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Series GSE188900 Query DataSets for GSE188900
Status Public on Mar 16, 2022
Title The confused cell identity is associated with aggressiveness in esophageal squamous cell carcinoma [scRNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Seven tumor samples and one distal normal sample from five pathologically confirmed ESCC patients were analyzed with 10X Genomics scRNA-seq. To better represent the squamous epithelial cells, we optimized the dissociation protocol. Total 44,206 cells were obtained, including 16,657 normal and malignant squamous epithelial cells. The squamous epithelial cells, glandular epithelial cells, immune cells, endothelial cells and other tumor microenvironmental cells were clearly separated and identified with classic markers.Seven tumor samples and one distal normal sample from five pathologically confirmed ESCC patients were analyzed with 10X Genomics scRNA-seq. To better represent the squamous epithelial cells, we optimized the dissociation protocol. Total 44,206 cells were obtained, including 16,657 normal and malignant squamous epithelial cells. The squamous epithelial cells, glandular epithelial cells, immune cells, endothelial cells and other tumor microenvironmental cells were clearly separated and identified with classic markers.
 
Overall design The cell identity of malignant cells and how they acquire it are fundamental for our understanding of cancer. Here, we report that esophageal squamous cell carcinoma (ESCC) cells display molecular features similar but distinct to all three types of normal esophageal epithelial cells, which we term as confused cell identity (CCI). CCI is an independent prognostic marker associated with poor prognosis in ESCC. Further, we identify tripomyosin 4 (TPM4) as a critical CCI gene that promotes the aggressiveness of ESCC in vitro and in vivo. And TPM4 creates CCI through activating the JAK/STAT-SOX2 pathway. Thus, our study suggests a precedent unrecognized feature of ESCC cells, which might be of value for clinic prognosis and potential interference.
 
Contributor(s) Pan X, Wang J, Guo L, Du J, Chen C, Liu Y
Citation(s) 35418165
Submission date Nov 15, 2021
Last update date Sep 16, 2022
Contact name Xaingyu Pan
E-mail(s) pangxueyu233@outlook.com
Organization name Sichuan University
Department State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.
Lab Chen & Liu Lab
Street address No.17 Renming road section3
City Chengdu, Cihna
State/province Sichuan
ZIP/Postal code 610041
Country China
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (8)
GSM5691642 Patient1
GSM5691643 Patient2
GSM5691644 Patient3
This SubSeries is part of SuperSeries:
GSE188955 The confused cell identity is associated with aggressiveness in esophageal squamous cell carcinoma
Relations
BioProject PRJNA780580
SRA SRP346244

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
GSE188900_RAW.tar 342.4 Mb (http)(custom) TAR (of TAR)
GSE188900_scESCC_rds.tar.gz 6.3 Gb (ftp)(http) TAR
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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