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Series GSE281111 Query DataSets for GSE281111
Status Public on Jan 22, 2025
Title Molecular landscape of tumor-associated tissue-resident memory T cells in tumor microenvironment of hepatocellular carcinoma [HCC_scTCR]
Organism Homo sapiens
Experiment type Other
Summary Immunotherapy for liver cancer is used to rejuvenate tumor-infiltrating lymphocytes by modulating the immune microenvironment. Thus, early protective functions of T cell subtypes with tissue-specific residency have been studied in the tumor microenvironment (TME). We identified tumor-associated tissue-resident memory T (TA-TRM) cells in hepatocellular carcinoma (HCC) and characterized their molecular signatures. We obtained single-cell RNA and single-cell TCR sequencing data from five patients with HCC. The heterogeneous characteristics of TRM cell subsets within the TME were then investigated and validated. We characterized two TRM clusters (CD69+ and CD103+) that expressed unique signature genes and validated their similar molecular patterns in an independent dataset. Risk scores based on core gene expression in TA-TRM cells were associated with survival in both datasets. Trajectory analysis revealed that the two lineages followed different trajectory paths with distinct marker gene expression across pseudo-time. CD103+ TA-TRM cells showed diverse clonotypes and shared clonotypes with other cell groups. Lower clonal diversity and distinct signaling interactions were observed in the recurrent than in the non-recurrent samples. The CXCL13-CXCR3 interaction between CD103+ TA-TRM and regulatory T cells was observed only in the recurrent samples. We identified two subtypes of TA-TRM cells in HCC and demonstrated their unique molecular signatures, relevance to survival, and distinct signaling networks according to recurrence. The study findings provide a better understanding of the molecular characteristics of TA-TRM cells in HCC and potential immunotherapeutic strategies.
 
Overall design We generated scRNA-seq of CD45+ immune cells from tumors and adjacent livers for HCC by fluorescence-activated cell sorting (FACS).

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Submitter declares that the raw data cannot be provided due to patient privacy concerns.
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Contributor(s) Park M, Jo H, Kim H, Kim J, Park W, Paik Y, Yoon Y, Kang W, Won H
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Submission date Nov 05, 2024
Last update date Jan 23, 2025
Contact name Hong-Hee Won
E-mail(s) wonhh@skku.edu
Organization name SungKyunKwan University
Street address 81, Irwon-ro
City Gangnam-gu
ZIP/Postal code 06351
Country South Korea
 
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL30209 MGISEQ-2000RS (Homo sapiens)
Samples (7)
GSM8610987 TRM_132_LIL, scTCRseq
GSM8610988 HCC_M1_LIL, scTCRseq
GSM8610989 TRM_113_LIL, scTCRseq
Relations
BioProject PRJNA1182296

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
GSE281111_HCC_M1_LIL_demuxlet.best.gz 1.3 Mb (ftp)(http) BEST
GSE281111_RAW.tar 1.3 Mb (http)(custom) TAR (of CSV)
Raw data not provided for this record

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