in tumor-reactive CD8+ T cells. Our study supports the involvement of DNA methylation in shaping tumor-reactive and bystander CD8+ TILs, and provides a valuable resource for the development of novel DNA methylation markers and future therapeutics.
 
Overall design We used whole-genome methylome profiling and RNA-seq to investigate the characteristics of tumor-reactive and bystander CD8+ TILs, as well as naive and effector memory CD8+ T cell subsets as controls from colorectal cancer patients. Raw sequence data access provided at: China Genomic Sequence Archive (GSA) (https://bigd.big.ac.cn/gsa-human/browse/HRA000059) under accession HRA000059.

****Raw sequence data access provided at: China Genomic Sequence Archive (GSA) (https://bigd.big.ac.cn/gsa-human/browse/HRA000059) under accession HRA000059.
 
Contributor(s) Yang R, Cheng S, Luo N, Gao R, Yu K, Kang B, Wang L, Zhang Q, Fang Q, Zhang L, Li C, He A, Hu X, Peng J, Ren X, Zhang Z
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Submission date Dec 11, 2019
Last update date Dec 12, 2019
Contact name Zemin Zhang
E-mail(s) zemin@pku.edu.cn
Organization name Peking University
Department School of Life Science
Lab Zhang Lab
Street address Haidian District, Beijing Summer Palace Road No. 5
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (73)
GSM4215308 RNA-seq: P0929_Naive
GSM4215309 RNA-seq: P0929_EM
GSM4215310 RNA-seq: P0929_DP
Relations
BioProject PRJNA595032

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
GSE141878_CD8Tcell_raw_counts.csv.gz 2.1 Mb (ftp)(http) CSV
GSE141878_DN.filt.DMR.bed.gz 24.5 Kb (ftp)(http) BED
GSE141878_DP.filt.DMR.bed.gz 33.8 Kb (ftp)(http) BED
GSE141878_EM.filt.DMR.bed.gz 5.9 Kb (ftp)(http) BED
GSE141878_Naive.filt.DMR.bed.gz 159.8 Kb (ftp)(http) BED
GSE141878_README.txt 273 b (ftp)(http) TXT
GSE141878_SP.filt.MDR.bed.gz 3.1 Kb (ftp)(http) BED
Processed data are available on Series record
Raw data not provided for this record

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