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SRX16716052: GSM6411768: Con, WGBS; Mus musculus; Bisulfite-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 408.7M spots, 122.6G bases, 39.3Gb downloads

External Id: GSM6411768_r1
Submitted by: Institute of Health Service and Transfusion Medicine
Study: Decitabine-induced T cell remodeling facilitates a high antitumor response to PD-1 blockade therapy by promoting the expansion and effector function of CD8+ progenitor exhausted T cells
show Abstracthide Abstract
CD8+ exhausted T (Tex) cells are heterogeneous with distinct transcriptional and epigenetic landscapes. PD-1 inhibitors reinvigorate progenitor Tex cells, which subsequently differentiate into irresponsive terminal Tex cells and impair the longlasting antitumor response of PD-1 blockade therapy. How to maintain durable proliferative capacity of progenitor Tex cells is important but remains largely unknown. Here, we showed that low-dose DNA demethylating agent decitabine-pretreated CD8+ progenitor Tex cells had enhanced cytolytic activity against tumors after anti-PD-1 treatment in vitro and could not reactivate the terminal Tex cells. Decitabine-plus-anti-PD-1 treatment promoted the activation and expansion of endogenous tumor-infiltrated CD8+ progenitor Tex cells and efficiently suppressed tumor growth in multiple mice tumor models. The single-cell RNA-sequencing, TCR-sequencing and ATAC-sequencing demonstrated that decitabine-plus-anti-PD-1 combination altered the transcriptional and epigenetic status of CD8+ Tex cells and markedly elevated the clonally expansion and effector function of progenitor Tex cells as compared with anti-PD-1 monotherapy, presenting increased expression of genes associated with T cell activation, proliferation, cytolytic activity, memory and mitochondrial metabolism. Strikingly, decitabine-plus-anti-PD-1 combination sustained the expression and activity of AP-1 transcription factor JunD, which was reduced following PD-1 blockade therapy. Suppressing JNK/AP-1 signaling in CD8+ T cells blunted decitabine-plus-anti-PD-1-induced activation of CD8+ T cells. Together, our findings show that the epigenetic therapy remodels CD8+ progenitor Tex subset, improves responsiveness to anti-PD-1 therapy and suppresses CD8+ T cell terminal differentiation. Overall design: scRNA-seq, scTCR-seq, ATAC-seq, and WGBS of T cells in the Control (C), decitabine(D), anti-PD-1(P), and decitabine-plus-anti-PD-1(DP) group.
Sample: Con, WGBS
SAMN30024310 • SRS14346004 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM6411768
Instrument: Illumina NovaSeq 6000
Strategy: Bisulfite-Seq
Source: GENOMIC
Selection: RANDOM
Layout: PAIRED
Construction protocol: The tumor tissues were minced and dissociated into single-cell suspensions using a tissue dissociation kit (Miltenyi Biotec). Cells were washed and re-suspended in PBS and stained with a Viability Dye, CD45 and CD3, the alive CD45+CD3+ TILs were sorted on a BD Bioscience cell sorter. Sorted cells were collected into cold PBS plus 2% FBS, and used for the scRNA-seq or ATAC-seq. For the ACT assay, the alive CD45.2+CD45.1-CD8+ transfered T cells were sorted and used for the scRNA-seq. For the WGBS assay, CD8+ naive T cells were treated with PBS or decitabine (10nM) in vitro. (scRNA-seq with paired scTCR-seq) Cells were loaded between 10,000 and 15,000 cells/chip position using the 10x Chromium Single Cell V(D)J Reagent Kits v1.1. Library was performed according to the manufacter's instructions (single cell 5' v1+TCR protocol). (ATAC-seq) ATAC-seq DNA library was constructed using TruePrepTM DNA Library Prep Kit V2 for Illumina. (WGBS) The C-T transformation was Bisufile processed according to EZ DNA Methylation-GoldTM Kit (D5006) process, and then WGBS library was constructed.
Runs: 1 run, 408.7M spots, 122.6G bases, 39.3Gb
Run# of Spots# of BasesSizePublished
SRR20694218408,681,220122.6G39.3Gb2022-07-29

ID:
23456135

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